From 38bed3b1b4d7888dcfed995871b3d0e44e66569e Mon Sep 17 00:00:00 2001
From: "Strope, Pooja" <pooja.strope@nih.gov>
Date: Thu, 25 Jul 2024 14:42:23 -0400
Subject: [PATCH 1/4] updating to v0.2

---
 LICENSE                                       |  11 +-
 examples/input_C_longicornis.yaml             |   2 +-
 examples/input_Gavia_stellata.yaml            |   2 +-
 .../{gnomon => default}/align_sort_sa/main.nf |   0
 .../ncbi/default/annot_builder/main.nf        |  26 +-
 .../ncbi/default/annotwriter/main.nf          |  10 +-
 .../ncbi/gnomon-training-iteration/main.nf    |  30 +-
 .../gnomon-training-iteration/utilities.nf    |  18 +-
 .../ncbi/gnomon/chainer_wnode/main.nf         |   6 +-
 nf/subworkflows/ncbi/gnomon/diamond/main.nf   | 112 +---
 .../ncbi/gnomon/gnomon_biotype/main.nf        |  10 +-
 .../ncbi/gnomon/gnomon_training/main.nf       |  11 +-
 .../ncbi/gnomon/locus_link/main.nf            | 116 ++++
 nf/subworkflows/ncbi/gnomon/main.nf           |  96 +++
 .../ncbi/gnomon/prot_gnomon_prepare/main.nf   |   6 +
 .../ncbi/gnomon/protein_filter/main.nf        |  59 +-
 nf/subworkflows/ncbi/main.nf                  | 132 ++--
 nf/subworkflows/ncbi/only_gnomon.nf           |  16 +-
 .../ncbi/orthology/diamond_orthology/main.nf  |  25 +
 .../extract_products_from_models/main.nf      |  45 ++
 .../ncbi/orthology/find_orthologs/main.nf     | 170 +++++
 nf/subworkflows/ncbi/orthology/main.nf        |  43 ++
 .../rnaseq_short/bam_bin_and_sort/main.nf     |   6 +-
 .../rnaseq_short/bam_strandedness/main.nf     |   6 +-
 .../rnaseq_short/convert_from_bam/main.nf     |  12 +-
 nf/subworkflows/ncbi/rnaseq_short/main.nf     |  78 +++
 .../ncbi/rnaseq_short/rnaseq_collapse/main.nf |   2 +-
 .../ncbi/rnaseq_short/sra_qry/main.nf         |   4 +-
 .../ncbi/rnaseq_short/star_index/main.nf      |   4 +-
 .../ncbi/rnaseq_short/star_wnode/main.nf      |  74 ++-
 nf/subworkflows/ncbi/setup/main.nf            |  38 +-
 nf/subworkflows/ncbi/shared/diamond/main.nf   | 107 +++
 .../target_proteins/best_aligned_prot/main.nf |   9 +-
 nf/subworkflows/ncbi/target_proteins/main.nf  |  37 ++
 .../ncbi/target_proteins/miniprot/main.nf     |  81 ++-
 .../ncbi/target_proteins/paf2asn/main.nf      |  16 +-
 nf/subworkflows/ncbi/utilities.nf             |  22 +-
 nf/ui.nf                                      |  68 +-
 third_party_licenses/LICENSE_diamond          | 622 ++++++++++++++++++
 .../{LICENSE_bamtools => LICENSE_seqkit}      |   5 +-
 ui/assets/config/docker_image.config          |   2 +-
 ui/assets/config/executor/aws.config          |  15 +-
 ui/assets/config/executor/ncbi-sge.config     |  29 +
 ui/assets/config/process_resources.config     |  33 +-
 ui/assets/default_task_params.yaml            |  23 +-
 ui/egapx.py                                   | 560 ++++++++++++++--
 46 files changed, 2322 insertions(+), 477 deletions(-)
 rename nf/subworkflows/ncbi/{gnomon => default}/align_sort_sa/main.nf (100%)
 create mode 100644 nf/subworkflows/ncbi/gnomon/locus_link/main.nf
 create mode 100644 nf/subworkflows/ncbi/gnomon/main.nf
 create mode 100644 nf/subworkflows/ncbi/orthology/diamond_orthology/main.nf
 create mode 100644 nf/subworkflows/ncbi/orthology/extract_products_from_models/main.nf
 create mode 100644 nf/subworkflows/ncbi/orthology/find_orthologs/main.nf
 create mode 100644 nf/subworkflows/ncbi/orthology/main.nf
 create mode 100644 nf/subworkflows/ncbi/rnaseq_short/main.nf
 create mode 100644 nf/subworkflows/ncbi/shared/diamond/main.nf
 create mode 100644 nf/subworkflows/ncbi/target_proteins/main.nf
 create mode 100644 third_party_licenses/LICENSE_diamond
 rename third_party_licenses/{LICENSE_bamtools => LICENSE_seqkit} (90%)
 create mode 100644 ui/assets/config/executor/ncbi-sge.config

diff --git a/LICENSE b/LICENSE
index 8a95065..d34a2eb 100644
--- a/LICENSE
+++ b/LICENSE
@@ -43,10 +43,15 @@ Authors:  Dana-Farber Cancer Institute
 License:  MIT License
           [https://github.com/lh3/miniprot/blob/master/LICENSE.txt]
 
-Location: img/gp/third-party/bamtools
-Authors:  Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
+Location: img/gp/third-party/diamond
+Authors:  Benjamin Buchfink
+License:  GNU GENERAL PUBLIC LICENSE
+          [https://github.com/bbuchfink/diamond/blob/master/LICENSE]
+
+Location: img/gp/third-party/seqkit
+Authors:  Wei Shen
 License:  MIT License
-          [https://github.com/pezmaster31/bamtools/blob/master/LICENSE]
+          [https://github.com/shenwei356/seqkit/blob/master/LICENSE]
 
 ================================================================================
 
diff --git a/examples/input_C_longicornis.yaml b/examples/input_C_longicornis.yaml
index 208f080..78887a2 100644
--- a/examples/input_C_longicornis.yaml
+++ b/examples/input_C_longicornis.yaml
@@ -1,3 +1,3 @@
 genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029//603/195/GCF_029603195.1_ASM2960319v2/GCF_029603195.1_ASM2960319v2_genomic.fna.gz
-reads_query: 'txid2530218[Organism] AND biomol_transcript[properties] NOT SRS024887[Accession]'
+reads: txid2530218[Organism] AND biomol_transcript[properties] NOT SRS024887[Accession]
 taxid: 2530218
\ No newline at end of file
diff --git a/examples/input_Gavia_stellata.yaml b/examples/input_Gavia_stellata.yaml
index 9196df1..ad08b5e 100644
--- a/examples/input_Gavia_stellata.yaml
+++ b/examples/input_Gavia_stellata.yaml
@@ -1,3 +1,3 @@
 genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/936/135/GCF_030936135.1_bGavSte3.hap2/GCF_030936135.1_bGavSte3.hap2_genomic.fna.gz
-reads_query: 'txid37040[Organism] AND biomol_transcript[properties] NOT SRS024887[Accession]'
+reads: txid37040[Organism] AND biomol_transcript[properties] NOT SRS024887[Accession]
 taxid: 37040
diff --git a/nf/subworkflows/ncbi/gnomon/align_sort_sa/main.nf b/nf/subworkflows/ncbi/default/align_sort_sa/main.nf
similarity index 100%
rename from nf/subworkflows/ncbi/gnomon/align_sort_sa/main.nf
rename to nf/subworkflows/ncbi/default/align_sort_sa/main.nf
diff --git a/nf/subworkflows/ncbi/default/annot_builder/main.nf b/nf/subworkflows/ncbi/default/annot_builder/main.nf
index 5c37ea6..66393a9 100644
--- a/nf/subworkflows/ncbi/default/annot_builder/main.nf
+++ b/nf/subworkflows/ncbi/default/annot_builder/main.nf
@@ -30,11 +30,13 @@ workflow annot_builder {
         def m = annot_builder_main('outdir', params).collect() 
         def i = annot_builder_input('outdir', m, '01', gnomon_file, params)
         // FIXME: intended params 4-5 to be lists of all input files and all input manifests, but it complained with only one entry
-        def (all, accept) = annot_builder_run('outdir', i[0], gencoll_asn, i[1], gnomon_file, genome_asn, params)
+        def (all, accept, accept_ftable, annot) = annot_builder_run('outdir', i[0], gencoll_asn, i[1], gnomon_file, genome_asn, params)
 
     emit:
         outputs = all
         accept_asn = accept
+        accept_ftable_annot = accept_ftable
+        annot_files = annot
 }
 
 
@@ -76,6 +78,7 @@ process annot_builder_main {
     stub:
     """
         touch annot_builder_main.ini
+        echo 'main' > annot_builder_main.ini
     """
 }
 
@@ -137,6 +140,8 @@ process annot_builder_input {
     """
         touch annot_builder_input.ini
         touch input_manifest_${provider_number}.mft
+        cp ${prior_file} annot_builder_input.ini
+        echo 'input ${provider_number}' >> annot_builder_input.ini 
     """
 }
 
@@ -152,8 +157,10 @@ process annot_builder_run {
         path genome_asn, stageAs: 'genome/*'
         val params
     output:
-        path "${outdir}/*"
-        path "${outdir}/ACCEPT/accept.asn", optional: true
+        path "${outdir}/*", emit: "all"
+        path "${outdir}/ACCEPT/accept.asn", emit: "accept", optional: true
+        path "${outdir}/ACCEPT/accept.ftable_annot", emit: "accept_ftable_annot", optional: true
+        path "${outdir}/ACCEPT/*.annot", optional: true
     script:
     """
     mkdir -p $outdir/ACCEPT
@@ -165,6 +172,7 @@ process annot_builder_run {
     lds2_indexer -source genome/ -db LDS2
     # EXCEPTION_STACK_TRACE_LEVEL=Warning DEBUG_STACK_TRACE_LEVEL=Warning DIAG_POST_LEVEL=Trace
     annot_builder -accept-output both -nogenbank -lds2 LDS2 -conffile $conffile -gc-assembly $gencoll_asn -logfile ${outdir}/annot_builder.log
+    cat ${outdir}/ACCEPT/*.ftable.annot > ${outdir}/ACCEPT/accept.ftable_annot
     """
     stub:
     """
@@ -174,7 +182,15 @@ process annot_builder_run {
     mkdir -p $outdir/REPORT
     mkdir -p $outdir/TEST
     
-    touch ${outdir}/annot_builder.log
-    touch ${outdir}/accept.asn
+    echo "1" > ${outdir}/annot_builder.log
+    echo "2" > ${outdir}/accept.asn
+    echo "3" > ${outdir}/accept.ftable.annot
+    
+
+    echo "4" > ${outdir}/ACCEPT/accept.asn
+    echo "5" > ${outdir}/ACCEPT/accept.ftable_annot
+    echo "S1" > ${outdir}/ACCEPT/S1.annot
+    echo "S2" > ${outdir}/ACCEPT/S2.annot
+
     """
 }
diff --git a/nf/subworkflows/ncbi/default/annotwriter/main.nf b/nf/subworkflows/ncbi/default/annotwriter/main.nf
index 3cd83be..9267e1f 100644
--- a/nf/subworkflows/ncbi/default/annotwriter/main.nf
+++ b/nf/subworkflows/ncbi/default/annotwriter/main.nf
@@ -17,17 +17,21 @@ process run_annotwriter {
     input:
         path accept_asn_file
     output:
-        path ('output/accept.gff')  , emit: 'annoted_file'
+        path ('output/accept.gff'), emit: 'annoted_file'
 
     script:
     """
     mkdir -p output
-    annotwriter -i ${accept_asn_file} -nogenbank -format gff3 -o output/accept.gff
+    if [ -s ${accept_asn_file} ]; then
+        annotwriter -i ${accept_asn_file} -nogenbank -format gff3 -o output/accept.gff
+    else
+        touch output/accept.gff
+    fi
     """
 
     stub:
     """
     mkdir -p output
-    touch output/accept.gff
+    echo "1"  > output/accept.gff
     """
 }
diff --git a/nf/subworkflows/ncbi/gnomon-training-iteration/main.nf b/nf/subworkflows/ncbi/gnomon-training-iteration/main.nf
index d30159c..82b2acc 100644
--- a/nf/subworkflows/ncbi/gnomon-training-iteration/main.nf
+++ b/nf/subworkflows/ncbi/gnomon-training-iteration/main.nf
@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 nextflow.enable.dsl=2
-nextflow.preview.recursion=true
+//nextflow.preview.recursion=true
 
 
 include { gnomon_training_iteration; gnomon_training_iteration as gnomon_training_iteration2; 
@@ -20,22 +20,21 @@ workflow gnomon_training_iterations {
         gnomon_softmask_lds2
         gnomon_softmask_lds2_source
         gnomon_scaffolds
-        chainer_parameters
-        gnomon_parameters
-        gnomon_training_parameters
+        max_intron
+        parameters
     main:
     gnomon_training_iteration(models_file, genome_asn, proteins_asn ,chainer_alignments,chainer_evidence_denylist,chainer_gap_fill_allowlist,
-               chainer_trusted_genes,  chainer_scaffolds, gnomon_softmask_lds2,
-               gnomon_softmask_lds2_source, gnomon_scaffolds, chainer_parameters, gnomon_parameters, gnomon_training_parameters)
+               chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
+               gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
     gnomon_training_iteration2(gnomon_training_iteration.out.hmm_params_file, genome_asn, proteins_asn ,chainer_alignments,
-               chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes,  chainer_scaffolds, gnomon_softmask_lds2,
-               gnomon_softmask_lds2_source, gnomon_scaffolds, chainer_parameters, gnomon_parameters, gnomon_training_parameters)
+               chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
+               gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
     gnomon_training_iteration3(gnomon_training_iteration2.out.hmm_params_file, genome_asn, proteins_asn ,chainer_alignments,
-               chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes,  chainer_scaffolds, gnomon_softmask_lds2,
-               gnomon_softmask_lds2_source, gnomon_scaffolds, chainer_parameters, gnomon_parameters, gnomon_training_parameters)
+               chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
+               gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
     gnomon_training_iteration4(gnomon_training_iteration3.out.hmm_params_file, genome_asn, proteins_asn ,chainer_alignments,
-               chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes,  chainer_scaffolds, gnomon_softmask_lds2,
-               gnomon_softmask_lds2_source, gnomon_scaffolds, chainer_parameters, gnomon_parameters, gnomon_training_parameters)
+               chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
+               gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
 
     emit:
         hmm_params_file = gnomon_training_iteration4.out.hmm_params_file
@@ -84,14 +83,13 @@ workflow gnomon_training_iterations {
         gnomon_softmask_lds2
         gnomon_softmask_lds2_source
         gnomon_scaffolds
-        chainer_parameters
-        gnomon_parameters
-        gnomon_training_parameters
+        max_intron
+        parameters
     main:
         gnomon_training_iteration
             .recurse(models_file, genome_asn, proteins_asn ,chainer_alignments,chainer_evidence_denylist,chainer_gap_fill_allowlist, 
                chainer_trusted_genes,  chainer_scaffolds, gnomon_softmask_lds2,
-               gnomon_softmask_lds2_source, gnomon_scaffolds, chainer_parameters, gnomon_parameters, gnomon_training_parameters)
+               gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
             .times(4)
     emit:
         hmm_params_file = gnomon_training_iteration.out.hmm_params_file
diff --git a/nf/subworkflows/ncbi/gnomon-training-iteration/utilities.nf b/nf/subworkflows/ncbi/gnomon-training-iteration/utilities.nf
index 06e01fd..0bdb480 100644
--- a/nf/subworkflows/ncbi/gnomon-training-iteration/utilities.nf
+++ b/nf/subworkflows/ncbi/gnomon-training-iteration/utilities.nf
@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 nextflow.enable.dsl=2
-nextflow.preview.recursion=true
+// nextflow.preview.recursion=true
 
 include { chainer_wnode as chainer } from '../gnomon/chainer_wnode/main'
 include { gnomon_wnode } from '../gnomon/gnomon_wnode/main'
@@ -20,14 +20,13 @@ workflow gnomon_training_iteration {
         gnomon_softmask_lds2
         gnomon_softmask_lds2_source
         gnomon_scaffolds
-        chainer_parameters
-        gnomon_parameters
-        gnomon_training_parameters
+        max_intron
+        parameters
     main:
 
-        chainer(chainer_alignments, models_file, chainer_evidence_denylist, chainer_gap_fill_allowlist, chainer_scaffolds, chainer_trusted_genes, genome_asn, proteins_asn, chainer_parameters)
-        gnomon_wnode(gnomon_scaffolds, chainer.out.chains, chainer.out.chains_slices, models_file, gnomon_softmask_lds2, gnomon_softmask_lds2_source, genome_asn, proteins_asn,  gnomon_parameters)
-        gnomon_training(genome_asn, gnomon_wnode.out.outputs, gnomon_training_parameters)
+        chainer(chainer_alignments, models_file, chainer_evidence_denylist, chainer_gap_fill_allowlist, chainer_scaffolds, chainer_trusted_genes, genome_asn, proteins_asn, parameters.get('chainer', [:]))
+        gnomon_wnode(gnomon_scaffolds, chainer.out.chains, chainer.out.chains_slices, models_file, gnomon_softmask_lds2, gnomon_softmask_lds2_source, genome_asn, proteins_asn,  parameters.get('gnomon', [:]))
+        gnomon_training(genome_asn, gnomon_wnode.out.outputs, max_intron, parameters.get('gnomon_training', [:]))
 
     emit:
         hmm_params_file = gnomon_training.out.hmm_params_file
@@ -41,7 +40,6 @@ workflow gnomon_training_iteration {
         gnomon_softmask_lds2 = gnomon_softmask_lds2
         gnomon_softmask_lds2_source = gnomon_softmask_lds2_source
         gnomon_scaffolds = gnomon_scaffolds
-        chainer_parameters = chainer_parameters
-        gnomon_parameters  = gnomon_parameters
-        gnomon_training_parameters = gnomon_training_parameters
+        max_intron = max_intron
+        parameters = parameters
 }
diff --git a/nf/subworkflows/ncbi/gnomon/chainer_wnode/main.nf b/nf/subworkflows/ncbi/gnomon/chainer_wnode/main.nf
index e645d8c..478eaf8 100644
--- a/nf/subworkflows/ncbi/gnomon/chainer_wnode/main.nf
+++ b/nf/subworkflows/ncbi/gnomon/chainer_wnode/main.nf
@@ -3,7 +3,7 @@ nextflow.enable.dsl=2
 
 
 include { merge_params } from '../../utilities'
-include { run_align_sort }  from '../align_sort_sa/main.nf'
+include { run_align_sort }  from '../../default/align_sort_sa/main.nf'
 
 split_count=16
 
@@ -145,8 +145,8 @@ process run_gpx_make_outputs {
     output:
         path "output/chains.*.out.gz", emit: 'chains'
         path "output/chains.*.out.gz.slices", emit: 'chains_slices'
-        path "output/evidence.*.out.gz", emit: 'evidence'
-        path "output/evidence.*.out.gz.slices", emit: 'evidence_slices'
+        path "output/evidence.*.out.gz", emit: 'evidence', optional: true
+        path "output/evidence.*.out.gz.slices", emit: 'evidence_slices', optional: true
     script:
     """
     ls -1 gpx_inputs/* > gpx_inputs.mft
diff --git a/nf/subworkflows/ncbi/gnomon/diamond/main.nf b/nf/subworkflows/ncbi/gnomon/diamond/main.nf
index 0ed88c1..ad37a5c 100644
--- a/nf/subworkflows/ncbi/gnomon/diamond/main.nf
+++ b/nf/subworkflows/ncbi/gnomon/diamond/main.nf
@@ -1,30 +1,8 @@
 #!/usr/bin/env nextflow
 nextflow.enable.dsl=2
 
-
-/*
- *Execution of: 
- * /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/bin/diamond 
- *    -asn-cache /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/sequence_cache 
- *    -blastp-args '--sam-query-len --comp-based-stats 0 --evalue 0.0001 --very-sensitive --max-hsps 3' 
- *    -diamond-executable /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/third-party/diamond/diamond 
- *    -lds2 /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/prot_gnomon_prepare.8202002/out/LDS2 
- *    -ofmt seq-align-set 
- *    -output-dir /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out 
- *    -output-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out/align.mft 
- *    -output-prefix hits 
- *    ## query is gnomon-made proteins 'gnl|GNOMON|23016146.p'
- *    ## query-fmt is <String, `fasta', `seq-ids'>
- *    -query-fmt seq-ids 
- *    -query-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/query_ids.mft 
- *    ## subject is swiss-prot ids 'sp|A0A009IHW8.1|ABTIR_ACIB9'
- *    -subject-fmt seq-ids 
- *    -subject-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/subject_ids.mft 
- *    -work-area /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/tmp
-
- */
-
 include { merge_params; to_map; shellSplit } from '../../utilities'
+include { run_diamond_egap;} from '../../shared/diamond/main'
 
 
 workflow diamond_worker {
@@ -35,92 +13,12 @@ workflow diamond_worker {
         swiss_prot_asn
         parameters  // Map : extra parameter and parameter update
     main:
-        String diamond_egap_params = merge_params('-query-fmt seq-ids -subject-fmt seq-ids -output-prefix hits -ofmt seq-align-set', parameters, 'diamond')
-        // move out or above?
-        //swiss_prot_asn = fetch_swiss_prot_asn()
-        //swiss_prot_ids = get_swiss_prot_ids(swiss_prot_asn)
+        String diamond_blastp_params = merge_params('--sam-query-len --very-sensitive --unal 0 --comp-based-stats 0 --masking 0', parameters, 'diamond_blastp')
+        String diamond_regular_params = merge_params('-ofmt seq-align-set -query-fmt seq-ids -subject-fmt seq-ids -output-prefix hits', parameters, 'diamond')
+        String diamond_egap_params = '-blastp-args \''  + diamond_blastp_params + '\' '  + diamond_regular_params
+        
         run_diamond_egap(gnomon_prot_ids, swiss_prot_ids, gnomon_prot_asn, swiss_prot_asn, diamond_egap_params)
 
     emit:
         alignments = run_diamond_egap.out
 }
-
-
-swiss_prot_url='https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/reference_sets/swissprot.asnb.gz'
-process fetch_swiss_prot_asn  {
-    input:
-    output:
-        path "output/swissprot.asnb"
-    script:
-    """
-        curl -O '$swiss_prot_url'
-        gunzip swissprot.asnb.gz
-        mkdir -p output
-        mv swissprot.asnb output/swissprot.asnb
-    """   
-    stub:
-    """
-        mkdir -p output
-        touch output/swissprot.asnb
-    """
-}
-
-process get_swiss_prot_ids {
-    input:
-        path swiss_prot_asn
-    output:
-        path "output/swiss_prot_ids"
-    script: 
-    """
-        mkdir -p output
-        lds2_indexer  -db lds -source  .
-        sqlite3 ./lds "SELECT txt_id FROM seq_id WHERE orig=1 AND int_id IS NULL;"    > output/swiss_prot_ids
-    """
-    stub:
-    """
-        mkdir -p output
-        touch output/swiss_prot_ids
-    """
-}
-
-process run_diamond_egap {
-    input:
-        path gnomon_prot_ids
-        path swiss_prot_ids
-        path gnomon_prot_asn, stageAs: 'indexed/*'
-        path swiss_prot_asn, stageAs: 'indexed/*'
-        val params
-    output:
-        path "output/*"
-    script:
-    print(params)
-    """
-   
-    ###diamond_bin=`which diamond`
-    #diamond_egap uses GP_HOME to build paths to both some gp apps, and third-party
-    #GP_HOME needs to be the directory that contains third-party, and the directory that contains bin/<gp apps> 
-    diamond_bin=\${GP_HOME}/third-party/diamond/diamond
-    
-    mkdir -p ./asncache/
-
-    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${gnomon_prot_asn} -oseq-ids /dev/null -split-sequences
-    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${swiss_prot_asn} -oseq-ids /dev/null -split-sequences
-
-    mkdir ./output
-    mkdir ./work
-
-    echo  ${params}
-
-    diamond_egap  ${params} -asn-cache ./asncache/ -nogenbank -query ${gnomon_prot_ids} -subject ${swiss_prot_ids} \
-        -output-dir ./output/ -work-area ./work/  -diamond-executable \${diamond_bin}
-    rm -rf ./work
-    """
-
-    stub:
-    """
-    mkdir -p output
-    touch output/diamond_output.asn
-    """
-}
-
-
diff --git a/nf/subworkflows/ncbi/gnomon/gnomon_biotype/main.nf b/nf/subworkflows/ncbi/gnomon/gnomon_biotype/main.nf
index 22adf6c..fd10c2a 100644
--- a/nf/subworkflows/ncbi/gnomon/gnomon_biotype/main.nf
+++ b/nf/subworkflows/ncbi/gnomon/gnomon_biotype/main.nf
@@ -15,7 +15,7 @@ workflow gnomon_biotype {
         parameters  // Map : extra parameter and parameter update
     main:
         default_params = ""
-        effective_params = merge_params(default_params, parameters, 'gnomon_training')
+        effective_params = merge_params(default_params, parameters, 'gnomon_biotype')
         run_gnomon_biotype(models_files, splices_files, denylist, gencoll_asn, swiss_prot_asn,  lds2_source, raw_blastp_hits, default_params)
     emit:
         biotypes = run_gnomon_biotype.out.biotypes
@@ -50,7 +50,12 @@ process run_gnomon_biotype {
     echo "${models_files.join('\n')}" > models.mft
     echo "prot_hits.asn" > prot_hits.mft
     echo "${splices_files.join('\n')}" > splices.mft
-    gnomon_biotype  -gc $gencoll_asn -asn-cache ./asncache/  -nogenbank -gnomon_models models.mft -o output/biotypes.tsv -o_prots_rpt output/prots_rpt.tsv -prot_denylist $denylist -prot_hits prot_hits.mft -prot_splices splices.mft
+    if [ -z "$denylist" ]
+    then
+      gnomon_biotype  -gc $gencoll_asn -asn-cache ./asncache/  -nogenbank -gnomon_models models.mft -o output/biotypes.tsv -o_prots_rpt output/prots_rpt.tsv -prot_hits prot_hits.mft -prot_splices splices.mft  -reftrack-server 'NONE' -allow_lt631 true
+    else
+      gnomon_biotype  -gc $gencoll_asn -asn-cache ./asncache/  -nogenbank -gnomon_models models.mft -o output/biotypes.tsv -o_prots_rpt output/prots_rpt.tsv -prot_denylist $denylist -prot_hits prot_hits.mft -prot_splices splices.mft  -reftrack-server 'NONE' -allow_lt631 true
+    fi
     """
     stub:
     """
@@ -59,3 +64,4 @@ process run_gnomon_biotype {
     touch output/biotypes.tsv
     """
 }
+
diff --git a/nf/subworkflows/ncbi/gnomon/gnomon_training/main.nf b/nf/subworkflows/ncbi/gnomon/gnomon_training/main.nf
index 4427ad9..bcb5957 100644
--- a/nf/subworkflows/ncbi/gnomon/gnomon_training/main.nf
+++ b/nf/subworkflows/ncbi/gnomon/gnomon_training/main.nf
@@ -7,32 +7,39 @@ workflow gnomon_training {
     take:
         genome_asn
         models_file
+        max_intron1 // max intron length, name modified from max_intron to pacify stupid Nextflow compiler
         parameters  // Map : extra parameter and parameter update
     main:
         default_params = "-b -asn -maxintron 1200000"
         effective_params = merge_params(default_params, parameters, 'gnomon_training')
-        run_gnomon_training(genome_asn, models_file, default_params)
+        run_gnomon_training(genome_asn, models_file, max_intron1, effective_params)
     emit:
         hmm_params_file = run_gnomon_training.out.hmm_params_file
 }
 
 
-
 process run_gnomon_training {
     input:
         path genome_asn, stageAs: 'indexed/*'
         path models_file
+        val max_intron1
         val parameters
     output:
         path ('output/hmm_params.asn'), emit: 'hmm_params_file'
 
     script:
+    // Substitute -maxintron with correct value coming from max_intron
+    def dummy = ["dummy" : "-maxintron ${max_intron1}"]
+    parameters = merge_params(parameters, dummy, "dummy")
     """
     mkdir -p output
     lds2_indexer -source indexed -db ./indexed_lds
     gnomon_training ${parameters} -nogenbank -lds2 ./indexed_lds  -input ${models_file} -out output/hmm_params.asn 
     """
     stub:
+    def dummy = ["dummy" : "-maxintron ${max_intron1}"]
+    parameters = merge_params(parameters, dummy, "dummy")
+    println("Gnomon training parameters: ${parameters}")
     """
     mkdir -p output
     touch  output/hmm_params.asn
diff --git a/nf/subworkflows/ncbi/gnomon/locus_link/main.nf b/nf/subworkflows/ncbi/gnomon/locus_link/main.nf
new file mode 100644
index 0000000..e4d3ffb
--- /dev/null
+++ b/nf/subworkflows/ncbi/gnomon/locus_link/main.nf
@@ -0,0 +1,116 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+include { merge_params } from '../../utilities'
+
+workflow locus_link {
+    take:
+        best_refseq_prot_hit
+        orthologs
+        annotation 
+        gencoll_asn
+        gnomon_lds2_source
+        best_prot_hit
+        track_loci
+        comparisons
+        curr_prev_compare
+        gnomon_biotypes
+        lxr_data
+        proteins_asn
+        name_from_ortholog
+        parameters  // Map : extra parameter and parameter update
+    main:
+        default_params = ""
+        effective_params = merge_params(default_params, parameters, 'locus_link')
+        run_locus_link(best_refseq_prot_hit, orthologs, annotation, 
+                 gencoll_asn, gnomon_lds2_source, best_prot_hit, track_loci, comparisons,  curr_prev_compare,  
+                 gnomon_biotypes, lxr_data, proteins_asn, name_from_ortholog,  default_params)
+    emit:
+        best_gnomon_prot_hit = run_locus_link.out.best_gnomon_prot_hit
+        best_refseq_prot_hit = run_locus_link.out.best_refseq_prot_hit
+        locustypes = run_locus_link.out.locustypes
+        locus = run_locus_link.out.locus
+        stats = run_locus_link.out.stats
+        all = run_locus_link.out.all
+}
+
+
+
+process run_locus_link {
+    input:
+        path best_refseq_prot_hit
+        path orthologs
+        path annotation 
+        path gencoll_asn
+        path gnomon_lds2_source, stageAs: 'genome/*'
+        path best_prot_hit
+        path track_loci
+        path comparisons
+        path curr_prev_compare
+        path gnomon_biotypes
+        path lxr_data
+        path proteins_asn
+        path name_from_ortholog
+        val parameters
+    output:
+        path ('output/best_gnomon_prot_hit.tsv'), emit: 'best_gnomon_prot_hit'
+        path ('output/best_refseq_prot_hit.tsv'), emit: 'best_refseq_prot_hit'
+        path ('output/locustypes.tsv'), emit: 'locustypes'
+        path ('output/locus.lnk'), emit: 'locus'
+        path ('output/stats.xml'), emit: 'stats'
+        path ('output/*'), emit: 'all'
+    script:
+    """
+    mkdir -p output
+    mkdir -p ./asncache/
+    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i $proteins_asn  -oseq-ids /dev/null -split-sequences
+    
+    lds2_indexer -source genome/ -db LDS2 
+    echo "${best_prot_hit.join('\n')}" > best_prot_hit.mft
+    extract_prot_names -alns best_prot_hit.mft  -nogenbank -o output/best_gnomon_prot_hit.tsv -asn-cache ./asncache/ -lds2 LDS2
+    echo "${best_refseq_prot_hit.join('\n')}" > best_refseq_prot_hit.mft
+    extract_prot_names -alns best_refseq_prot_hit.mft -nogenbank -o output/best_refseq_prot_hit.tsv -asn-cache ./asncache/ -lds2 LDS2 
+    echo "${annotation.join('\n')}" > annotation.mft
+    echo "${curr_prev_compare.join('\n')}" > curr_prev_compare.mft
+    echo  "${comparisons.join('\n')}"  > comparisons.mft
+    str=""
+    if [ ! -z "$orthologs" ]
+    then
+        str="\$str -orthologs $orthologs"
+    fi
+    if [ ! -z "$lxr_data" ]
+    then
+        str="\$str -lxr $lxr_data"
+    else
+        touch lxr_data
+        str="\$str -lxr lxr_data"
+    fi
+
+    if [ ! -z "$track_loci" ]
+    then
+        str="\$str -locus_track $track_loci"
+    else
+        touch track_loci
+        str="\$str -locus_track track_loci"
+    fi
+    if [ ! -z "$name_from_ortholog" ]
+    then
+        str="\$str -name_from_ortholog_rpt $name_from_ortholog"
+    else
+	    touch name_from_ortholog
+        str="\$str -name_from_ortholog_rpt name_from_ortholog"
+    fi
+
+    locus_type  -no_acc_reserve  -annots annotation.mft -gc $gencoll_asn -gnomon_biotype $gnomon_biotypes -o_stats output/stats.xml -o_locustypes output/locustypes.tsv -o_locus_lnk output/locus.lnk  -annotcmp comparisons.mft  -annotcmp_pb curr_prev_compare.mft \$str
+    """
+    stub:
+    """
+    mkdir -p output
+    touch output/best_gnomon_prot_hit.tsv
+    touch output/best_refseq_prot_hit.tsv
+    touch output/locustypes.tsv
+    touch output/locus.lnk
+    touch output/stats.xml
+    """
+}
+
diff --git a/nf/subworkflows/ncbi/gnomon/main.nf b/nf/subworkflows/ncbi/gnomon/main.nf
new file mode 100644
index 0000000..5787e1b
--- /dev/null
+++ b/nf/subworkflows/ncbi/gnomon/main.nf
@@ -0,0 +1,96 @@
+#!/usr/bin/env nextflow
+// gnomon plane workflow
+// route data to tasks
+
+nextflow.enable.dsl=2
+
+include { chainer_wnode as chainer } from './chainer_wnode/main'
+include { gnomon_wnode } from './gnomon_wnode/main'
+include { prot_gnomon_prepare } from './prot_gnomon_prepare/main'
+include { gnomon_training_iterations } from '../gnomon-training-iteration/main'
+
+include { diamond_worker} from './diamond/main'
+include { best_protein_hits } from './protein_filter/main'
+include { gnomon_biotype} from './gnomon_biotype/main'
+include { fetch_swiss_prot_asn; get_swiss_prot_ids } from '../shared/diamond/main'
+include { diamond_orthology } from '../orthology/diamond_orthology/main'
+include { locus_link } from './locus_link/main'
+
+
+params.intermediate = false
+
+workflow gnomon_plane {
+    take:
+        genome_asn
+        scaffolds
+        gencoll_asn
+        proteins_asn
+        alignments // list of all relevent input alignments
+
+        // Alternative parameters, one of them should be set
+        // tax_id - NCBI tax id of the closest taxon to the genome
+        // hmm_params - HMM parameters
+        tax_id          // NCBI tax id of the closest taxon to the genome
+        hmm_params      // HMM parameters
+        hmm_taxid       // NCBI tax id of the taxon of the HMM
+        //
+        softmask        // softmask for GNOMON, optional
+        max_intron      // max intron length
+        task_params     // task parameters for every task
+    main:
+        // GNOMON
+        def effective_hmm
+        if (tax_id == hmm_taxid) {
+            effective_hmm = hmm_params
+        } else {
+            effective_hmm = gnomon_training_iterations(hmm_params, genome_asn, proteins_asn, alignments, /* evidence_denylist */ [], /* gap_fill_allowlist */ [],
+                /* trusted_genes */ [], scaffolds, softmask,
+                softmask, scaffolds,
+                max_intron,
+                task_params)
+        }
+
+        chainer(alignments, effective_hmm, /* evidence_denylist */ [], /* gap_fill_allowlist */ [], scaffolds, /* trusted_genes */ [], genome_asn, proteins_asn, task_params.get('chainer', [:]))
+
+        def gn_models = []
+        gnomon_wnode(scaffolds, chainer.out.chains, chainer.out.chains_slices, effective_hmm, [], softmask, genome_asn, proteins_asn, task_params.get('gnomon', [:]))
+       
+    emit:
+        gnomon_models = gnomon_wnode.out.outputs
+        // trained_hmm = effective_hmm
+}
+
+
+
+workflow post_gnomon_plane {
+    take:
+        gnomon_models
+        gencoll_asn
+        orthologs
+
+
+        // Alternative parameters, one of them should be set
+        // tax_id - NCBI tax id of the closest taxon to the genome
+        // hmm_params - HMM parameters
+        tax_id          // NCBI tax id of the closest taxon to the genome
+        task_params     // task parameters for every task
+    main:
+        // Post GNOMON
+        // might come its own plane
+        def swiss_prot_asn = fetch_swiss_prot_asn()
+        def swiss_prot_ids = get_swiss_prot_ids(swiss_prot_asn)
+
+        prot_gnomon_prepare(gnomon_models, task_params.get('prot_gnomon_prepare', [:]))
+        // Seed Protein-Model Hits
+        diamond_worker(prot_gnomon_prepare.out.prot_ids, swiss_prot_ids, gnomon_models, swiss_prot_asn, task_params.get('diamond', [:]))
+        best_protein_hits(gnomon_models, swiss_prot_asn,  diamond_worker.out.alignments , task_params.get('protein_filter', [:]))
+
+        gnomon_biotype([] /*models*/,/*splices_file  -- constant*/ [],  /*denylist -- constant*/ [], gencoll_asn, swiss_prot_asn, gnomon_models, diamond_worker.out.alignments,task_params.get('gnomon_biotype', [:]))
+        locus_link(/*best_refseq_prot_hit  -- best protein hits from refseq plane*/ [], orthologs, []  /*annot_builder.out.annot_files*/, 
+                gencoll_asn, gnomon_models, best_protein_hits.out.alignments , /*track_loci*/ [], /*comparisons*/ [],  /*curr_prev_compare*/ [], 
+                gnomon_biotype.out.biotypes, /*lxr_data*/ [], swiss_prot_asn, /*name_from_ortholog */ [],  task_params.get('locus_link', [:]))
+
+       
+    emit:
+        locus = locus_link.out.locus
+}
diff --git a/nf/subworkflows/ncbi/gnomon/prot_gnomon_prepare/main.nf b/nf/subworkflows/ncbi/gnomon/prot_gnomon_prepare/main.nf
index ba5db1e..715eddd 100644
--- a/nf/subworkflows/ncbi/gnomon/prot_gnomon_prepare/main.nf
+++ b/nf/subworkflows/ncbi/gnomon/prot_gnomon_prepare/main.nf
@@ -14,6 +14,9 @@ workflow prot_gnomon_prepare {
         prot_gnomon_prepare_p(models, prot_gnomon_prepare_params)
     emit:
         outputs = prot_gnomon_prepare_p.out.outputs
+        LDS2 = prot_gnomon_prepare_p.out.LDS2
+        prot_ids = prot_gnomon_prepare_p.out.prot_ids
+        nuc_ids = prot_gnomon_prepare_p.out.nuc_ids
 }
 
 
@@ -23,6 +26,9 @@ process prot_gnomon_prepare_p {
         val params
     output:
         path "*", emit: 'outputs'
+        path "LDS2", emit: 'LDS2'
+        path "prot_ids.seq_id", emit: 'prot_ids'
+        path "nuc_ids.seq_id", emit: 'nuc_ids'
     script:
     """
     echo ${models} |tr ' ' '\\n' > models.mft
diff --git a/nf/subworkflows/ncbi/gnomon/protein_filter/main.nf b/nf/subworkflows/ncbi/gnomon/protein_filter/main.nf
index f07639a..7381ef6 100644
--- a/nf/subworkflows/ncbi/gnomon/protein_filter/main.nf
+++ b/nf/subworkflows/ncbi/gnomon/protein_filter/main.nf
@@ -2,32 +2,13 @@
 nextflow.enable.dsl=2
 
 
+
 /*
- *Execution of: 
- * /netmnt/vast01/gpi/prod/GPIPE_PROD/system/current/arch/x86_64/bin/gp_makeblastdb 
-    -nogenbank
-    -asn-cache ''
-    -db ./spdb
-    -asnb swissprot.asnb
-    -dbtype prot
-    -title 'BLASTdb used for naming tasks in GPipe'
-
- * /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/bin/align_sort 
- *   -ifmt seq-align-set -input-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/protein_filter.8201942/inp/blast_align.mft 
- *   -k query,query_start,-query_end,query_strand,subject,subject_start,-subject_end,subject_strand,-num_ident,gap_count 
- *   -o /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/protein_filter.8201942/var/blast_align_sorted.asnb 
- *   -tmp /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/protein_filter.8201942/var 
- *   -nogenbank -limit-mem 13G 
- * /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/bin/protein_filter 
- *   -lds2 /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/prot_gnomon_prepare.8202002/out/LDS2 
- *   -asn-cache /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/sequence_cache 
- *   -filter 'pct_coverage >= 50' 
- *   -input /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/protein_filter.8201942/var/blast_align_sorted.asnb 
- *   -nr-path /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/create_nr_blast_db.8200792/out/blastdb 
- *   -output /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/protein_filter.8201942/out/blast.asn 
- *   -taxid 37040 
+ *   align_filter -filter 'pct_coverage >= 50' -nogenbank 
+ *      | align_sort -ifmt seq-align-set -k query,-bit_score,slen,-align_length -group 1 -top 1 -nogenbank
  */
 
+
 include { merge_params; to_map; shellSplit } from '../../utilities'
 
 
@@ -36,49 +17,41 @@ workflow best_protein_hits {
         gnomon_prot_asn
         swiss_prot_asn
         prot_alignments
-        taxid
         parameters  // Map : extra parameter and parameter update
     main:
-        String align_sort_params = merge_params('-nogenbank', parameters, 'align_sort')
-        String protein_filter_params = merge_params('-nogenbank', parameters, 'protein_filter')
+        String align_filter_params = merge_params(' -ifmt seq-align-set -filter \'pct_coverage >= 50\' -nogenbank', parameters, 'align_filter')
+        String align_sort_params = merge_params(' -ifmt seq-align-set -k query,-bit_score,slen,-align_length -group 1 -top 1 -nogenbank', parameters, 'align_sort')
 
-        run_protein_filter(gnomon_prot_asn, swiss_prot_asn, prot_alignments, taxid, align_sort_params, protein_filter_params)
+        run_protein_filter_replacement(gnomon_prot_asn, swiss_prot_asn, prot_alignments, align_filter_params, align_sort_params)
 
     emit:
-        alignments = run_protein_filter.out
+        alignments = run_protein_filter_replacement.out
 }
 
 
-
-process run_protein_filter {
+process run_protein_filter_replacement {
     input:
         path gnomon_prot_asn, stageAs: 'indexed/*'
         path swiss_prot_asn, stageAs: 'indexed/*'
         path input_prot_alignments, stageAs: "input_alignments.asnb"
-        val taxid
+        val align_filter_params
         val align_sort_params
-        val protein_filter_params
     output:
         path "output/*"
     script:
     """
-    
     mkdir -p ./asncache/
-
     prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${gnomon_prot_asn} -oseq-ids /dev/null -split-sequences
     prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${swiss_prot_asn} -oseq-ids /dev/null -split-sequences
 
-    mkdir ./output
-    mkdir ./work
-    mkdir ./spdb
-
-    /netmnt/vast01/gpi/prod/GPIPE_PROD/system/current/arch/x86_64/bin/gp_makeblastdb -nogenbank -asn-cache ./asncache/ -db ./spdb/spdb -asnb ${swiss_prot_asn} -dbtype prot -title 'BLASTdb used for naming tasks in GPipe'
+    mkdir -p ./output
 
-    align_sort $align_sort_params -asn-cache ./asncache/ -input $input_prot_alignments -o ./sorted_prot_alignments.asnb  -tmp ./work/ 
+    align_filter $align_filter_params -asn-cache ./asncache  -i ./input_alignments.asnb -o - | align_sort -i - $align_sort_params -asn-cache ./asncache  -o - | align_pack -ifmt seq-align -i - -ofmt seq-align-set -o ./output/best_protein_hits.asnb 
+    ##align_filter $align_filter_params -asn-cache ./asncache  -i ./input_alignments.asnb -o ./t1.asnb 
+    ##align_sort -i ./t1.asnb $align_sort_params -asn-cache ./asncache  -o ./t2.asnb     
+    ##align_pack -ifmt seq-align -i ./t2.asnb -ofmt seq-align-set -o ./t3.asnb
+    ##cp ./t3.asnb ./output/best_protein_hits.asnb
 
-    protein_filter $protein_filter_params -asn-cache ./asncache/ -taxid $taxid -input ./sorted_prot_alignments.asnb -output ./output/best_protein_hits.asnb -nr-path ./spdb/spdb
-    
-    rm -rf ./work
     """
 
     stub:
diff --git a/nf/subworkflows/ncbi/main.nf b/nf/subworkflows/ncbi/main.nf
index de959bd..fe19bd1 100644
--- a/nf/subworkflows/ncbi/main.nf
+++ b/nf/subworkflows/ncbi/main.nf
@@ -4,35 +4,25 @@
 
 nextflow.enable.dsl=2
 
+include { rnaseq_short_plane } from './rnaseq_short/main'
+include { target_proteins_plane } from './target_proteins/main'
+include { gnomon_plane; post_gnomon_plane } from './gnomon/main'
+include { orthology_plane } from './orthology/main'
 include { setup_genome; setup_proteins } from './setup/main'
-include { sra_query } from './rnaseq_short/sra_qry/main'
-include { fetch_sra_fasta } from './rnaseq_short/fetch_sra_fasta/main'
-include { star_index } from './rnaseq_short/star_index/main'
-include { star_wnode_simplified as star_simplified; star_wnode as star } from './rnaseq_short/star_wnode/main'
-include { bam_strandedness } from './rnaseq_short/bam_strandedness/main'
-include { bam_bin_and_sort } from './rnaseq_short/bam_bin_and_sort/main'
-include { bam2asn } from './rnaseq_short/convert_from_bam/main'
-include { rnaseq_collapse } from './rnaseq_short/rnaseq_collapse/main'
-include { get_hmm_params; run_get_hmm } from './default/get_hmm_params/main'
-include { chainer_wnode as chainer } from './gnomon/chainer_wnode/main'
-include { gnomon_wnode } from './gnomon/gnomon_wnode/main'
-include { prot_gnomon_prepare } from './gnomon/prot_gnomon_prepare/main'
 include { annot_builder } from './default/annot_builder/main'
 include { annotwriter } from './default/annotwriter/main'
-include { miniprot } from './target_proteins/miniprot/main'
-include { align_filter_sa } from './target_proteins/align_filter_sa/main'
-include { best_aligned_prot } from './target_proteins/best_aligned_prot/main'
-include { paf2asn } from './target_proteins/paf2asn/main'
-include { run_align_sort} from './gnomon/align_sort_sa/main'
-include { gnomon_training_iterations; gnomon_no_training } from './gnomon-training-iteration/main'
+
 
 params.intermediate = false
+params.use_orthology = false
+params.use_post_gnomon = false
 
 
 workflow egapx {
     take:
         genome          // path to genome
         proteins        // path to proteins, optional
+
         // Alternative groups of parameters, one of them should be set
         // reads_query - SRA query in the form accepted by NCBI
         // reads_ids - list of SRA IDs
@@ -42,71 +32,48 @@ workflow egapx {
         reads           // path to reads
         reads_metadata  // path to reads metadata 13 tab-delimited fields, 1-st - SRA ID, 3-rd paired or unpaired, everything else - not used, but must be present
                         // 4, 5, 13 - numbers, 5 - non zero number
+
         organelles      // path to organelle list
         // Alternative parameters, one of them should be set
         // tax_id - NCBI tax id of the closest taxon to the genome
         // hmm_params - HMM parameters
         tax_id          // NCBI tax id of the closest taxon to the genome
         hmm_params      // HMM parameters
+        hmm_taxid       // NCBI tax id of the HMM
         //
         softmask        // softmask for GNOMON, optional
+        //
+        max_intron      // max intron length
+        genome_size_threshold // the threshold for calculating actual max intron length
         task_params     // task parameters for every task
     main:
-        def (scaffolds, gencoll_asn, unpacked_genome, genome_asn) = setup_genome(genome, organelles, task_params.get('setup', [:]))
+        print "workflow.container: ${workflow.container}"
+
+        def setup_genome_params = task_params.get('setup', [:])
+        setup_genome_params['max_intron'] = max_intron
+        setup_genome_params['genome_size_threshold'] = genome_size_threshold
+        def (scaffolds, gencoll_asn, unpacked_genome, genome_asn, genome_asnb, eff_max_intron) = setup_genome(genome, organelles, setup_genome_params)
 
         // Protein alignments
         def protein_alignments = []
         def unpacked_proteins
         def proteins_asn = []
+        def proteins_asnb = []
         if (proteins) {
             // miniprot plane
             (unpacked_proteins, proteins_asn) = setup_proteins(proteins, task_params.get('setup', [:]))
-            miniprot(unpacked_genome, unpacked_proteins, task_params.get('miniprot', [:]))
-            paf2asn(genome_asn, proteins_asn, miniprot.out.miniprot_file, task_params.get('paf2asn', [:]))
-            best_aligned_prot(genome_asn, proteins_asn, paf2asn.out.asn_file, gencoll_asn, task_params.get('best_aligned_prot', [:]))
-            align_filter_sa(genome_asn, proteins_asn, best_aligned_prot.out.asn_file, task_params.get('align_filter_sa', [:]))
-            protein_alignments = run_align_sort(genome_asn, proteins_asn,align_filter_sa.out.filtered_file, 
-                "-k subject,subject_start,-subject_end,subject_strand,query,query_start,-query_end,query_strand,-num_ident,gap_count" )
+            target_proteins_plane(unpacked_genome, genome_asn, gencoll_asn, unpacked_proteins, proteins_asn, eff_max_intron, task_params)
+            protein_alignments = target_proteins_plane.out.protein_alignments
         }
 
         // RNASeq short alignments
         def rnaseq_alignments = []
-        // Satisfy quirks of Nextflow compiler
-        def reads_query1 = reads_query
-        def reads_ids1 = reads_ids
-        // Conditional code on SRA reads source
         if (reads_query || reads_ids || reads) {
-            def index = star_index(unpacked_genome, task_params.get('star_index', [:]))
-            def ch_align, ch_align_index, sra_metadata, sra_run_list
-            if (reads_query || reads_ids) {
-                def query = reads_query1 ? reads_query1 : reads_ids1.join("[Accession] OR ") + "[Accession]"
-                (sra_metadata, sra_run_list) = sra_query(query, task_params.get('sra_qry', [:]))
-                def reads_fasta_pairs = fetch_sra_fasta(sra_run_list, task_params.get('fetch_sra_fasta', [:]))
-                (ch_align, ch_align_index) = star(scaffolds, reads_fasta_pairs, genome_asn, index, task_params.get('star_wnode', [:]))
-            } else {
-                sra_metadata = reads_metadata
-                (ch_align, ch_align_index) = star_simplified(scaffolds, reads, genome_asn, index, task_params.get('star_wnode', [:]))
-            }
-            //
-
-            bam_strandedness(ch_align.collect(), sra_metadata, task_params.get('bam_strandedness', [:]))
-            def strandedness = bam_strandedness.out.strandedness
-            
-            // Run bam_bin_and_sort
-            bam_bin_and_sort(ch_align, ch_align_index, unpacked_genome, organelles, task_params.get('bam_bin_and_sort', [:]))
-            def bam_bins = bam_bin_and_sort.out.sorted
-
-            // Run BAM2ASN
-            bam2asn(bam_bins, strandedness, genome_asn, task_params.get('convert_from_bam', [:]))
-            def asn_align = bam2asn.out.align.collect()
-            def keylist = bam2asn.out.keylist.collect()
-
-            rnaseq_collapse(genome_asn, keylist, asn_align, sra_metadata, 10, task_params.get('rnaseq_collapse', [:]))
-            rnaseq_alignments = rnaseq_collapse.out.alignments
+            rnaseq_short_plane(genome_asn, scaffolds, unpacked_genome, reads_query, reads_ids, reads, reads_metadata, organelles, tax_id, eff_max_intron, task_params) 
+            rnaseq_alignments = rnaseq_short_plane.out.rnaseq_alignments
         }
 
         // Combine RNASeq and protein alignments
-
         def alignments
         if (proteins && (reads_query || reads_ids || reads)) [
             alignments = rnaseq_alignments.combine(protein_alignments)
@@ -118,41 +85,32 @@ workflow egapx {
 
         // GNOMON
 
+        def gnomon_models = []
         def effective_hmm
-        if (hmm_params) {
-            effective_hmm = hmm_params
-        } else {
-            tmp_hmm = run_get_hmm(tax_id)
-            b = tmp_hmm | splitText( { it.split('\n') } ) | flatten | collect
-            c = b | branch { n ->
-                    exact: n[0] == tax_id.toString()
-                        return n[1]
-                    closest:  n[0] != tax_id.toString()
-                        return n[1]
-                }
-            hmm_params_closest = gnomon_training_iterations(c.closest, genome_asn, proteins_asn ,alignments , /* evidence_denylist */ [], /* gap_fill_allowlist */ [],
-               /* trusted_genes */ [], scaffolds, softmask,
-               softmask, scaffolds, task_params.get('chainer', [:]), task_params.get('gnomon', [:]), task_params.get('gnomon_training', [:]))
-            hmm_params_exact = gnomon_no_training (c.exact)
-            tmp_channel1 = Channel.of() 
-            tmp_channel2 = tmp_channel1.concat(hmm_params_closest) 
-            tmp_channel3 = tmp_channel2.concat(hmm_params_exact)
-            effective_hmm = tmp_channel3 | last
+        gnomon_plane(genome_asn, scaffolds, gencoll_asn, proteins_asn, alignments, tax_id, hmm_params, hmm_taxid, softmask, eff_max_intron, task_params) 
+        gnomon_models = gnomon_plane.out.gnomon_models
+
+
+        // outputs 
+        annot_builder(gencoll_asn, gnomon_models, genome_asn, task_params.get('annot_builder', [:]))
+        def accept_annot_file = annot_builder.out.accept_ftable_annot 
+        def annot_files = annot_builder.out.annot_files
+
+        if (params.use_orthology) {
+            // ORTHOLOGY
+            orthology_plane(genome_asnb, gencoll_asn, gnomon_models, annot_files, task_params)
+            def orthologs = orthology_plane.out.orthologs
+            if (params.use_post_gnomon) {
+                //POST GNOMON
+                post_gnomon_plane(gnomon_models, gencoll_asn, orthologs, tax_id, task_params)
+            }
         }
 
-        chainer(alignments, effective_hmm, /* evidence_denylist */ [], /* gap_fill_allowlist */ [], scaffolds, /* trusted_genes */ [], genome_asn, proteins_asn, task_params.get('chainer', [:]))
-
-        gnomon_wnode(scaffolds, chainer.out.chains, chainer.out.chains_slices, effective_hmm, [], softmask, genome_asn, proteins_asn, task_params.get('gnomon', [:]))
-        def models = gnomon_wnode.out.outputs
+        annotwriter(accept_annot_file, [:])
+        annotwriter.out.annoted_file     
 
-        // prot_gnomon_prepare(models, task_params.get('prot_gnomon_prepare', [:]))
-        
-        annot_builder(gencoll_asn, models, genome_asn, task_params.get('annot_builder', [:]))
-        def accept_asn = annot_builder.out.accept_asn
-        
-        annotwriter(accept_asn, [:])
-        annotwriter.out.annoted_file
     emit:
         out_files = annotwriter.out.annoted_file
         annot_builder_output = annot_builder.out.outputs
+        // locus = post_gnomon_plane.out.locus
 }
diff --git a/nf/subworkflows/ncbi/only_gnomon.nf b/nf/subworkflows/ncbi/only_gnomon.nf
index 524fa86..c18e512 100644
--- a/nf/subworkflows/ncbi/only_gnomon.nf
+++ b/nf/subworkflows/ncbi/only_gnomon.nf
@@ -5,13 +5,12 @@
 nextflow.enable.dsl=2
 
 include { setup_genome; setup_proteins } from './setup/main'
-include { get_hmm_params; run_get_hmm } from './default/get_hmm_params/main'
 include { chainer_wnode as chainer } from './gnomon/chainer_wnode/main'
 include { gnomon_wnode } from './gnomon/gnomon_wnode/main'
 include { prot_gnomon_prepare } from './gnomon/prot_gnomon_prepare/main'
 include { annot_builder } from './default/annot_builder/main'
 include { annotwriter } from './default/annotwriter/main'
-include { run_align_sort} from './gnomon/align_sort_sa/main'
+include { run_align_sort} from './default/align_sort_sa/main'
 
 params.intermediate = false
 
@@ -29,6 +28,7 @@ workflow only_gnomon {
         // hmm_params - HMM parameters
         tax_id          // NCBI tax id of the closest taxon to the genome
         hmm_params      // HMM parameters
+        hmm_taxid       // NCBI tax id of the taxon of the HMM
         //
         softmask        // softmask for GNOMON, optional
         task_params     // task parameters for every task
@@ -63,17 +63,7 @@ workflow only_gnomon {
 
         // GNOMON
 
-        def effective_hmm
-        if (hmm_params) {
-            effective_hmm = hmm_params
-        } else {
-            tmp_hmm = run_get_hmm(tax_id)
-            b = tmp_hmm | splitText( { it.split('\n') } ) | flatten 
-            c = b | last
-            effective_hmm = c
-        }
-
-        chainer(alignments, effective_hmm, /* evidence_denylist */ [], /* gap_fill_allowlist */ [], scaffolds, /* trusted_genes */ [], genome_asn, proteins_asn, task_params.get('chainer', [:]))
+        chainer(alignments, hmm_params, /* evidence_denylist */ [], /* gap_fill_allowlist */ [], scaffolds, /* trusted_genes */ [], genome_asn, proteins_asn, task_params.get('chainer', [:]))
 
         gnomon_wnode(scaffolds, chainer.out.chains, chainer.out.chains_slices, effective_hmm, [], softmask, genome_asn, proteins_asn, task_params.get('gnomon', [:]))
         def models = gnomon_wnode.out.outputs
diff --git a/nf/subworkflows/ncbi/orthology/diamond_orthology/main.nf b/nf/subworkflows/ncbi/orthology/diamond_orthology/main.nf
new file mode 100644
index 0000000..8efd88d
--- /dev/null
+++ b/nf/subworkflows/ncbi/orthology/diamond_orthology/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+include { merge_params;} from '../../utilities'
+include { run_diamond_egap;} from '../../shared/diamond/main'
+
+
+
+workflow diamond_orthology {
+    take:
+        gnomon_prot_ids
+        proteins_ids
+        gnomon_prot_asn
+        proteins_asn
+        parameters  // Map : extra parameter and parameter update
+    main:
+        String diamond_blastp_params = merge_params('--sam-query-len --very-sensitive --unal 0 --comp-based-stats 0 --masking 0', parameters, 'diamond_orthology_blastp')
+        String diamond_regular_params = merge_params('-ofmt seq-align-set -query-fmt seq-ids -subject-fmt seq-ids -output-prefix hits', parameters, 'diamond_orthology')
+        String diamond_egap_params = '-blastp-args \''  + diamond_blastp_params + '\' '  + diamond_regular_params
+                                                    
+        run_diamond_egap(gnomon_prot_ids, proteins_ids, gnomon_prot_asn, proteins_asn, diamond_egap_params)
+
+    emit:
+        alignments = run_diamond_egap.out
+}
diff --git a/nf/subworkflows/ncbi/orthology/extract_products_from_models/main.nf b/nf/subworkflows/ncbi/orthology/extract_products_from_models/main.nf
new file mode 100644
index 0000000..d6b68e8
--- /dev/null
+++ b/nf/subworkflows/ncbi/orthology/extract_products_from_models/main.nf
@@ -0,0 +1,45 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+include { merge_params } from '../../utilities'
+
+// extract_products -input-manifest models.mft -it -ifmt seq-annot -rna-ids out/rna.ids -prot-ids out/prot.ids
+
+workflow extract_products_from_models {
+    take:
+        models     //path: models
+        parameters          // Map : extra parameter and parameter update
+    main:
+        default_params = ""
+        effective_params = merge_params(default_params, parameters, 'extract_products_from_models')
+        run_extract_products_from_models(models, effective_params)
+
+    emit:
+        rna_ids = run_extract_products_from_models.out.rna_ids
+        prot_ids = run_extract_products_from_models.out.prot_ids
+        all = run_extract_products_from_models.out.all
+}
+
+
+process run_extract_products_from_models {
+    input:
+        path models
+        val parameters
+    output:
+        path ('output/rna.ids'), emit: 'rna_ids'
+        path ('output/prot.ids'), emit: 'prot_ids'
+        path ('output/*'), emit: 'all'
+    script:
+    """
+    mkdir -p output
+    echo "${models.join('\n')}"  > models.mft
+    extract_products -input-manifest models.mft -it -ifmt seq-annot -rna-ids output/rna.ids -prot-ids output/prot.ids
+
+    """
+    stub:
+    """
+    mkdir -p output
+    touch output/rna.ids
+    touch output/prot.ids
+    """
+}
diff --git a/nf/subworkflows/ncbi/orthology/find_orthologs/main.nf b/nf/subworkflows/ncbi/orthology/find_orthologs/main.nf
new file mode 100644
index 0000000..475dd3f
--- /dev/null
+++ b/nf/subworkflows/ncbi/orthology/find_orthologs/main.nf
@@ -0,0 +1,170 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+include { merge_params } from '../../utilities'
+
+workflow find_orthologs {
+    take:
+        input_gencoll_asn     //path: gencoll
+        ref_gencoll_asn     //path: gencoll
+        input_annotations       //path: annotations
+        ref_annotations        //path: annotations
+        prot_hits
+        blastdb
+        input_proteins_asn
+        ref_proteins_asn
+        input_genome_asn
+        ref_genome_asn
+        parameters  // Map : extra parameter and parameter update
+    main:
+        default_params = "-check_exome -annots1_serial_type Seq-annot -annots2_serial_type Seq-annot "
+        effective_params = merge_params(default_params, parameters, 'find_orthologs')
+        run_find_orthologs(input_gencoll_asn, ref_gencoll_asn, input_annotations, ref_annotations, prot_hits, blastdb, 
+                input_proteins_asn, ref_proteins_asn, input_genome_asn, ref_genome_asn, effective_params)
+
+    emit:
+        orthologs = run_find_orthologs.out.orthologs
+        stats = run_find_orthologs.out.stats
+        all = run_find_orthologs.out.all
+}
+
+
+process run_find_orthologs {
+    input:
+        path input_gencoll_asn     
+        path ref_gencoll_asn, stageAs: 'input/ref_gencoll.asn'
+        path input_annotations   
+        path ref_annotations
+        path prot_hits
+        path blastdb
+        path input_proteins_asn
+        path ref_proteins_asn
+        path input_genome_asn
+        path ref_genome_asn, stageAs: 'input/ref_genome.asn'
+        val parameters
+    output:
+        path ('output/orthologs.rpt'), emit: 'orthologs'
+        path ('output/stats.xml'), emit: 'stats'
+        path ('output/*'), emit: 'all'
+    script:
+    """
+    mkdir -p output
+    echo "${input_annotations.join('\n')}"  > annotations1.mft
+    echo "${ref_annotations.join('\n')}"  > annotations2.mft
+    str=""
+    if [ -z "$blastdb" ]
+    then
+        mkdir -p ./asncache/
+        prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i $ref_proteins_asn  -oseq-ids /dev/null -split-sequences
+        prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i $input_genome_asn  -oseq-ids /dev/null -split-sequences
+        prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i $input_proteins_asn  -oseq-ids /dev/null -split-sequences
+        prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i input/ref_genome.asn  -oseq-ids /dev/null -split-sequences
+        str="-asn-cache ./asncache/  -prot_hits_serial_type Seq-align-set"
+    else
+        str="-blastdb $blastdb/prot.blastdb,$blastdb/nucl.blastdb -prot_hits_serial_type Seq-align"
+    fi
+    find_orthologs $parameters -gc1 $input_gencoll_asn -gc2 input/ref_gencoll.asn -annots1 annotations1.mft  -annots2 annotations2.mft  \
+                 \$str  -o_orthologs output/orthologs.rpt   -prot_hits $prot_hits \
+                 -o_stats output/stats.xml -nogenbank
+
+    """
+    stub:
+    """
+    mkdir -p output
+    touch output/stats.xml
+    touch output/orthologs.rpt
+    """
+}
+
+
+
+
+ref_prot_url='https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/ortholog_references/9606/current/GCF_000001405.40_GRCh38.p14_protein.faa.gz'
+ref_genf_url='https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/ortholog_references/9606/current/GCF_000001405.40_GRCh38.p14_genomic.fna.gz'
+ref_geng_url='https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/ortholog_references/9606/current/GCF_000001405.40_GRCh38.p14_genomic.gff.gz' 
+process fetch_ortholog_references  {
+    input:
+    output:
+        path "output/p14_protein.faa", emit: "p14_protein_faa"
+        path "output/p14_genomic.fna", emit: "p14_genomic_fna"
+        path "output/gc1.annot.asnt.gz", emit: "annot_file"
+    script:
+    """
+        curl -O '$ref_prot_url'
+        curl -O '$ref_genf_url'
+        curl -O '$ref_geng_url'
+        gunzip GCF_000001405.40_GRCh38.p14_protein.faa.gz
+        gunzip GCF_000001405.40_GRCh38.p14_genomic.fna.gz
+        #gunzip GCF_000001405.40_GRCh38.p14_genomic.gff.gz
+        mkdir -p output
+        zcat GCF_000001405.40_GRCh38.p14_genomic.gff.gz | multireader -format gff3 | gzip -c > output/gc1.annot.asnt.gz
+        mv GCF_000001405.40_GRCh38.p14_protein.faa output/p14_protein.faa
+        mv GCF_000001405.40_GRCh38.p14_genomic.fna output/p14_genomic.fna
+        #mv GCF_000001405.40_GRCh38.p14_genomic.gff output/p14_genomic.gff
+        
+    """   
+    stub:
+    """
+        mkdir -p output
+        touch output/p14_protein.faa
+        touch output/p14_genomic.fna
+        touch output/gc1.annot.asnt.gz
+    """
+}
+
+
+/*
+#!/usr/bin/bash
+set -exuo pipefail
+
+gc1=GCF_000364345.1   # macaca       ([Q]uery)
+gc2=GCF_000001405.40  # homo sapiens ([S]ubject)
+
+inp_dir1=/am/ftp-genomes/all/GCF/000/364/345/GCF_000364345.1_Macaca_fascicularis_5.0/
+inp_dir2=/am/ftp-genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/
+
+
+cleanup() {
+    kill -- -$$
+}
+trap cleanup SIGTERM
+
+
+mkdir -p data
+
+# Required by find_orthologs
+gc_get_assembly -acc $gc1 -level 2 -o data/$gc1.gc.asn
+gc_get_assembly -acc $gc2 -level 2 -o data/$gc2.gc.asn
+
+# Convert GFF3 to ASN.1
+zcat $inp_dir1/*_genomic.gff.gz | multireader -format gff3 | gzip -c > data/$gc1.annot.asnt.gz
+zcat $inp_dir2/*_genomic.gff.gz | multireader -format gff3 | gzip -c > data/$gc2.annot.asnt.gz
+
+# Genomic sequence required for aligning nucleotide neighborhood beween putative pairs of orthologs (-check_exome)                                                                                      
+# Protein sequence required for computing ortholog-specific scores.
+# (takes about 5 minutes)
+zcat $inp_dir1/*_genomic.fna.gz $inp_dir2/*_genomic.fna.gz | makeblastdb -dbtype nucl -input_type fasta -parse_seqids -title nucs  -out data/nucl.blastdb                                               
+zcat $inp_dir1/*_protein.faa.gz $inp_dir2/*_protein.faa.gz | makeblastdb -dbtype prot -input_type fasta -parse_seqids -title prots -out data/prot.blastdb                                               
+
+# Make diamond-db for subject sequences
+zcat $inp_dir2/*_protein.faa.gz | diamond makedb --db $gc2.prots
+
+# Compute protein hits (takes about 3 minutes with 96 CPUs)
+time zcat $inp_dir1/*_protein.faa.gz |
+    nice -n19 diamond blastp --db ./$gc2.prots.dmnd --very-sensitive --sam-query-len --outfmt sam |
+    sam2asn -diamond -align-type prot-to-prot -nogenbank |
+    gzip -c > data/$gc1-$gc2.prot-hits.seq-align.asnb.gz
+
+# Compute orthologs (takes about 10 minutes)
+zcat data/$gc1-$gc2.prot-hits.seq-align.asnb.gz |
+    time find_orthologs -prot_hits - -prot_hits_serial_type Seq-align \
+        -gc1 data/$gc1.gc.asn \
+        -gc2 data/$gc2.gc.asn \
+        -annots1_serial_type Seq-annot -annots1 <(ls data/$gc1.annot.asnt.gz) \
+        -annots2_serial_type Seq-annot -annots2 <(ls data/$gc2.annot.asnt.gz) \
+        -check_exome \
+        -blastdb data/prot.blastdb,data/nucl.blastdb \
+        -o_orthologs orthologs.rpt \
+        -nogenbank
+
+*/
diff --git a/nf/subworkflows/ncbi/orthology/main.nf b/nf/subworkflows/ncbi/orthology/main.nf
new file mode 100644
index 0000000..2ce9fd5
--- /dev/null
+++ b/nf/subworkflows/ncbi/orthology/main.nf
@@ -0,0 +1,43 @@
+#!/usr/bin/env nextflow
+// main nextflow script for EGAPx execution
+// route data to subworkflows
+
+nextflow.enable.dsl=2
+
+
+include { extract_products_from_models } from './extract_products_from_models/main'
+include { find_orthologs; fetch_ortholog_references; } from './find_orthologs/main'
+include { diamond_orthology } from './diamond_orthology/main'
+include { setup_genome; setup_proteins } from './../setup/main'
+include { get_swiss_prot_ids as get_prot_ref_ids } from '../shared/diamond/main'
+
+params.intermediate = false
+
+
+workflow orthology_plane {
+    take:
+        genome_asnb
+        gencoll_asn
+        models
+        annot_files
+        task_params     // task parameters for every task
+    main:
+        // Protein alignments
+        fetch_ortholog_references()
+        def (scaffolds_ref, gencoll_ref_asn, unpacked_genome_ref, genome_ref_asn, genome_ref_asnb) = setup_genome(fetch_ortholog_references.out.p14_genomic_fna, [], task_params.get('setup', [:]))
+        def (unpacked_proteins_ref, proteins_ref_asn, proteins_ref_asnb) = setup_proteins(fetch_ortholog_references.out.p14_protein_faa, task_params.get('setup', [:]))
+        def prot_ref_ids  = get_prot_ref_ids(proteins_ref_asnb)
+        //orthology plane
+        extract_products_from_models(annot_files, task_params.get('extract_products_from_models', [:]))
+        // reference side. 1) gencoll, annotation , genome and protein sequence --> asn cashe or LDS demon
+        
+        diamond_orthology(extract_products_from_models.out.prot_ids, prot_ref_ids , models, proteins_ref_asnb , task_params.get('diamond_orthology', [:]))
+
+        // input side 1) gencoll asn from setup, genome_asn from setup, protein from gnomon_wnode.out, annotation it is from annotbuilder annot_files or accepts_asn
+        find_orthologs( gencoll_asn,  gencoll_ref_asn,  annot_files, fetch_ortholog_references.out.annot_file, diamond_orthology.out.alignments, [],
+                        models, proteins_ref_asnb , genome_asnb, genome_ref_asnb ,  task_params.get('find_orthologs', [:]))
+
+    emit:
+        orthologs = find_orthologs.out.orthologs
+}
+
diff --git a/nf/subworkflows/ncbi/rnaseq_short/bam_bin_and_sort/main.nf b/nf/subworkflows/ncbi/rnaseq_short/bam_bin_and_sort/main.nf
index 9a7ddff..ba3e9c5 100644
--- a/nf/subworkflows/ncbi/rnaseq_short/bam_bin_and_sort/main.nf
+++ b/nf/subworkflows/ncbi/rnaseq_short/bam_bin_and_sort/main.nf
@@ -26,6 +26,7 @@ workflow bam_bin_and_sort {
 
 
 process calc_assembly_sizes {
+    label 'large_disk'
     input:
         path bam_files
     output:
@@ -127,6 +128,7 @@ process bam_bin {
 
 
 process merge_prepare {
+    label 'large_disk'
     input:
         path runs
     output:
@@ -168,6 +170,7 @@ process merge_prepare {
 
 process merge {
     label 'big_job'
+    label 'large_disk'
     input:
         path merge_args
         path bins
@@ -181,4 +184,5 @@ process merge {
     stub:
     """
         touch 1.bam
-    """}
+    """
+}
diff --git a/nf/subworkflows/ncbi/rnaseq_short/bam_strandedness/main.nf b/nf/subworkflows/ncbi/rnaseq_short/bam_strandedness/main.nf
index 1b91c18..a59193d 100644
--- a/nf/subworkflows/ncbi/rnaseq_short/bam_strandedness/main.nf
+++ b/nf/subworkflows/ncbi/rnaseq_short/bam_strandedness/main.nf
@@ -21,9 +21,8 @@ workflow bam_strandedness {
 }
 
 
-
-
 process rnaseq_divide_by_strandedness {
+    label 'large_disk'
     input:
         path bam_list
         path metadata_file
@@ -47,5 +46,4 @@ process rnaseq_divide_by_strandedness {
     touch output/stranded.list
     touch output/unstranded.list
     """
- }
-
+}
diff --git a/nf/subworkflows/ncbi/rnaseq_short/convert_from_bam/main.nf b/nf/subworkflows/ncbi/rnaseq_short/convert_from_bam/main.nf
index e59b733..1dbbcb0 100644
--- a/nf/subworkflows/ncbi/rnaseq_short/convert_from_bam/main.nf
+++ b/nf/subworkflows/ncbi/rnaseq_short/convert_from_bam/main.nf
@@ -20,19 +20,25 @@ workflow bam2asn {
 
 
 process convert {
+    label 'long_job'
+    label 'large_disk'
     input:
         path in_bam
         path strandedness
         path genome, stageAs: 'genome/*'
         val  conv_param
     output:
-        path "${prefix}.align.asnb.gz", emit: 'align'
-        path "${prefix}.align_counts.txt", emit: 'keylist'
+        path "${prefix}.align.asnb.gz", emit: 'align', optional: true
+        path "${prefix}.align_counts.txt", emit: 'keylist', optional: true
     script:
         prefix = in_bam.name.replaceAll(/\.bam$/, '')
+        min_file_size = 100000
     """
-    tmpdir=`mktemp -d`
     samtools=`which samtools`
+    if [ `stat -L -c%s $in_bam` -lt $min_file_size ] && [ `\$samtools view -c $in_bam` -eq 0 ]; then
+        exit 0
+    fi
+    tmpdir=`mktemp -d`
     lds2_indexer -source genome/ -db LDS2
     # EXCEPTION_STACK_TRACE_LEVEL=Warning DEBUG_STACK_TRACE_LEVEL=Warning DIAG_POST_LEVEL=Trace
     sam2asn $conv_param -refs-local-by-default  -nogenbank -lds2 LDS2 -tmp-dir \$tmpdir -align-counts "${prefix}.align_counts.txt" -o "${prefix}.align.asnb.gz" -strandedness $strandedness -input $in_bam -samtools-path \$samtools
diff --git a/nf/subworkflows/ncbi/rnaseq_short/main.nf b/nf/subworkflows/ncbi/rnaseq_short/main.nf
new file mode 100644
index 0000000..a69c790
--- /dev/null
+++ b/nf/subworkflows/ncbi/rnaseq_short/main.nf
@@ -0,0 +1,78 @@
+#!/usr/bin/env nextflow
+// rnaseq short  EGAPx execution
+// route data to tasks
+
+nextflow.enable.dsl=2
+
+include { sra_query } from './sra_qry/main'
+include { fetch_sra_fasta } from './fetch_sra_fasta/main'
+include { star_index } from './star_index/main'
+include { star_wnode as star } from './star_wnode/main'
+include { bam_strandedness } from './bam_strandedness/main'
+include { bam_bin_and_sort } from './bam_bin_and_sort/main'
+include { bam2asn } from './convert_from_bam/main'
+include { rnaseq_collapse } from './rnaseq_collapse/main'
+
+params.intermediate = false
+
+
+workflow rnaseq_short_plane {
+    take:
+        genome_asn
+        scaffolds
+        unpacked_genome_fasta
+
+        // Alternative groups of parameters, one of them should be set
+        // reads_query - SRA query in the form accepted by NCBI
+        // reads_ids - list of SRA IDs
+        // reads, reads_metadata - path to reads accompanied by metadata
+        reads_query     // SRA query
+        reads_ids       // list of SRA IDs
+        reads           // path to reads
+        reads_metadata  // path to reads metadata 13 tab-delimited fields, 1-st - SRA ID, 3-rd paired or unpaired, everything else - not used, but must be present
+                        // 4, 5, 13 - numbers, 5 - non zero number
+        organelles      // path to organelle list
+        // Alternative parameters, one of them should be set
+        // tax_id - NCBI tax id of the closest taxon to the genome
+        // hmm_params - HMM parameters
+        tax_id          // NCBI tax id of the closest taxon to the genome
+        max_intron      // max intron length
+        task_params     // task parameters for every task
+    main:
+        // Satisfy quirks of Nextflow compiler
+        def reads_query1 = reads_query
+        def reads_ids1 = reads_ids
+        def ch_reads = Channel.fromList(reads)
+        // Conditional code on SRA reads source
+        if (reads_query || reads_ids || reads) {
+            def index = star_index(unpacked_genome_fasta, task_params.get('star_index', [:]))
+            def ch_align, ch_align_index, sra_metadata, sra_run_list
+            if (reads_query || reads_ids) {
+                def query = reads_query1 ? reads_query1 : reads_ids1.join("[Accession] OR ") + "[Accession]"
+                (sra_metadata, sra_run_list) = sra_query(query, task_params.get('sra_qry', [:]))
+                def reads_fasta_pairs = fetch_sra_fasta(sra_run_list, task_params.get('fetch_sra_fasta', [:]))
+                (ch_align, ch_align_index) = star(scaffolds, reads_fasta_pairs, genome_asn, index, max_intron, task_params.get('star_wnode', [:]))
+            } else {
+                sra_metadata = reads_metadata
+                (ch_align, ch_align_index) = star(scaffolds, ch_reads, genome_asn, index, max_intron, task_params.get('star_wnode', [:]))
+            }
+            //
+
+            bam_strandedness(ch_align.collect(), sra_metadata, task_params.get('bam_strandedness', [:]))
+            def strandedness = bam_strandedness.out.strandedness
+            
+            // Run bam_bin_and_sort
+            bam_bin_and_sort(ch_align, ch_align_index, unpacked_genome_fasta, organelles, task_params.get('bam_bin_and_sort', [:]))
+            def bam_bins = bam_bin_and_sort.out.sorted
+
+            // Run BAM2ASN
+            bam2asn(bam_bins, strandedness, genome_asn, task_params.get('convert_from_bam', [:]))
+            def asn_align = bam2asn.out.align.collect()
+            def keylist = bam2asn.out.keylist.collect()
+
+            rnaseq_collapse(genome_asn, keylist, asn_align, sra_metadata, 10, task_params.get('rnaseq_collapse', [:]))
+        }
+        
+    emit:
+        rnaseq_alignments = rnaseq_collapse.out.alignments 
+}
diff --git a/nf/subworkflows/ncbi/rnaseq_short/rnaseq_collapse/main.nf b/nf/subworkflows/ncbi/rnaseq_short/rnaseq_collapse/main.nf
index 5bdaae9..07ea393 100644
--- a/nf/subworkflows/ncbi/rnaseq_short/rnaseq_collapse/main.nf
+++ b/nf/subworkflows/ncbi/rnaseq_short/rnaseq_collapse/main.nf
@@ -14,7 +14,7 @@ workflow rnaseq_collapse {
         parameters        // Map: extra parameter and parameter update
     main:
         String create_jobs_params =  merge_params("-alignments-per-job 50000 -min-range 100000", parameters, 'rnaseq_collapse_create_jobs')
-        String rnaseq_collapse_params = merge_params("-backlog 1 -max-jobs 1 -rank-counts-precalculated", parameters, 'rnaseq_collapse')
+        String rnaseq_collapse_params = merge_params("-backlog 1 -max-jobs 1 -support-non-sra", parameters, 'rnaseq_collapse')
         String gpx_make_outputs_params =  merge_params("-default-output-name align -slices-for affinity -sort-by job-id -unzip align", parameters, 'gpx_make_outputs')
 
         def (jobs, lines_per_file) = generate_jobs(genome, scaffold_list, max_jobs, create_jobs_params)
diff --git a/nf/subworkflows/ncbi/rnaseq_short/sra_qry/main.nf b/nf/subworkflows/ncbi/rnaseq_short/sra_qry/main.nf
index f488c90..443d74b 100644
--- a/nf/subworkflows/ncbi/rnaseq_short/sra_qry/main.nf
+++ b/nf/subworkflows/ncbi/rnaseq_short/sra_qry/main.nf
@@ -37,6 +37,7 @@ process run_sra_query {
     #!/usr/bin/env python3
     # sra_query.py - proxy compliant replacement for sra_query
 
+    import csv
     import json
     from urllib.request import urlopen
     from urllib.parse import quote
@@ -76,7 +77,8 @@ process run_sra_query {
             line = line.strip()
             if not line:
                 continue
-            parts = line.split(",")
+            for l in  csv.reader([line], quotechar='"', delimiter=',', quoting=csv.QUOTE_ALL, skipinitialspace=True):
+                parts = l
             printable = []
             paired = False
             for k in ["Run", "Sample", "LibraryLayout", "spots", "bases", "NA", "NA", "Platform", "Model", "Experiment", "SRAStudy", "BioSample", "ProjectID", "BioProject", "ScientificName", "TaxID", "ReleaseDate"]:
diff --git a/nf/subworkflows/ncbi/rnaseq_short/star_index/main.nf b/nf/subworkflows/ncbi/rnaseq_short/star_index/main.nf
index fa9f3b2..10d5d68 100644
--- a/nf/subworkflows/ncbi/rnaseq_short/star_index/main.nf
+++ b/nf/subworkflows/ncbi/rnaseq_short/star_index/main.nf
@@ -5,6 +5,7 @@ include { merge_params } from '../../utilities'
 
 
 process build_index {
+    label 'big_job'
     input:
         path genome_file
         val parameters
@@ -14,7 +15,8 @@ process build_index {
         out_dir = genome_file.toString().replaceFirst(/\.(fa(sta)?|fna)$/, ".index")
     """
     echo "in $genome_file, out $out_dir"
-    STAR  $parameters --runMode genomeGenerate --genomeDir $out_dir --genomeFastaFiles $genome_file 
+    STAR  $parameters --runMode genomeGenerate --genomeDir $out_dir --genomeFastaFiles $genome_file
+    chmod a+rx $out_dir
     """
 
     stub:
diff --git a/nf/subworkflows/ncbi/rnaseq_short/star_wnode/main.nf b/nf/subworkflows/ncbi/rnaseq_short/star_wnode/main.nf
index e52d088..47a5cda 100644
--- a/nf/subworkflows/ncbi/rnaseq_short/star_wnode/main.nf
+++ b/nf/subworkflows/ncbi/rnaseq_short/star_wnode/main.nf
@@ -4,45 +4,70 @@ nextflow.enable.dsl=2
 include { merge_params } from '../../utilities'
 
 
-process exec {
+def get_effective_params(parameters, use_zcat, max_intron) {
+    def effective_star_params = ""
+    // Check that parameters for star_wnode doesn't contain 'star-params'
+    boolean back_compat = parameters.get("star_wnode", "").contains("-star-params")
+    if (!back_compat) {
+        def star_params = "--alignSJoverhangMin 8 --outFilterMultimapNmax 200 --outFilterMismatchNmax 50 --runThreadN 16 --genomeLoad NoSharedMemory --outSAMtype SAM --outSAMattributes 'NH HI AS nM NM MD jM jI XS MC' --outSAMprimaryFlag AllBestScore --outFilterMultimapScoreRange 50 --seedSearchStartLmax 15 --limitOutSAMoneReadBytes 1000000 --outSJtype None"
+        effective_star_params = ' -star-params "' + (use_zcat ? "--readFilesCommand zcat " : "") + merge_params(star_params, parameters, 'star-params') + '"'
+    }
+    def default_params = "-cpus-per-worker 4 -csi-threshold 512000000 -max-intron ${max_intron} -preserve-star-logs"
+    def effective_params = merge_params(default_params, parameters, 'star_wnode') + effective_star_params
+    if (!back_compat) {
+        // Ad-hoc post processing - remove single quotes from effective_params
+        effective_params = effective_params.replaceAll("'", "")
+    }
+    return effective_params
+}
+
+
+process run_star {
     label 'huge_job'
     label 'long_job'
     input:
         path seqid_list
         tuple val(sampleID), path(fasta_rna_file)
+        val  use_zcat
         path genome_file, stageAs: 'genome/*'
         path Star_Index
-        val parameters
+        val  max_intron
+        val  parameters
     output:
-        path "${assembly}-${sampleID}-Aligned.out.Sorted.bam", emit: 'align'
-        path "${assembly}-${sampleID}-Aligned.out.Sorted.bam.bai", emit: 'align_index'
+        path "*-Aligned.out.Sorted.bam", emit: 'align'
+        path "*-Aligned.out.Sorted.bam.bai", emit: 'align_index'
         // path "per_run_counts.txt", emit: 'per_run_counts'
     script:
-        assembly=genome_file.baseName.toString().replaceFirst(/\.(fa(sta)?|asn[bt]?)$/, "")
+        def assembly=genome_file.baseName.toString().replaceFirst(/\.(fa(sta)?|asn[bt]?)$/, "")
+        seqkit_cmd = ""
         if ( fasta_rna_file[0] && fasta_rna_file[1] ) {
             query_str = "${fasta_rna_file[0]},${fasta_rna_file[1]}"
+            seqkit_cmd = "seqkit stats ${fasta_rna_file[0]} ${fasta_rna_file[1]}"
         } else {
             query_str = fasta_rna_file[0]
+            seqkit_cmd = "seqkit stats ${fasta_rna_file[0]} "
         }
+        def effective_params = get_effective_params(parameters, use_zcat, max_intron)
+        // println("Effective STAR parameters: $effective_params")
     """
+    echo "Assembly: ${assembly} sampleID: ${sampleID} Query: ${query_str}"
     echo "${seqid_list.join('\n')}" > seqid_list.mft
     lds2_indexer -source genome
     mkdir -p out
     mkdir -p wrkarea
-    #echo "${fasta_rna_file[0]}"
-    #echo "${fasta_rna_file[1]}"
-    echo "$query_str"
-    #echo "<job query =\\\"lcl|${fasta_rna_file[0]}\\\" subject=\\\"$Star_Index\\\"></job>"
-    ##echo "<job query =\\\"lcl|${fasta_rna_file[0]},${fasta_rna_file[1]}\\\" subject=\\\"$Star_Index\\\"></job>" > jobfile
     echo "<job query =\\\"lcl|${query_str}\\\" subject=\\\"$Star_Index\\\"></job>" > jobfile
     star=\$(which star-with-filter)
     samtools=\$(which samtools)
     fastq=\$(which fasterq-dump)
-    star_wnode $parameters -input-jobs jobfile -genome-sequences-manifest seqid_list.mft -fastq-executable \$fastq  -samtools-executable \$samtools -star-executable \$star -output-dir . -work-area wrkarea -O out -lds2 genome/lds2.db
+    ${seqkit_cmd};
+    star_wnode ${effective_params} -input-jobs jobfile -genome-sequences-manifest seqid_list.mft -fastq-executable \$fastq  -samtools-executable \$samtools -star-executable \$star -output-dir . -work-area wrkarea -O out -lds2 genome/lds2.db
     """
     
     stub:
-        assembly=genome_file.baseName.toString().replaceFirst(/\.(fa(sta)?|asn[bt]?)$/, "")
+        def assembly=genome_file.baseName.toString().replaceFirst(/\.(fa(sta)?|asn[bt]?)$/, "")
+        println("Assembly: ${assembly} sampleID: ${sampleID}, max_intron: ${max_intron}")
+        def effective_params = get_effective_params(parameters, use_zcat, max_intron)
+        println("Effective STAR parameters: $effective_params")
     """
     touch ${assembly}-${sampleID}-Aligned.out.Sorted.bam
     touch ${assembly}-${sampleID}-Aligned.out.Sorted.bam.bai
@@ -54,19 +79,17 @@ workflow star_wnode {
     take: 
         seqid_list  // path:  list of seq ids in the index (SEQID_LIST)
         reads       // channel: FASTA file pairs generated from SRA reads, see e.g., https://www.nextflow.io/docs/latest/channel.html#fromfilepairs
-        genome_file //path: genome file, fasta or ASN
+        genome_file // path: genome file, fasta or ASN
         star_index  // path: index path
+        max_intron  // int: maximum intron length
         parameters  // Map : extra parameter and parameter update
     main:
    
-        star_params = "\" --alignSJoverhangMin 8 --outFilterMultimapNmax 200 --outFilterMismatchNmax 50 --runThreadN 16 --genomeLoad NoSharedMemory --outSAMtype SAM --outSAMattributes NH HI AS nM NM MD jM jI XS MC --outSAMprimaryFlag AllBestScore --outFilterMultimapScoreRange 50 --seedSearchStartLmax 15 --limitOutSAMoneReadBytes 1000000 --outSJtype None \""
-        default_params = "-cpus-per-worker 4 -csi-threshold 512000000  -max-intron 1200000  -star-params $star_params -preserve-star-logs"
-        effective_params = merge_params(default_params, parameters, 'star_wnode')
-        // println("Effective parameters: $effective_params")
-        exec(seqid_list, reads, genome_file, star_index, effective_params)
+        def use_zcat_ch = reads.map { it[1][0] ==~ /.*gz$/ }
+        run_star(seqid_list, reads, use_zcat_ch, genome_file, star_index, max_intron, parameters)
     emit:
-        align = exec.out.align
-        align_index = exec.out.align_index
+        align = run_star.out.align
+        align_index = run_star.out.align_index
 }
 
 
@@ -74,18 +97,17 @@ workflow star_wnode_simplified {
     take:
         seqid_list  // path:  list of seq ids in the index (SEQID_LIST)
         reads       // list of FASTA read files, expects pairs in form SRAxxx.1, SRAxxx.2
-        genome_file //path: genome file, fasta or ASN
+        genome_file // path: genome file, fasta or ASN
         star_index  // path: index path
+        max_intron  // int: maximum intron length
         parameters  // Map : extra parameter and parameter update
     main:
         def filePairs = Channel.of(reads).flatten().map { read ->
-            def m = read =~ /\/([A-Za-z0-9]+).{1,2}$/
+            def m = read =~ /\/([^\/]+).[12](.gz)?$/
             [m[0][1], read]
         }.groupTuple()
-        star_params = "\" --alignSJoverhangMin 8 --outFilterMultimapNmax 200 --outFilterMismatchNmax 50 --runThreadN 16 --genomeLoad NoSharedMemory --outSAMtype SAM --outSAMattributes NH HI AS nM NM MD jM jI XS MC --outSAMprimaryFlag AllBestScore --outFilterMultimapScoreRange 50 --seedSearchStartLmax 15 --limitOutSAMoneReadBytes 1000000 --outSJtype None \""
-        default_params = "-cpus-per-worker 4 -csi-threshold 512000000  -max-intron 1200000  -star-params $star_params -preserve-star-logs"
-        effective_params = merge_params(default_params, parameters, 'star_wnode')
-        exec(seqid_list, filePairs, genome_file, star_index, effective_params)
+        def use_zcat_ch = filePairs.map { it[1][0] ==~ /.*gz$/ }
+        run_star(seqid_list, filePairs, use_zcat_ch, genome_file, star_index, max_intron, parameters)
     emit:
         align = exec.out.align
         align_index = exec.out.align_index
diff --git a/nf/subworkflows/ncbi/setup/main.nf b/nf/subworkflows/ncbi/setup/main.nf
index 21eb9b0..15b6fa2 100644
--- a/nf/subworkflows/ncbi/setup/main.nf
+++ b/nf/subworkflows/ncbi/setup/main.nf
@@ -9,24 +9,30 @@ workflow setup_genome {
         organelles
         parameters  // Map : extra parameter and parameter update
     main:
-        get_genome_info(genome, organelles)
+        get_genome_info(genome, organelles, parameters)
     emit:
         seqid_list = get_genome_info.out.seqid_list
         gencoll_asn = get_genome_info.out.gencoll_asn
         unpacked_genome = get_genome_info.out.fasta
         genome_asn = get_genome_info.out.genome_asn
+        genome_asnb = get_genome_info.out.genome_asnb
+        max_intron = get_genome_info.out.max_intron
 }
 
 
 process get_genome_info {
+    debug true
     input:
         path fasta_genome_file, stageAs: 'src/*'
         path organelles
+        val  parameters
     output:
         path '*.seqids', emit: 'seqid_list'
         path '*.asn', emit: 'gencoll_asn'
         path "${out_fasta}", emit: 'fasta'
         path "${genome_asn}", emit: 'genome_asn'
+        path "${genome_asnb}", emit: 'genome_asnb'
+        env  max_intron, emit: 'max_intron'
     script:
         need_zcat = fasta_genome_file.toString().endsWith('.gz')
         base_name_stripped = fasta_genome_file.baseName.toString().replaceAll(/\.(fa(sta)?|fna)(\.gz)?$/, "")
@@ -38,8 +44,11 @@ process get_genome_info {
         fasta_dir = "fasta"
         out_fasta = fasta_dir + "/" + indexed_fasta_name
         genome_asn = genome_dir + "/" + base_name_stripped + ".asn"
+        genome_asnb = genome_dir + "/" + base_name_stripped + ".asnb"
+        max_intron = parameters.max_intron
+        genome_size_threshold = parameters.genome_size_threshold        
     """
-    echo "need_zcat: ${need_zcat}, out_fasta: ${out_fasta}"
+    # echo "need_zcat: ${need_zcat}, out_fasta: ${out_fasta}"
     mkdir -p ${genome_dir}
     mkdir -p ${fasta_dir}
     if [[ ${need_zcat} == true ]]; then
@@ -54,13 +63,24 @@ process get_genome_info {
     # Old way, now use gc_get_molecules. For multipart ids with gi first use the second part
     # grep -oP "^>\\K[^ ]+" ${out_fasta} | sed 's/^\\(gi|[0-9]\\+\\)|\\([^|]\\+|[^|]\\+\\)|\\?/\\2/' >list.seqids
     multireader -flags ParseRawID -out-format asn_text -input ${out_fasta} -output ${genome_asn}
+    multireader -flags ParseRawID -out-format asn_binary -input ${out_fasta} -output ${genome_asnb}
     lds2_indexer -source ${genome_dir}/ -db LDS2
     # Using all parts of multipart ids is preferrable, but slower - one more pass over genomic FASTA
     gc_create -unplaced ${out_fasta} -unplaced-fmt fasta -fasta-parse-raw-id -gc-assm-name "EGAPx Test Assembly" -nogenbank -lds2 LDS2 >gencoll.asn
-    # gc_create -unplaced list.seqids -unplaced-fmt seq-id -gc-assm-name "EGAPx Test Assembly" -nogenbank -lds2 LDS2 >gencoll.asn
     gc_get_molecules -gc-assembly gencoll.asn -filter all -level top-level > list.seqids
 
     #TODO: subtract organelles from list
+
+    # This is a rough estimate because we don't need the more accurate size
+    genome_size=`wc -c <${out_fasta}`
+    # Max intron logic
+    if [ $genome_size_threshold -gt 0 ] && [ \$genome_size -lt $genome_size_threshold ]; then
+        # scale max intron to genome size, rounding up to nearest 100kb
+        (( max_intron = ($max_intron * genome_size / $genome_size_threshold + 99999) / 100000 * 100000 ))
+        # echo "Setting max_intron to \$max_intron"
+    else
+        max_intron=$max_intron
+    fi
     """
     
     stub:
@@ -73,14 +93,18 @@ process get_genome_info {
         fasta_dir = "fasta"
         out_fasta = fasta_dir + "/" + indexed_fasta_name
         genome_asn = genome_dir + "/" + base_name_stripped + ".asn"
- 
+        genome_asnb = genome_dir + "/" + base_name_stripped + ".asnb"
     """
     mkdir -p $genome_dir
     mkdir -p $fasta_dir
     touch $out_fasta
     touch $genome_asn
+    touch $genome_asnb
     touch gencoll.asn
     touch list.seqids
+    max_intron=10000
+    echo "Processing genome $fasta_genome_file"
+    echo "Setting max_intron to \$max_intron"
     """
 }
 
@@ -94,6 +118,7 @@ workflow setup_proteins {
     emit:
         unpacked_proteins = convert_proteins.out.unpacked_proteins
         proteins_asn = convert_proteins.out.proteins_asn
+        proteins_asnb = convert_proteins.out.proteins_asnb
 }
 
 
@@ -103,6 +128,7 @@ process convert_proteins {
     output:
         path out_fasta, emit: 'unpacked_proteins'
         path proteins_asn, emit: 'proteins_asn'
+        path proteins_asnb, emit: 'proteins_asnb'
     script:
         need_zcat = fasta_proteins_file.toString().endsWith('.gz')
         base_name_stripped = fasta_proteins_file.baseName.toString().replaceAll(/\.(fa(sta)?|faa)(\.gz)?$/, "")
@@ -112,6 +138,7 @@ process convert_proteins {
         fasta_dir = "fasta"
         out_fasta = fasta_dir + "/" + fasta_name
         proteins_asn = asn_dir + "/" + base_name_stripped + ".asn"
+        proteins_asnb = asn_dir + "/" + base_name_stripped + ".asnb"
     """
     mkdir -p ${asn_dir}
     mkdir -p ${fasta_dir}
@@ -121,6 +148,7 @@ process convert_proteins {
         sed 's/>\\([^ |]\\+\\)\\( .*\\)\\?\$/>lcl\\|\\1\\2/' ${fasta_proteins_file} > ${out_fasta}
     fi
     multireader -flags ParseRawID -out-format asn_text -input ${out_fasta} -output ${proteins_asn}
+    multireader -flags ParseRawID -out-format asn_binary -input ${out_fasta} -output ${proteins_asnb}
     """
 
     stub:
@@ -130,12 +158,14 @@ process convert_proteins {
         fasta_dir = "fasta"
         out_fasta = fasta_dir + "/" + fasta_name
         proteins_asn = asn_dir + "/" + base_name_stripped + ".asn"
+        proteins_asnb = asn_dir + "/" + base_name_stripped + ".asnb"
     
     """
     mkdir -p $asn_dir
     mkdir -p $fasta_dir
     touch $out_fasta
     touch $proteins_asn
+    touch $proteins_asnb
     """
 
 }
diff --git a/nf/subworkflows/ncbi/shared/diamond/main.nf b/nf/subworkflows/ncbi/shared/diamond/main.nf
new file mode 100644
index 0000000..1ef6801
--- /dev/null
+++ b/nf/subworkflows/ncbi/shared/diamond/main.nf
@@ -0,0 +1,107 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+
+/*
+ *Execution of: 
+ * /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/bin/diamond 
+ *    -asn-cache /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/sequence_cache 
+ *    -blastp-args '--sam-query-len --comp-based-stats 0 --evalue 0.0001 --very-sensitive --max-hsps 3' 
+ *    -diamond-executable /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/third-party/diamond/diamond 
+ *    -lds2 /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/prot_gnomon_prepare.8202002/out/LDS2 
+ *    -ofmt seq-align-set 
+ *    -output-dir /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out 
+ *    -output-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out/align.mft 
+ *    -output-prefix hits 
+ *    ## query is gnomon-made proteins 'gnl|GNOMON|23016146.p'
+ *    ## query-fmt is <String, `fasta', `seq-ids'>
+ *    -query-fmt seq-ids 
+ *    -query-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/query_ids.mft 
+ *    ## subject is swiss-prot ids 'sp|A0A009IHW8.1|ABTIR_ACIB9'
+ *    -subject-fmt seq-ids 
+ *    -subject-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/subject_ids.mft 
+ *    -work-area /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/tmp
+
+ */
+
+include {to_map; shellSplit } from '../../utilities'
+
+
+swiss_prot_url='https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/reference_sets/swissprot.asnb.gz'
+process fetch_swiss_prot_asn  {
+    input:
+    output:
+        path "output/swissprot.asnb", emit: "swiss_prot_asn"
+    script:
+    """
+        curl -O '$swiss_prot_url'
+        gunzip swissprot.asnb.gz
+        mkdir -p output
+        mv swissprot.asnb output/swissprot.asnb
+    """   
+    stub:
+    """
+        mkdir -p output
+        touch output/swissprot.asnb
+    """
+}
+
+process get_swiss_prot_ids {
+    input:
+        path swiss_prot_asn
+    output:
+        path "output/swiss_prot_ids"
+    script: 
+    """
+        mkdir -p output
+        lds2_indexer  -db lds -source  .
+        sqlite3 ./lds "SELECT txt_id FROM seq_id WHERE orig=1 AND int_id IS NULL;"    > output/swiss_prot_ids
+    """
+    stub:
+    """
+        mkdir -p output
+        touch output/swiss_prot_ids
+    """
+}
+
+process run_diamond_egap {
+    input:
+        path gnomon_prot_ids
+        path swiss_prot_ids
+        path gnomon_prot_asn, stageAs: 'indexed/*'
+        path swiss_prot_asn, stageAs: 'indexed/*'
+        val params
+    output:
+        path "output/*"
+    script:
+    // print(params)
+    """
+   
+    ###diamond_bin=`which diamond`
+    #diamond_egap uses GP_HOME to build paths to both some gp apps, and third-party
+    #GP_HOME needs to be the directory that contains third-party, and the directory that contains bin/<gp apps> 
+    diamond_bin=\${GP_HOME}/third-party/diamond/diamond
+    
+    mkdir -p ./asncache/
+
+    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${gnomon_prot_asn} -oseq-ids /dev/null -split-sequences
+    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${swiss_prot_asn} -oseq-ids /dev/null -split-sequences
+
+    mkdir ./output
+    mkdir ./work
+
+    echo  ${params}
+    echo "${gnomon_prot_ids.join('\n')}" > query.mft
+    diamond_egap  ${params} -asn-cache ./asncache/ -nogenbank -query-manifest query.mft -subject ${swiss_prot_ids} \
+        -output-dir ./output/ -work-area ./work/  -diamond-executable \${diamond_bin}
+    rm -rf ./work
+    """
+
+    stub:
+    """
+    mkdir -p output
+    touch output/diamond_output.asn
+    """
+}
+
+
diff --git a/nf/subworkflows/ncbi/target_proteins/best_aligned_prot/main.nf b/nf/subworkflows/ncbi/target_proteins/best_aligned_prot/main.nf
index f98a8bc..5e7a7ef 100644
--- a/nf/subworkflows/ncbi/target_proteins/best_aligned_prot/main.nf
+++ b/nf/subworkflows/ncbi/target_proteins/best_aligned_prot/main.nf
@@ -26,9 +26,9 @@ workflow best_aligned_prot {
 
 process run_best_aligned_prot {
     input:
-        path (genome, stageAs: 'LDS_Index/genome.asnt')
-        path (proteins,  stageAs: 'LDS_Index/proteins.asnt')
-        path alignment_asn_file
+        path genome, stageAs: 'LDS_Index/genome.asnt'
+        path proteins,  stageAs: 'LDS_Index/proteins.asnt'
+        path alignment_asn_file // list of alignment files
         path gencoll_file
         val parameters
     output:
@@ -39,10 +39,11 @@ process run_best_aligned_prot {
     """
     mkdir -p output
     lds2_indexer -source LDS_Index
-    echo "$alignment_asn_file" > align.mft
+    echo "${alignment_asn_file.join('\n')}" > align.mft
     best_placement ${parameters}  -lds2 LDS_Index/lds2.db  -nogenbank  -gc_path $gencoll_file -in_alns align.mft -out_alns output/align.asn -out_rpt  output/report.txt
     """
     stub:
+        print("Best aligned prot input ${alignment_asn_file}")
     """
     mkdir -p output
     touch output/align.asn
diff --git a/nf/subworkflows/ncbi/target_proteins/main.nf b/nf/subworkflows/ncbi/target_proteins/main.nf
new file mode 100644
index 0000000..6e3d705
--- /dev/null
+++ b/nf/subworkflows/ncbi/target_proteins/main.nf
@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+// main nextflow script for EGAPx execution
+// route data to subworkflows
+
+nextflow.enable.dsl=2
+
+include { miniprot } from './miniprot/main'
+include { align_filter_sa } from './align_filter_sa/main'
+include { best_aligned_prot } from './best_aligned_prot/main'
+include { paf2asn } from './paf2asn/main'
+include { run_align_sort} from '../default/align_sort_sa/main'
+
+params.intermediate = false
+
+
+workflow target_proteins_plane {
+    take:
+        unpacked_genome_fasta
+        genome_asn
+        gencoll_asn
+        unpacked_proteins_fasta
+        proteins_asn
+        max_intron
+        task_params     // task parameters for every task
+    main:
+        // Protein alignments
+        miniprot(unpacked_genome_fasta, unpacked_proteins_fasta, max_intron, task_params.get('miniprot', [:]))
+        def miniprot_file = miniprot.out.miniprot_file
+        paf2asn(genome_asn, proteins_asn, miniprot_file, task_params.get('paf2asn', [:]))
+        def converted_asn = paf2asn.out.asn_file
+        best_aligned_prot(genome_asn, proteins_asn, converted_asn.collect(), gencoll_asn, task_params.get('best_aligned_prot', [:]))
+        align_filter_sa(genome_asn, proteins_asn, best_aligned_prot.out.asn_file, task_params.get('align_filter_sa', [:]))
+        run_align_sort(genome_asn, proteins_asn,align_filter_sa.out.filtered_file,
+            "-k subject,subject_start,-subject_end,subject_strand,query,query_start,-query_end,query_strand,-num_ident,gap_count" )
+    emit:
+        protein_alignments = run_align_sort.out
+}
diff --git a/nf/subworkflows/ncbi/target_proteins/miniprot/main.nf b/nf/subworkflows/ncbi/target_proteins/miniprot/main.nf
index 74763c1..5f54118 100644
--- a/nf/subworkflows/ncbi/target_proteins/miniprot/main.nf
+++ b/nf/subworkflows/ncbi/target_proteins/miniprot/main.nf
@@ -5,43 +5,104 @@ nextflow.enable.dsl=2
 include { merge_params } from '../../utilities'
 
 
+def get_effective_params(parameters, max_intron) {
+    def default_params = "-t 8 -G ${max_intron}"
+    def value = parameters.get("miniprot", "")
+    value = value.replaceFirst("-cpu-count", "-t")
+    value = value.replaceFirst("-max-intron", "-G")
+    parameters['miniprot'] = value
+    def effective_params = merge_params(default_params, parameters, "miniprot")
+    return effective_params
+}
+
 workflow miniprot {
     take:
         fasta_genome_file  //path: genome fasta file
         fasta_proteins_file  //path: protein fasta file
+        max_intron          //int: max intron length
         parameters      // Map : extra parameter and parameter update
     main:
-        default_params = "-t 8"
-        def value = parameters.get('miniprot', "")
-        value = value.replaceFirst("-cpu-count", "-t")
-        value = value.replaceFirst("-max-intron", "-G")
-        parameters['miniprot'] = value
-        effective_params = merge_params(default_params, parameters, 'miniprot')
-        run_miniprot(fasta_genome_file, fasta_proteins_file, effective_params)
+        // println("Miniprot max intron: ${max_intron}")
+        def items_per_chunk = merge_params("-n 1000000000", parameters, "split_proteins").replaceFirst("-n ", "").toInteger()
+        def protein_chunks
+        if (items_per_chunk == 1000000000) {
+            protein_chunks = fasta_proteins_file
+        } else {
+            protein_chunks = split_proteins(fasta_proteins_file, items_per_chunk)
+        }
+        run_miniprot(fasta_genome_file, protein_chunks.flatten(), max_intron, parameters)
 
     emit:
         miniprot_file = run_miniprot.out.miniprot_file
 }
 
 
+process split_proteins {
+    input:
+        path fasta_proteins_file
+        val  items_per_chunk
+    output:
+        path 'output/*'
+    script:
+    """
+    #!/usr/bin/env python3
+    import os
+
+    os.makedirs("output", exist_ok=True)
+    with open("${fasta_proteins_file}", 'rt') as f:
+        items = 0
+        chunk = []
+        nextfile = 1
+        for line in f:
+            if line and line[0] == '>':
+                items += 1
+                if items >= ${items_per_chunk}:
+                    with open(f"output/{nextfile}.fa", "w") as outf:
+                        outf.write(''.join(chunk))
+                        chunk = []
+                        nextfile += 1
+                        items = 1
+            chunk.append(line)
+        if chunk:
+            with open(f"output/{nextfile}.fa", "w") as outf:
+                outf.write(''.join(chunk))
+    """
+    stub:
+    print("items_per_chunk ${items_per_chunk}")
+    """
+    mkdir -p output
+    touch output/1.fa
+    touch output/2.fa
+    touch output/3.fa
+    """
+}
+
+
 process run_miniprot {
     label 'huge_job'
     label 'long_job'
     input:
         path fasta_genome_file
         path fasta_proteins_file
+        val max_intron
         val parameters
     output:
-        path ('output/aligns.paf'), emit: 'miniprot_file'
+        path ('output/*.paf'), emit: 'miniprot_file'
 
     script:
+        def paf_name = fasta_proteins_file.baseName.toString() + ".paf"
+        def effective_params = get_effective_params(parameters, max_intron)
+        // println("Miniprot params: ${effective_params}")
     """
     mkdir -p output
-    miniprot ${parameters}  ${fasta_genome_file} ${fasta_proteins_file} > output/aligns.paf
+    miniprot ${effective_params}  ${fasta_genome_file} ${fasta_proteins_file} > output/${paf_name}
     """
     stub:
+        def paf_name = fasta_proteins_file.baseName.toString() + ".paf"
+        def effective_params = get_effective_params(parameters, max_intron)
+        println("Miniprot params: ${effective_params}")
     """
     mkdir -p output
-    touch output/aligns.paf
+    touch output/${paf_name}
     """
 }
diff --git a/nf/subworkflows/ncbi/target_proteins/paf2asn/main.nf b/nf/subworkflows/ncbi/target_proteins/paf2asn/main.nf
index 0b5f291..ce33e59 100644
--- a/nf/subworkflows/ncbi/target_proteins/paf2asn/main.nf
+++ b/nf/subworkflows/ncbi/target_proteins/paf2asn/main.nf
@@ -22,22 +22,26 @@ workflow paf2asn {
 
 
 process run_paf2asn {
+    label 'long_job'
     input:
-        path (genome,  stageAs: 'LDS_Index/genome.asnt')
-        path (proteins,  stageAs: 'LDS_Index/proteins.asnt')
-        path paf_file
+        path genome,  stageAs: 'LDS_Index/genome.asnt'
+        path proteins,  stageAs: 'LDS_Index/proteins.asnt'
+        path paf_file  // list of PAF files to convert
         val parameters
     output:
-        path 'output/align.asn', emit: 'asn_file'
+        path 'output/*.asn', emit: 'asn_file'
     script:
+        def asn_name = paf_file.baseName.toString() + ".asn"    
     """
     mkdir -p output
     lds2_indexer -source LDS_Index
-    paf2asn ${parameters}  -lds2 LDS_Index/lds2.db  -nogenbank -input ${paf_file} -o output/align.asn
+    echo "${paf_file.join('\n')}" > input.mft
+    paf2asn ${parameters}  -lds2 LDS_Index/lds2.db  -nogenbank -input-manifest input.mft -o output/${asn_name}
     """
     stub:
+        def asn_name = paf_file.baseName.toString() + ".asn"    
     """
     mkdir -p output
-    touch output/align.asn
+    touch output/${asn_name}
     """
 }
diff --git a/nf/subworkflows/ncbi/utilities.nf b/nf/subworkflows/ncbi/utilities.nf
index cbb5135..57c66a6 100644
--- a/nf/subworkflows/ncbi/utilities.nf
+++ b/nf/subworkflows/ncbi/utilities.nf
@@ -44,18 +44,18 @@ def List<String> shellSplit(CharSequence s) {
 // Convert a parameter list into a map
 def Map<String, String> to_map(List<String> list )
 {
-    map = [:]
-    s = list.size()
-    i = 0
+    def map = [:]
+    def s = list.size()
+    def i = 0
     while (i < s)
     {
-        elem = list.get(i)
+        def elem = list.get(i)
         i = i + 1
         if (elem.size() > 0 && elem[0] == '-')
         {
             if (i < s) {
-                val = list.get(i)
-                if (val.size() > 0 && (val[0] != '-'  || (val[0] == '-' &&  val.contains(' '))))
+                def val = list.get(i)
+                if ( val.size() > 0 && (val[0] != '-' || val.contains(' ')) )
                 {
                     map[elem] = val
                     i = i + 1
@@ -64,13 +64,13 @@ def Map<String, String> to_map(List<String> list )
                 }
             } else {
                 map[elem] = ""
-            } 
+            }
         } else {
-            println("Error: parameter string not well formed")
-            return map 
+            println("Error: parameter string not well formed, map ${map}, elem ${elem}, i ${i}, s ${s}")
+            return map
         }
     }
-    return map 
+    return map
 }
 
 
@@ -102,7 +102,7 @@ def merge_params(default_params, parameters, section_name)
             l << quote(value)
         }
     }
-     
+
     return l.join(" ")
 }
 
diff --git a/nf/ui.nf b/nf/ui.nf
index 8742883..bd8506c 100644
--- a/nf/ui.nf
+++ b/nf/ui.nf
@@ -15,6 +15,7 @@ process export {
     input:
         path out_files
         path annot_builder_output, stageAs: 'annot_builder_output/*'
+        // path locus
     output:
         path "*", includeInputs: true
     script:
@@ -40,53 +41,48 @@ workflow {
     def organelles = input_params.get('organelles', []) ?: []
     def tax_id = input_params.get('taxid', [])
     def hmm_params = input_params.get('hmm', []) ?: []
+    def hmm_taxid = input_params.get('hmm_taxid', []) ?: []
     def softmask = input_params.get('softmask', []) ?: []
+    def max_intron = input_params.get('max_intron', [])
+    def genome_size_threshold = input_params.get('genome_size_threshold', [])
     def rnaseq_alignments = input_params.get('rnaseq_alignments', []) ?: []
     def protein_alignments = input_params.get('protein_alignments', []) ?: []
     def task_params = params.get('tasks', [:])
     def func_name = params.get('func_name', '')
     if (params.verbose) {
-        println("input params:\ngenome")
-        print(genome)
-        println("proteins")
-        print(proteins)
-        println("reads_query")
-        print(reads_query)
-        println("reads_ids")
-        print(reads_ids)
-        println("reads")
-        print(reads)
-        println("reads_metadata")
-        print(reads_metadata)
-        println("organelles")
-        print(organelles)
-        println("tax_id")
-        print(tax_id)
-        println("hmm_params")
-        print(hmm_params)
-        println("softmask")
-        print(softmask)
-        println("task_params")
-        print(task_params)
-     
-        println("rnaseq_alignments")
-        print(rnaseq_alignments)
-        println("protein_alignments")
-        print(protein_alignments)
-        println("func_name")
-        print(func_name)
-   
+        println("input params:\ngenome ${genome}")
+        println("proteins ${proteins}")
+        println("reads_query ${reads_query}")
+        println("reads_ids ${reads_ids}")
+        println("reads ${reads}")
+        println("reads_metadata ${reads_metadata}")
+        println("organelles ${organelles}")
+        println("tax_id ${tax_id}")
+        println("hmm_params ${hmm_params}")
+        println("hmm_taxid ${hmm_taxid}")
+        println("softmask ${softmask}")
+        println("max_intron ${max_intron}")
+        println("genome_size_threshold ${genome_size_threshold}")
+        println("rnaseq_alignments ${rnaseq_alignments}")
+        println("protein_alignments ${protein_alignments}")
+        println("func_name ${func_name}")
+        // Keep it last as it is large
+        println("task_params ${task_params}")
     }
     
-    if(func_name == 'only_gnomon') { 
-        print('in gnomon block')
-        only_gnomon(genome, proteins, rnaseq_alignments, protein_alignments, organelles, tax_id, hmm_params, softmask, task_params)
+    if(func_name == 'only_gnomon') {
+        if (params.verbose) {
+            print('in gnomon block')
+        }
+        only_gnomon(genome, proteins, rnaseq_alignments, protein_alignments, organelles, tax_id, hmm_params, hmm_taxid, softmask, task_params)
         export(only_gnomon.out.out_files, only_gnomon.out.evidence)
     }
     else {
-        print('in egapx block')
-        egapx(genome, proteins, reads_query, reads_ids, reads, reads_metadata, organelles, tax_id, hmm_params, softmask, task_params)
+        if (params.verbose) {
+            print('in egapx block')
+        }
+        egapx(genome, proteins, reads_query, reads_ids, reads, reads_metadata, organelles, tax_id, hmm_params, hmm_taxid, softmask, max_intron, genome_size_threshold, task_params)
+        // export(egapx.out.out_files, egapx.out.annot_builder_output, egapx.out.locus)
         export(egapx.out.out_files, egapx.out.annot_builder_output)
     }
-    // Export egapx results
 }
diff --git a/third_party_licenses/LICENSE_diamond b/third_party_licenses/LICENSE_diamond
new file mode 100644
index 0000000..0a2daba
--- /dev/null
+++ b/third_party_licenses/LICENSE_diamond
@@ -0,0 +1,622 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
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+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work.  The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
diff --git a/third_party_licenses/LICENSE_bamtools b/third_party_licenses/LICENSE_seqkit
similarity index 90%
rename from third_party_licenses/LICENSE_bamtools
rename to third_party_licenses/LICENSE_seqkit
index eaee1fd..590e25d 100644
--- a/third_party_licenses/LICENSE_bamtools
+++ b/third_party_licenses/LICENSE_seqkit
@@ -1,6 +1,6 @@
-The MIT License
+The MIT License (MIT)
 
-Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
+Copyright © 2016-2019 Wei Shen, 2019 Oxford Nanopore Technologies.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
-
diff --git a/ui/assets/config/docker_image.config b/ui/assets/config/docker_image.config
index 26abebf..203e80b 100644
--- a/ui/assets/config/docker_image.config
+++ b/ui/assets/config/docker_image.config
@@ -1 +1 @@
-process.container = 'ncbi/egapx:latest'
+process.container = '737128524250.dkr.ecr.us-east-2.amazonaws.com/ncbi-egapx:latest'
\ No newline at end of file
diff --git a/ui/assets/config/executor/aws.config b/ui/assets/config/executor/aws.config
index 3b82227..8fd958e 100644
--- a/ui/assets/config/executor/aws.config
+++ b/ui/assets/config/executor/aws.config
@@ -1,5 +1,16 @@
-process.executor = 'awsbatch'
-process.queue = 'egapx-small-and-medium-ds'
+process {
+    executor = 'awsbatch'
+    // Queue points to a compute environment with a mix of r6i.2xlarge, r6i.4xlarge, and r6i.8xlarge
+    // with 200GB EBS gp3 disks, using modified Amazon Linux 2 image with aws cli and docker installed
+    // as described in https://www.nextflow.io/docs/latest/aws.html
+    queue = 'egapx-small-and-medium-ds'
+    // If jobs fail with the message 'out of disk space', create compute environment
+    // with r6i.4xlarge instances with 1000GB EBS gp3 disk, connect a queue to it
+    // and put the queue name here
+    withLabel: 'large_disk' {
+        queue = 'egapx-large-disk'
+    }
+}
 
 aws {
     region = 'us-east-2'
diff --git a/ui/assets/config/executor/ncbi-sge.config b/ui/assets/config/executor/ncbi-sge.config
new file mode 100644
index 0000000..41daf3b
--- /dev/null
+++ b/ui/assets/config/executor/ncbi-sge.config
@@ -0,0 +1,29 @@
+// This is an example of SGE executor configuration
+// It is specific for internal NCBI use, you need to supply -P and -A parameters specific to your HPC
+// account. Keep -V, maybe adjust osverfull parameters (set to use Alma Linux 8)
+// This configuration uses binaries setup directly on network accessible drive. We currently don't support
+// such configurations for third party, use docker or singularity for this. Uncomment corresponding line below
+//docker.enabled = true
+//singularity.enabled = true
+process {
+    executor = 'sge'
+    clusterOptions = "-m n -V -P progressive -w n -A annotations-euk -l express=TRUE,h_vmem=INFINITY,m_core=12,osverfull='8*'"
+}
+env.GP_HOME="/netmnt/vast01/egapx/bin/"
+env.PATH = "/netmnt/vast01/egapx/bin:/netmnt/vast01/egapx/bin/gp:/netmnt/vast01/egapx/bin/third-party/STAR/bin/Linux_x86_64:\$PATH"
+process {
+    memory = 60.GB
+    time = 3.h
+
+    withLabel: 'big_job' {
+        memory = 120.GB
+    }
+
+    withLabel: 'huge_job' {
+        memory = 200.GB
+    }
+
+    withLabel: 'long_job' {
+        time = 6.h
+    }
+}
diff --git a/ui/assets/config/process_resources.config b/ui/assets/config/process_resources.config
index a7e81db..efdf076 100644
--- a/ui/assets/config/process_resources.config
+++ b/ui/assets/config/process_resources.config
@@ -4,7 +4,9 @@
 process {
     memory = 60.GB
     cpus = 7
-    time = 3.h
+    time = 6.h
+    errorStrategy = 'retry'
+    maxRetries = 3
 
     withLabel: 'big_job' {
         memory = 120.GB
@@ -17,6 +19,33 @@ process {
     }
 
     withLabel: 'long_job' {
-        time = 6.h
+        time = 16.h
     }
 }
+
+profiles {
+
+    stubrun {
+        
+        process {
+            memory = 1.GB
+            cpus = 1
+            time = 1.h
+
+            withLabel: 'big_job' {
+                memory = 1.GB
+                cpus = 1
+            }
+
+            withLabel: 'huge_job' {
+                memory = 1.GB
+                cpus = 1
+            }
+
+            withLabel: 'long_job' {
+                time = 1.h
+            }
+        }
+    }
+
+}
diff --git a/ui/assets/default_task_params.yaml b/ui/assets/default_task_params.yaml
index 145e28d..9569214 100644
--- a/ui/assets/default_task_params.yaml
+++ b/ui/assets/default_task_params.yaml
@@ -37,21 +37,22 @@ tasks:
     gpx_make_outputs: -default-output-name align -slices-for affinity -sort-by job-id
       -unzip align
     gpx_qsubmit: -affinity subject
-    rnaseq_collapse: -backlog 1 -max-jobs 1 -rank-counts-precalculated
+    rnaseq_collapse: -backlog 1 -max-jobs 1 -support-non-sra
+    # -rank-counts-precalculated
     rnaseq_collapse_create_jobs: -alignments-per-job 50000 -min-range 100000
   star_index:
     STAR: --runThreadN 8
   star_wnode:
     gpx_qdump: -unzip '*'
     gpx_qsubmit: -affinity subject
-    star_wnode: -cpus-per-worker 16 -csi-threshold 512000000 -max-intron 600000 -star-params
-      '--alignSJoverhangMin 8 --outFilterMultimapNmax 200 --outFilterMismatchNmax
+    star_wnode: -cpus-per-worker 16 -csi-threshold 512000000 -preserve-star-logs
+    star-params: --alignSJoverhangMin 8 --outFilterMultimapNmax 200 --outFilterMismatchNmax
       50 --runThreadN 16 --genomeLoad NoSharedMemory --outSAMtype SAM --outSAMattributes
-      NH HI AS nM NM MD jM jI XS MC --outSAMprimaryFlag AllBestScore --outFilterMultimapScoreRange
-      50 --seedSearchStartLmax 15 --limitOutSAMoneReadBytes 1000000 --outSJtype None'
-      -preserve-star-logs
+      'NH HI AS nM NM MD jM jI XS MC' --outSAMprimaryFlag AllBestScore --outFilterMultimapScoreRange
+      50 --seedSearchStartLmax 15 --limitOutSAMoneReadBytes 1000000 --outSJtype None 
   miniprot:
-    miniprot: -t 31 -p 0.4 --outs=0.4 -G 600000
+    split_proteins: -n 100000
+    miniprot: -t 31 -p 0.4 --outs=0.4
   paf2asn:
     paf2asn: -prosplign-refinement
   best_aligned_prot:
@@ -61,4 +62,10 @@ tasks:
   align_filter_sa:
     align_filter:  -filter 'rank=1 OR (pct_identity_gapopen_only > 58 AND (pct_coverage > 50 OR align_length_ungap > 1000))' -ifmt seq-align  
   gnomon_training:
-    gnomon_training: -maxintron 1200000 -asn -b
+    gnomon_training: -asn -b
+  diamond:
+    diamond: -query-fmt seq-ids -subject-fmt seq-ids -output-prefix hits -ofmt seq-align-set
+    diamond_blastp:  --sam-query-len --very-sensitive --unal 0 --comp-based-stats 0 --masking 0
+  diamond_orthology:
+    diamond_orhtology: -ofmt seq-align-set -query-fmt seq-ids -subject-fmt seq-ids -output-prefix hits
+    diamond_orthology_blastp: --sam-query-len --very-sensitive --unal 0 --comp-based-stats 0 --masking 0 
diff --git a/ui/egapx.py b/ui/egapx.py
index 1f822ad..490f0a3 100755
--- a/ui/egapx.py
+++ b/ui/egapx.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 # requires pip install pyyaml
-
+#
 import shlex
 import shutil
 import sys
@@ -9,33 +9,181 @@
 import subprocess
 import tempfile
 import re
+import time
+import datetime
 from collections import defaultdict
+from ftplib import FTP
+from ftplib import FTP_TLS
+import ftplib
 from pathlib import Path
 from typing import List
 from urllib.request import urlopen
 import json
+import sqlite3
+import stat
+
 import yaml
 
 VERBOSITY_DEFAULT=0
 VERBOSITY_QUIET=-1
 VERBOSITY_VERBOSE=1
 
+FTP_EGAP_PROTOCOL = "https"
+FTP_EGAP_SERVER = "ftp.ncbi.nlm.nih.gov"
+FTP_EGAP_ROOT_PATH = "genomes/TOOLS/EGAP/support_data"
+FTP_EGAP_ROOT = f"{FTP_EGAP_PROTOCOL}://{FTP_EGAP_SERVER}/{FTP_EGAP_ROOT_PATH}"
+DATA_VERSION = "current"
+dataset_taxonomy_url = "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/taxonomy/taxon/"
+
+user_cache_dir = ''
+
 def parse_args(argv):
     parser = argparse.ArgumentParser(description="Main script for EGAPx")
-    parser.add_argument("filename", help="YAML file with input: section with at least genome: and reads: parameters")
-    parser.add_argument("-o", "--output", help="Output path", required=True, default="")
+    group = parser.add_argument_group('run')
+    group.add_argument("filename", nargs='?', help="YAML file with input: section with at least genome: and reads: parameters")
+    group.add_argument("-o", "--output", help="Output path", default="")
     parser.add_argument("-e", "--executor", help="Nextflow executor, one of docker, singularity, aws, or local (for NCBI internal use only). Uses corresponding Nextflow config file", default="local")
     parser.add_argument("-c", "--config-dir", help="Directory for executor config files, default is ./egapx_config. Can be also set as env EGAPX_CONFIG_DIR", default="")
     parser.add_argument("-w", "--workdir", help="Working directory for cloud executor", default="")
     parser.add_argument("-r", "--report", help="Report file prefix for report (.report.html) and timeline (.timeline.html) files, default is in output directory", default="")
     parser.add_argument("-n", "--dry-run", action="store_true", default=False)
     parser.add_argument("-st", "--stub-run", action="store_true", default=False)
+    parser.add_argument("-so", "--summary-only", help="Print result statistics only if available, do not compute result", action="store_true", default=False)
+    group = parser.add_argument_group('download')
+    group.add_argument("-dl", "--download-only", help="Download external files to local storage, so that future runs can be isolated", action="store_true", default=False)
+    parser.add_argument("-lc", "--local-cache", help="Where to store the downloaded files", default="")
     parser.add_argument("-q", "--quiet", dest='verbosity', action='store_const', const=VERBOSITY_QUIET, default=VERBOSITY_DEFAULT)
     parser.add_argument("-v", "--verbose", dest='verbosity', action='store_const', const=VERBOSITY_VERBOSE, default=VERBOSITY_DEFAULT)
     parser.add_argument("-fn", "--func_name", help="func_name", default="")
     return parser.parse_args(argv[1:])
 
 
+class FtpDownloader:
+    def __init__(self):
+        self.ftp = None
+
+    def connect(self, host):
+        self.host = host
+        self.reconnect() 
+
+    def reconnect(self):
+        self.ftp = FTP(self.host)
+        self.ftp.login()
+        self.ftp.set_debuglevel(0)
+       
+    ##ftp_types = set()
+    def download_ftp_file(self, ftp_name, local_path):
+        # print(f"file: {ftp_name}")
+        # print(f"f: { os.path.dirname(local_path)}")
+
+        os.makedirs(os.path.dirname(local_path), exist_ok=True)
+        try:
+            with open(local_path, 'wb') as f:
+                self.ftp.retrbinary("RETR {0}".format(ftp_name), f.write)
+            # print("downloaded: {0}".format(local_path))
+            return True
+        except FileNotFoundError:
+            print("FAILED FNF: {0}".format(local_path))
+        except EOFError:
+            print("FAILED EOF: {0}".format(local_path))
+            time.sleep(1)
+            self.reconnect()
+            print("retrying...")
+            r = self.download_ftp_file(ftp_name, local_path)
+            print("downloaded on retry: {0}".format(local_path))
+            return r
+        except BrokenPipeError:
+            print("FAILED BP: {0}".format(local_path))
+        except IsADirectoryError:
+            ## same as 550 but pre-exists
+            ## os.remove(local_path)
+            return 550
+        except ftplib.error_perm:
+            ## ftplib.error_perm: 550 genomes/TOOLS/EGAP/ortholog_references/9606/current: Not a regular file
+            ## its a symlink to a dir.
+            os.remove(local_path)
+            return 550
+        return False
+
+    # item: ('Eublepharis_macularius', {'modify': '20240125225739', 'perm': 'fle', 'size': '4096', 'type': 'dir', 'unique': '6CU599079F', 'unix.group': '562', 'unix.mode': '0444', 'unix.owner': '14'}
+    def should_download_file(self, ftp_item, local_name):
+        metadata = ftp_item[1]
+        ftp_modify = datetime.datetime.strptime(metadata['modify'], '%Y%m%d%H%M%S')
+        ftp_size = int(metadata['size'])
+        ftp_type = metadata['type']
+
+        local_stat = []
+        try:
+            local_stat = os.stat(local_name)
+        except FileNotFoundError:
+            return True
+        except NotADirectoryError:
+            return True
+        local_is_dir = stat.S_ISDIR(local_stat.st_mode)
+        #print(f"item: {ftp_item}")
+        #print(f"stat: {local_stat}") 
+ 
+        local_stat_dt = datetime.datetime.fromtimestamp(local_stat.st_mtime)
+
+        #print(f"should_dl: {ftp_size != local_stat.st_size}  {ftp_modify > local_stat_dt}  ")
+
+        if (ftp_type == 'file' and ftp_size != local_stat.st_size) or (ftp_type=='OS.unix=symlink' and ftp_size >= local_stat.st_size):
+            return True
+
+        if ftp_modify > local_stat_dt:
+            return True
+
+        return False
+
+    ## types
+    ## cdir and pdir: . and ..: do nothing
+    ## file: a file
+    ## dir: a dir
+    ## OS.unix=symlink: symlink to a file, treat like a file
+    def download_ftp_dir(self, ftp_path, local_path):
+        """ replicates a directory on an ftp server recursively """
+        for ftp_item in self.ftp.mlsd(ftp_path):
+            # print(f"ftp_item: {ftp_item}")
+            ##print(f"  name: {ftp_item[0]}")
+            ##print(f"  type: {ftp_item[1]['type']}")
+            name = ftp_item[0]
+            next_ftp_name="/".join([ftp_path,name])
+            next_local_name=os.sep.join([local_path,name])
+            ftp_type = ftp_item[1]['type']
+            ##ftp_types.add(ftp_type)
+            if ftp_type=='dir':
+                self.download_ftp_dir(next_ftp_name, next_local_name)
+            elif ftp_type=='file' or ftp_type=='OS.unix=symlink':
+                if self.should_download_file(ftp_item, next_local_name):
+                    r = self.download_ftp_file(next_ftp_name, next_local_name)
+                    if r == 550:
+                        self.download_ftp_dir(next_ftp_name, next_local_name)
+                    ##time.sleep(0.1)
+            ## else: . or .. do nothing
+
+
+def download_egapx_ftp_data(local_cache_dir):
+    global user_cache_dir
+    manifest_url = f"{FTP_EGAP_ROOT}/{DATA_VERSION}.mft"
+    manifest = urlopen(manifest_url)
+    manifest_path = f"{user_cache_dir}/{DATA_VERSION}.mft"
+    manifest_list = []
+    for line in manifest:
+        line = line.decode("utf-8").strip()
+        if not line or line[0] == '#':
+            continue
+        manifest_list.append(line)
+        print(f"Downloading {line}")
+        ftpd = FtpDownloader()
+        ftpd.connect(FTP_EGAP_SERVER)
+        ftpd.download_ftp_dir(FTP_EGAP_ROOT_PATH+f"/{line}", f"{local_cache_dir}/{line}")
+    if user_cache_dir:
+        with open(manifest_path, 'wt') as f:
+            for line in manifest_list:
+                f.write(f"{line}\n")
+    return 0
+
+
 def repackage_inputs(run_inputs):
     "Repackage input parameters into 'input' key if not already there"
     if 'input' in run_inputs:
@@ -57,8 +205,8 @@ def convert_value(value):
     elif isinstance(value, list):
         return [convert_value(v) for v in value]
     else:
-        if value == '' or re.match(r'^[a-z0-9]{2,5}://.*', value):
-            # do not convert - this is a URL or empty string
+        if value == '' or re.match(r'[a-z0-9]{2,5}://', value) or not os.path.exists(value):
+            # do not convert - this is a URL or empty string or non-file
             return value
         # convert to absolute path
         return str(Path(value).absolute())
@@ -78,40 +226,119 @@ def convert_paths(run_inputs):
         run_inputs['output'] = convert_value(run_inputs['output'])
 
 
-def generate_reads_metadata(run_inputs):
-    "Generate reads metadata file with minimal information - paired/unpaired and valid for existing libraries"
+def prepare_reads(run_inputs):
+    """Reformat reads input to be in 'fromPairs' format expected by egapx, i.e. [sample_id, [read1, read2]]
+    Generate reads metadata file with minimal information - paired/unpaired and valid for existing libraries"""
     if 'reads' not in run_inputs['input'] or 'output' not in run_inputs:
-        return None
-    output = run_inputs['output']
+        return
     prefixes = defaultdict(list)
-    with tempfile.NamedTemporaryFile(mode='w', delete=False, dir=output, prefix='egapx_reads_metadata_', suffix='.tsv') as f:
-        for rf in run_inputs['input']['reads']:
-            mo = re.match(r'([A-Za-z0-9]+)([^A-Za-z0-9].*)', Path(rf).parts[-1])
-            if mo:
-                prefixes[mo.group(1)].append(mo.group(2))
-        for k, v in prefixes.items():
-            paired = 'paired' if len(v) == 2 else 'unpaired'
-            # SRR9005248	NA	paired	2	2	NA	NA	NA	NA	NA	NA	NA	0
-            rec = "\t".join([k, 'NA', paired, '2', '2', 'NA', 'NA', 'NA', 'NA', 'NA', 'NA', 'NA', '0'])
-            f.write(rec + '\n')
-        f.flush()
-        run_inputs['input']['reads_metadata'] = f.name
-        return f.name
-
-
-def validate_params(run_inputs):
-    "Validate input parameters"
+    reads = run_inputs['input']['reads']
+    if type(reads) == str:
+        del run_inputs['input']['reads']
+        run_inputs['input']['reads_query'] = reads
+        return
+    # Create fake metadata file for reads containing only one meaningful information piece - pairedness
+    # Have an entry in this file only for SRA runs - files with prefixes SRR, ERR, and DRR and digits
+    # Non-SRA reads are handled by rnaseq_collapse internally
+    has_files = False
+    for rf in run_inputs['input']['reads']:
+        if type(rf) == str:
+            name = Path(rf).parts[-1]
+            mo = re.match(r'([^._]+)', name)
+            if mo and mo.group(1) != name:
+                has_files = True
+                prefixes[mo.group(1)].append(rf)
+        elif type(rf) == list:
+            has_files = True
+            names = list(map(lambda x: re.match(r'([^.]+)', Path(x).parts[-1]).group(1), rf))
+            # Find common prefix
+            names.sort()
+            if len(names) == 1:
+                sample_id = names[0]
+            else:
+                for i in range(min(len(names[0]), len(names[-1]))):
+                    if names[0][i] != names[-1][i]:
+                        break
+                sample_id = names[0][0:i]
+            # Dont end prefix with . or _
+            i = len(sample_id) - 1
+            while i > 0 and sample_id[-1] in "._":
+                sample_id = sample_id[:-1]
+                i -= 1
+            prefixes[sample_id] = rf
+    if has_files: # len(prefixes):
+        # Always create metadata file even if it's empty
+        output = run_inputs['output']
+        with tempfile.NamedTemporaryFile(mode='w', delete=False, dir=output, prefix='egapx_reads_metadata_', suffix='.tsv') as f:
+            for k, v in prefixes.items():
+                if re.fullmatch(r'([DES]RR[0-9]+)', k):
+                    paired = 'paired' if len(v) == 2 else 'unpaired'
+                    # SRR9005248	NA	paired	2	2	NA	NA	NA	NA	NA	NA	NA	0
+                    rec = "\t".join([k, 'NA', paired, '2', '2', 'NA', 'NA', 'NA', 'NA', 'NA', 'NA', 'NA', '0'])
+                    f.write(rec + '\n')
+            f.flush()
+            run_inputs['input']['reads_metadata'] = f.name
+        run_inputs['input']['reads'] = [ [k, v] for k, v in prefixes.items() ]
+    elif reads:
+        del run_inputs['input']['reads']
+        run_inputs['input']['reads_query'] = "[Accession] OR ".join(reads) + "[Accession]"
+
+
+def expand_and_validate_params(run_inputs):
+    """ Expand implicit parameters and validate inputs
+    Args:
+        run_inputs (dict): Input parameters
+    Returns:
+        bool: True if parameters are valid, False otherwise
+    """
     inputs = run_inputs['input']
-    success = True
-    has_genome = 'genome' in inputs
+
+    if 'taxid' not in inputs:
+        print("ERROR: Missing parameter: 'taxid'")
+        return False
+
+    taxid = inputs['taxid']
+
+    if 'genome' not in inputs:
+        print("ERROR: Missing parameter: 'genome'")
+        return False
+
+    # Check for proteins input and if empty or no input at all, add closest protein bag
+    if 'proteins' not in inputs:
+        proteins = get_closest_protein_bag(taxid)
+        if not proteins:
+            # Proteins are not specified explicitly and not found by taxid
+            print(f"ERROR: Proteins are not found for tax id {inputs['taxid']}")
+            print("  This organism is not supported by current NCBI protein database")
+            print("  You can specify proteins manually using 'proteins' parameter")
+            return False
+        inputs['proteins'] = proteins
+
     has_rnaseq = 'reads' in inputs or 'reads_ids' in inputs or 'reads_query' in inputs
-    has_taxid = 'taxid' in inputs
-    has_proteins = 'proteins' in inputs or ('taxid' in inputs and get_closest_protein_bag(inputs['taxid']))
-    if not has_genome or not has_taxid or not (has_rnaseq or has_proteins):
-        print("Missing parameter: 'genome', 'taxid', and either 'proteins', or 'reads' should be specified")
-        print("  proteins can be indirectly specified by 'taxid'")
-        success = False
-    return success
+    if not has_rnaseq:
+        if inputs['proteins']:
+            print("WARNING: It is strongly advised to specify RNA-seq reads using 'reads' parameter\n")
+        else:
+            print("ERROR: Either proteins or RNA-seq reads should be provided for annotation")
+            return False
+
+    if 'hmm' not in inputs:
+        best_taxid, best_hmm = get_closest_hmm(taxid)
+        inputs['hmm'] = best_hmm
+        inputs['hmm_taxid'] = best_taxid
+    else:
+        # We assume the user knows what they're doing and the training is not necessary
+        inputs['hmm_taxid'] = taxid
+
+    if 'max_intron' not in inputs:
+        max_intron, genome_size_threshold = get_max_intron(taxid)
+        inputs['max_intron'] = max_intron
+        inputs['genome_size_threshold'] = genome_size_threshold
+    else:
+        # Given max_intron is a hard limit, no further calculation is necessary
+        inputs['genome_size_threshold'] = 0
+
+    return True
 
 
 def manage_workdir(args):
@@ -131,6 +358,64 @@ def manage_workdir(args):
     return True
 
 
+def get_cache_dir():
+    global user_cache_dir
+    if user_cache_dir and os.path.exists(user_cache_dir):
+        return user_cache_dir
+    ##elif os.path.exists("/am/ftp-genomes/TOOLS/EGAP"):
+    ##    return "/am/ftp-genomes/TOOLS/EGAP"
+    return ""
+
+
+data_version_cache = {}
+def get_versioned_path(subsystem, filename):
+    global data_version_cache
+    global user_cache_dir
+    if not data_version_cache:
+        manifest_path = f"{user_cache_dir}/{DATA_VERSION}.mft"
+        if user_cache_dir and os.path.exists(manifest_path):
+            with open(manifest_path, 'rt') as f:
+                for line in f:
+                    line = line.strip()
+                    if not line or line[0] == '#':
+                        continue
+                    parts = line.split('/')
+                    if len(parts) == 2:
+                        data_version_cache[parts[0]] = parts[1]
+        else:
+            manifest_url = f"{FTP_EGAP_ROOT}/{DATA_VERSION}.mft"
+            manifest = urlopen(manifest_url)
+            manifest_list = []
+            for line in manifest:
+                line = line.decode("utf-8").strip()
+                if not line or line[0] == '#':
+                    continue
+                parts = line.split('/')
+                if len(parts) == 2:
+                    data_version_cache[parts[0]] = parts[1]
+                    manifest_list.append(line)
+            if user_cache_dir:
+                with open(manifest_path, 'wt') as f:
+                    for line in manifest_list:
+                        f.write(f"{line}\n")
+
+    if subsystem not in data_version_cache:
+        return os.path.join(subsystem, filename)
+    version = data_version_cache[subsystem]
+    return os.path.join(subsystem, version, filename)
+
+
+# Get file path for subsystem, either from cache or from remote server
+def get_file_path(subsystem, filename):
+    cache_dir = get_cache_dir()
+    vfn = get_versioned_path(subsystem, filename)
+    file_path = os.path.join(cache_dir, vfn)
+    file_url = f"{FTP_EGAP_ROOT}/{vfn}"
+    if os.path.exists(file_path):
+        return file_path
+    return file_url
+
+
 def get_config(script_directory, args):
     config_file = ""
     config_dir = args.config_dir if args.config_dir else os.environ.get("EGAPX_CONFIG_DIR")
@@ -171,13 +456,55 @@ def get_config(script_directory, args):
     return ",".join(config_files)
 
 
+lineage_cache = {}
+def get_lineage(taxid):
+    global lineage_cache
+    if not taxid:
+        return []
+    if taxid in lineage_cache:
+        return lineage_cache[taxid]
+    # Try cached taxonomy database
+    taxonomy_db_name = os.path.join(get_cache_dir(), get_versioned_path("taxonomy", "taxonomy4blast.sqlite3"))
+    if os.path.exists(taxonomy_db_name):
+        conn = sqlite3.connect(taxonomy_db_name)
+        if conn:
+            c = conn.cursor()
+            lineage = [taxid]
+            cur_taxid = taxid
+            while cur_taxid != 1:
+                c.execute("SELECT parent FROM TaxidInfo WHERE taxid = ?", (cur_taxid,))
+                cur_taxid = c.fetchone()[0]
+                lineage.append(cur_taxid)
+            lineage.reverse()
+            lineage_cache[taxid] = lineage
+            return lineage
+    
+    # Fallback to API
+    taxon_json_file = urlopen(dataset_taxonomy_url+str(taxid))
+    taxon = json.load(taxon_json_file)["taxonomy_nodes"][0]
+    lineage = taxon["taxonomy"]["lineage"]
+    lineage.append(taxon["taxonomy"]["tax_id"])
+    lineage_cache[taxid] = lineage
+    return lineage
+
+
+def get_tax_file(subsystem, tax_path):
+    vfn = get_versioned_path(subsystem, tax_path)
+    taxids_path = os.path.join(get_cache_dir(), vfn)
+    taxids_url = f"{FTP_EGAP_ROOT}/{vfn}"
+    taxids_file = []
+    if os.path.exists(taxids_path):
+        with open(taxids_path, "rb") as r:
+            taxids_file = r.readlines()
+    else:
+        taxids_file = urlopen(taxids_url)
+    return taxids_file
+
 def get_closest_protein_bag(taxid):
     if not taxid:
         return ''
-    taxon_str = str(taxid)
-    dataset_taxonomy_url = "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/taxonomy/taxon/"
 
-    taxids_file = urlopen("https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/target_proteins/taxid.list")
+    taxids_file = get_tax_file("target_proteins", "taxid.list")
     taxids_list = []
     for line in taxids_file:
         line = line.decode("utf-8").strip()
@@ -188,12 +515,7 @@ def get_closest_protein_bag(taxid):
             t = parts[0]
             taxids_list.append(int(t))
 
-    taxon_json_file = urlopen(dataset_taxonomy_url+taxon_str)
-    taxon = json.load(taxon_json_file)["taxonomy_nodes"][0]
-    lineage = taxon["taxonomy"]["lineage"]
-    lineage.append(taxon["taxonomy"]["tax_id"])
-    # print(lineage)
-    # print(taxon["taxonomy"]["organism_name"])
+    lineage = get_lineage(taxid)
 
     best_taxid = None
     best_score = 0
@@ -208,9 +530,75 @@ def get_closest_protein_bag(taxid):
 
     if best_score == 0:
         return ''
+    # print(best_taxid, best_score)
+    return get_file_path("target_proteins", f"{best_taxid}.faa.gz")
+
+
+def get_closest_hmm(taxid):
+    if not taxid:
+        return 0, ""
+
+    taxids_file = get_tax_file("gnomon", "hmm_parameters/taxid.list")
+
+    taxids_list = []
+    lineages = []
+    for line in taxids_file:
+        parts = line.decode("utf-8").strip().split('\t')
+        if len(parts) > 0:
+            t = parts[0]
+            taxids_list.append(t)
+            if len(parts) > 1:
+                l = map(lambda x: int(x) if x[-1] != ';' else int(x[:-1]), parts[1].split())
+                lineages.append((int(t), list(l)+[int(t)]))
+
+    #if len(lineages) < len(taxids_list):
+    #    taxonomy_json_file = urlopen(dataset_taxonomy_url+','.join(taxids_list))
+    #    taxonomy = json.load(taxonomy_json_file)["taxonomy_nodes"]
+    #    lineages = [ (t["taxonomy"]["tax_id"], t["taxonomy"]["lineage"] + [t["taxonomy"]["tax_id"]]) for t in taxonomy ]
+
+    lineage = get_lineage(taxid)
+
+    best_lineage = None
+    best_taxid = None
+    best_score = 0
+    for (t, l) in lineages:
+        pos1 = 0
+        last_match = 0
+        for pos in range(len(lineage)):
+            tax_id = lineage[pos]
+            while tax_id != l[pos1]:
+                if pos1 + 1 < len(l):
+                    pos1 += 1
+                else:
+                    break
+            if tax_id == l[pos1]:
+                last_match = pos1
+            else:
+                break
+        if last_match > best_score:
+            best_score = last_match
+            best_taxid = t
+            best_lineage = l
+
+    if best_score == 0:
+        return 0, ""
     # print(best_lineage)
     # print(best_taxid, best_score)
-    return f'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/target_proteins/{best_taxid}.faa.gz'
+    return best_taxid, get_file_path("gnomon", f"hmm_parameters/{best_taxid}.params")
+
+
+PLANTS=33090
+VERTEBRATES=7742
+def get_max_intron(taxid):
+    if not taxid:
+        return 0, 0
+    lineage = get_lineage(taxid)
+    if PLANTS in lineage:
+        return 300000, 3000000000
+    elif VERTEBRATES in lineage:
+        return 1200000, 2000000000
+    else:
+        return 600000, 500000000
 
 
 def to_dict(x: List[str]):
@@ -255,6 +643,26 @@ def merge_params(task_params, run_inputs):
     return task_params
 
 
+def print_statistics(output):
+    accept_gff = Path(output) / 'accept.gff'
+    print(f"Statistics for {accept_gff}")
+    counter = defaultdict(int)
+    if accept_gff.exists():
+        with open(accept_gff, 'rt') as f:
+            for line in f:
+                line = line.strip()
+                if not line or line[0] == '#':
+                    continue
+                parts = line.split()
+                if len(parts) < 3:
+                    continue
+                counter[parts[2]] += 1
+    keys = list(counter.keys())
+    keys.sort()
+    for k in keys:
+        print(f"{k:12s} {counter[k]}")
+
+
 def main(argv):
     "Main script for EGAPx"
     #warn user that this is an alpha release
@@ -263,6 +671,28 @@ def main(argv):
     # Parse command line
     args = parse_args(argv)
 
+    global user_cache_dir
+    if args.local_cache:
+        # print(f"Local cache: {args.local_cache}")
+        user_cache_dir = args.local_cache
+    if args.download_only:
+        if args.local_cache:
+            if not args.dry_run:
+                # print(f"Download only: {args.download_only}")
+                os.makedirs(args.local_cache, exist_ok=True)
+                download_egapx_ftp_data(args.local_cache)
+            else:
+                print(f"Download only to {args.local_cache}")
+            return 0
+        else:
+            print("Local cache not set")
+            return 1
+    else:
+        # Check that input and output set
+        if not args.filename or not args.output:
+            print("Input file and output directory must be set")
+            return 1
+
     packaged_distro = bool(getattr(sys, '_MEIPASS', ''))
     script_directory = getattr(sys, '_MEIPASS', os.path.abspath(os.path.dirname(__file__)))
     config_file = get_config(script_directory, args)
@@ -272,22 +702,19 @@ def main(argv):
     # Check for workdir, set if not set, and manage last used workdir
     if not manage_workdir(args):
         return 1
-    
+   
     files_to_delete = []
     
     # Read default task parameters into a dict
     task_params = yaml.safe_load(open(Path(script_directory) / 'assets' / 'default_task_params.yaml', 'r'))
     run_inputs = repackage_inputs(yaml.safe_load(open(args.filename, 'r')))
 
-    # Check for proteins input and if empty or no input at all, add closest protein bag
-    if 'proteins' not in run_inputs['input'] and 'taxid' in run_inputs['input']:
-        run_inputs['input']['proteins'] = get_closest_protein_bag(run_inputs['input']['taxid'])
+    if not expand_and_validate_params(run_inputs):
+        return 1
 
     # Command line overrides manifest input
     if args.output:
         run_inputs['output'] = args.output
-    if not validate_params(run_inputs):
-        return 1
 
     # Convert inputs to absolute paths
     convert_paths(run_inputs)
@@ -295,8 +722,19 @@ def main(argv):
     # Create output directory if needed
     os.makedirs(run_inputs['output'], exist_ok=True)
 
-    # Add reads_metadata.tsv file
-    generate_reads_metadata(run_inputs)
+    if args.summary_only:
+        print_statistics(run_inputs['output'])
+        return 0
+
+    # Reformat reads into pairs in fromPairs format and add reads_metadata.tsv file
+    prepare_reads(run_inputs)
+
+
+    ##if True or args.download_only:
+    ##    with open("./dumped_input.yaml", 'w') as f:
+    ##        yaml.dump(run_inputs, f)
+    ##        f.flush()
+    ##return 0 
 
     # Add to default task parameters, if input file has some task parameters they will override the default
     task_params = merge_params(task_params, run_inputs)
@@ -323,7 +761,7 @@ def main(argv):
         main_nf = Path(script_directory) / '..' / 'nf' / 'ui.nf'
     nf_cmd = ["nextflow", "-C", config_file, "-log", f"{output}/nextflow.log", "run", main_nf, "--output", output]
     if args.stub_run:
-        nf_cmd += ["-stub-run"]
+        nf_cmd += ["-stub-run", "-profile", "stubrun"]
     if args.report:
         nf_cmd += ["-with-report", f"{args.report}.report.html", "-with-timeline", f"{args.report}.timeline.html"]
     else:
@@ -344,16 +782,24 @@ def main(argv):
             f.flush()
         if args.verbosity >= VERBOSITY_VERBOSE:
             print(" ".join(map(str, nf_cmd)))
+        resume_file = Path(output) / "resume.sh"
+        with open(resume_file, 'w') as f:
+            f.write("#!/bin/bash\n")
+            f.write(" ".join(map(str, nf_cmd)))
+            f.write(" -resume")
+            if os.environ.get('NXF_WORK'):
+                f.write(" -work-dir " + os.environ['NXF_WORK'])
+            f.write("\n")
         try:
             subprocess.run(nf_cmd, check=True, capture_output=(args.verbosity <= VERBOSITY_QUIET), text=True)
         except subprocess.CalledProcessError as e:
             print(e.stderr)
-            print("To resume execution, run:")
-            nf_cmd.append("-resume")
-            print(" ".join(map(str, nf_cmd)))
+            print(f"To resume execution, run: sh {resume_file}")
             if files_to_delete:
                 print(f"Don't forget to delete file(s) {' '.join(files_to_delete)}")
             return 1
+    if not args.dry_run and not args.stub_run:
+        print_statistics(output)
     # TODO: Use try-finally to delete the metadata file
     for f in files_to_delete:
         os.unlink(f)

From 52aaa080c1332fcb477f6ab80ef182eb8f2075a9 Mon Sep 17 00:00:00 2001
From: "Strope, Pooja" <pooja.strope@nih.gov>
Date: Thu, 25 Jul 2024 17:55:23 -0400
Subject: [PATCH 2/4] update from prod

---
 nf/subworkflows/ncbi/only_gnomon.nf  | 13 ++++++++++++-
 ui/assets/config/docker_image.config |  3 ++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/nf/subworkflows/ncbi/only_gnomon.nf b/nf/subworkflows/ncbi/only_gnomon.nf
index c18e512..3544dba 100644
--- a/nf/subworkflows/ncbi/only_gnomon.nf
+++ b/nf/subworkflows/ncbi/only_gnomon.nf
@@ -5,6 +5,7 @@
 nextflow.enable.dsl=2
 
 include { setup_genome; setup_proteins } from './setup/main'
+include { get_hmm_params; run_get_hmm } from './default/get_hmm_params/main'
 include { chainer_wnode as chainer } from './gnomon/chainer_wnode/main'
 include { gnomon_wnode } from './gnomon/gnomon_wnode/main'
 include { prot_gnomon_prepare } from './gnomon/prot_gnomon_prepare/main'
@@ -63,7 +64,17 @@ workflow only_gnomon {
 
         // GNOMON
 
-        chainer(alignments, hmm_params, /* evidence_denylist */ [], /* gap_fill_allowlist */ [], scaffolds, /* trusted_genes */ [], genome_asn, proteins_asn, task_params.get('chainer', [:]))
+        def effective_hmm
+        if (hmm_params) {
+            effective_hmm = hmm_params
+        } else {
+            tmp_hmm = run_get_hmm(tax_id)
+            b = tmp_hmm | splitText( { it.split('\n') } ) | flatten 
+            c = b | last
+            effective_hmm = c
+        }
+
+        chainer(alignments, effective_hmm, /* evidence_denylist */ [], /* gap_fill_allowlist */ [], scaffolds, /* trusted_genes */ [], genome_asn, proteins_asn, task_params.get('chainer', [:]))
 
         gnomon_wnode(scaffolds, chainer.out.chains, chainer.out.chains_slices, effective_hmm, [], softmask, genome_asn, proteins_asn, task_params.get('gnomon', [:]))
         def models = gnomon_wnode.out.outputs
diff --git a/ui/assets/config/docker_image.config b/ui/assets/config/docker_image.config
index 203e80b..17f1797 100644
--- a/ui/assets/config/docker_image.config
+++ b/ui/assets/config/docker_image.config
@@ -1 +1,2 @@
-process.container = '737128524250.dkr.ecr.us-east-2.amazonaws.com/ncbi-egapx:latest'
\ No newline at end of file
+#process.container = '737128524250.dkr.ecr.us-east-2.amazonaws.com/ncbi-egapx:latest'
+process.container = 'ncbi/egapx:0.2-alpha'

From ac29bd5baebc02defd9f108ce75957c154ce2930 Mon Sep 17 00:00:00 2001
From: Pooja Strope <pstrope@users.noreply.github.com>
Date: Thu, 25 Jul 2024 18:01:45 -0400
Subject: [PATCH 3/4] Update docker_image.config

---
 ui/assets/config/docker_image.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/ui/assets/config/docker_image.config b/ui/assets/config/docker_image.config
index 17f1797..aa41657 100644
--- a/ui/assets/config/docker_image.config
+++ b/ui/assets/config/docker_image.config
@@ -1,2 +1 @@
-#process.container = '737128524250.dkr.ecr.us-east-2.amazonaws.com/ncbi-egapx:latest'
 process.container = 'ncbi/egapx:0.2-alpha'

From a886af6c8179a0949427fca152dfc2e2b2d359e5 Mon Sep 17 00:00:00 2001
From: "Strope, Pooja" <pooja.strope@nih.gov>
Date: Thu, 25 Jul 2024 18:34:49 -0400
Subject: [PATCH 4/4] protein sets posted

---
 README.md | 152 ++++++++++++++++++++++++++++++++++++++++++++----------
 1 file changed, 126 insertions(+), 26 deletions(-)

diff --git a/README.md b/README.md
index d46fa65..08bc731 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,14 @@ EGAPx is the publicly accessible version of the updated NCBI [Eukaryotic Genome
 
 EGAPx takes an assembly fasta file, a taxid of the organism, and RNA-seq data. Based on the taxid, EGAPx will pick protein sets and HMM models. The pipeline runs `miniprot` to align protein sequences, and `STAR` to align RNA-seq to the assembly. Protein alignments and RNA-seq read alignments are then passed to `Gnomon` for gene prediction. In the first step of `Gnomon`, the short alignments are chained together into putative gene models. In the second step, these predictions are further supplemented by _ab-initio_ predictions based on HMM models. The final annotation for the input assembly is produced as a `gff` file. 
 
-We currently have protein datasets posted for most vertebrates (mammals, sauropsids, ray-finned fishes), hymenoptera, diptera, lepidoptera and choleoptera. We will be adding datasets for more arthropods, vertebrates and plants in the next couple of months. Fungi, protists and nematodes are currently out-of-scope for EGAPx pending additional refinements.
+We currently have protein datasets posted that are suitable for most vertebrates and arthropods:
+  - Chordata - Mammalia, Sauropsida, Actinopterygii (ray-finned fishes)
+  - Insecta - Hymenoptera, Diptera, Lepidoptera, Coleoptera, Hemiptera 
+  - Arthropoda - Arachnida, other Arthropoda
+
+We will be adding datasets for plants and other invertebrates in the next couple of months. Fungi, protists and nematodes are currently out-of-scope for EGAPx pending additional refinements.
+
+We currently have protein datasets posted for most vertebrates (mammals, sauropsids, ray-finned fishes) and arthropods. We will be adding datasets for more arthropods, vertebrates and plants in the next couple of months. Fungi, protists and nematodes are currently out-of-scope for EGAPx pending additional refinements.
 
 **Warning:**
 The current version is an alpha release with limited features and organism scope to collect initial feedback on execution. Outputs are not yet complete and not intended for production use. Please open a GitHub [Issue](https://github.com/ncbi/egapx/issues)  if you encounter any problems with EGAPx. You can also write to cgr@nlm.nih.gov to give us your feedback or if you have any questions.  
@@ -41,23 +48,46 @@ Notes:
 
 Input to EGAPx is in the form of a YAML file. 
 
-- The following two are the _required_ key-value pairs for the input file:
+- The following are the _required_ key-value pairs for the input file:
 
   ```
   genome: path to assembled genome in FASTA format
   taxid: NCBI Taxonomy identifier of the target organism 
+  reads: RNA-seq data
   ```
   You can obtain taxid from the [NCBI Taxonomy page](https://www.ncbi.nlm.nih.gov/taxonomy).
 
 
-- The following are the _optional_ key-value pairs for the input file:
+  - RNA-seq data can be supplied in any one of the following ways:
 
-  - RNA-seq data. Use one of the following options:
     ```
-    reads: [ array of paths to reads FASTA files]
-    reads_ids: [ array of SRA run ids ]
-    reads_query: query for reads SRA
+    reads: [ array of paths to reads FASTA or FASTQ files]
+    reads: [ array of SRA run IDs ]
+    reads: [SRA Study ID]
+    reads: SRA query for reads
+    ```
+  - If you are using your local reads, then the FASTA/FASTQ headers need to be in the following format:
     ```
+    head SRR8506572_1.fasta| grep ">"
+    >SRR8506572.1.1
+    >SRR8506572.2.1
+  
+    head SRR8506572_2.fasta| grep ">"
+    >SRR8506572.1.2
+    >SRR8506572.2.2
+  
+    head SRR8506572_2.fastq| grep "@"
+    @SRR8506572.1.2
+    @SRR8506572.2.2
+  
+    head SRR8506572_1.fastq| grep "@"
+    @SRR8506572.1.1
+    @SRR8506572.2.1
+    ```
+
+  - If you provide an SRA Study ID, all the SRA run ID's belonging to that Study ID will be included in the EGAPx run.    
+
+- The following are the _optional_ key-value pairs for the input file:  
 
   - A protein set. A taxid-based protein set will be chosen if no protein set is provided.
     ```
@@ -86,19 +116,19 @@ Input to EGAPx is in the form of a YAML file.
     - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/data/Dermatophagoides_farinae_small/SRR9005248.2
   ```
 
-- To specify an array of NCBI SRA datasets using `reads_ids:`
+- To specify an array of NCBI SRA datasets:
    ```
-   reads_ids:
+   reads:
      - SRR8506572
      - SRR9005248
    ```
 
-- To specify an SRA entrez query using `reads_query:`
+- To specify an SRA entrez query:
     ```
-    reads_query: 'txid6954[Organism] AND biomol_transcript[properties] NOT SRS024887[Accession] AND (SRR8506572[Accession] OR SRR9005248[Accession] )'
+    reads: 'txid6954[Organism] AND biomol_transcript[properties] NOT SRS024887[Accession] AND (SRR8506572[Accession] OR SRR9005248[Accession] )'
     ```
 
-  **Note:** Both the above examples `reads_ids` and `reads_query` will have more RNA-seq data than the `input_D_farinae_small.yaml` example. To make sure the `reads_query` does not produce a large number of SRA runs, please run it first at the [NCBI SRA page](https://www.ncbi.nlm.nih.gov/sra). If there are too many SRA runs, then select a few of them and use the `reads_ids` option.   
+  **Note:** Both the above examples will have more RNA-seq data than the `input_D_farinae_small.yaml` example. To make sure the entrez query does not produce a large number of SRA runs, please run it first at the [NCBI SRA page](https://www.ncbi.nlm.nih.gov/sra). If there are too many SRA runs, then select a few of them and list it in the input yaml.   
 
 - First, test EGAPx on the example provided (`input_D_farinae_small.yaml`, a dust mite) to make sure everything works. This example usually runs under 30 minutes depending upon resource availability. There are other examples you can try: `input_C_longicornis.yaml`, a green fly, and `input_Gavia_tellata.yaml`, a bird. These will take close to two hours.  You can prepare your input YAML file following these examples.  
 
@@ -144,40 +174,57 @@ Input to EGAPx is in the form of a YAML file.
     - use `-e aws` for AWS batch using Docker image
     - use `-e docker` for using Docker image
     - use `-e singularity` for using the Singularity image
-    - use `-e slurm` for using SLURM in your HPC.
+    - use `-e biowulf_cluster` for Biowulf cluster using Singularity image
+    - use '-e slurm` for using SLURM in your HPC.
         - Note that for this option, you have to edit `./egapx_config/slurm.config` according to your cluster specifications.
     - type `python3 ui/egapx.py  -h ` for the help menu 
 
       ```
-      $ ./egapx.py  -h
-
+      $ ui/egapx.py  -h
+      
+      
       !!WARNING!!
       This is an alpha release with limited features and organism scope to collect initial feedback on execution. Outputs are not yet complete and not intended for production use.
 
-      usage: egapx.py [-h] [-e EXECUTOR] [-c CONFIG_DIR] [-o OUTPUT] [-w WORKDIR] [-r REPORT] [-n] [-q] [-v] [-fn FUNC_NAME] filename
+      usage: egapx.py [-h] [-o OUTPUT] [-e EXECUTOR] [-c CONFIG_DIR] [-w WORKDIR] [-r REPORT] [-n] [-st]
+                [-so] [-dl] [-lc LOCAL_CACHE] [-q] [-v] [-fn FUNC_NAME]
+                [filename]
 
       Main script for EGAPx
 
-      positional arguments:
-        filename              YAML file with input: section with at least genome: and reads: parameters
-
       optional arguments:
         -h, --help            show this help message and exit
         -e EXECUTOR, --executor EXECUTOR
-                              Nextflow executor, one of local, docker, aws. Uses corresponding Nextflow config file
+                        Nextflow executor, one of docker, singularity, aws, or local (for NCBI
+                        internal use only). Uses corresponding Nextflow config file
         -c CONFIG_DIR, --config-dir CONFIG_DIR
-                              Directory for executor config files, default is ./egapx_config. Can be also set as env EGAPX_CONFIG_DIR
-        -o OUTPUT, --output OUTPUT
-                              Output path
+                        Directory for executor config files, default is ./egapx_config. Can be also
+                        set as env EGAPX_CONFIG_DIR
         -w WORKDIR, --workdir WORKDIR
-                              Working directory for cloud executor
+                        Working directory for cloud executor
         -r REPORT, --report REPORT
-                              Report file prefix for report (.report.html) and timeline (.timeline.html) files, default is in output directory
+                        Report file prefix for report (.report.html) and timeline (.timeline.html)
+                        files, default is in output directory
         -n, --dry-run
+        -st, --stub-run
+        -so, --summary-only   Print result statistics only if available, do not compute result
+        -lc LOCAL_CACHE, --local-cache LOCAL_CACHE
+                        Where to store the downloaded files
         -q, --quiet
         -v, --verbose
         -fn FUNC_NAME, --func_name FUNC_NAME
                         func_name
+
+      run:
+        filename              YAML file with input: section with at least genome: and reads: parameters
+        -o OUTPUT, --output OUTPUT
+                        Output path
+
+      download:
+        -dl, --download-only  Download external files to local storage, so that future runs can be
+                        isolated
+
+      
       ```
 
 
@@ -270,9 +317,60 @@ $ aws s3 ls s3://temp_datapath/D_farinae/96/621c4ba4e6e87a4d869c696fe50034/outpu
 2024-03-27 11:20:24   17127134 aligns.paf
 ```
 
+## Offline mode
+
+If you do not have internet access from your cluster, you can run EGAPx in offline mode. To do this, you would first pull the Singularity image, then download the necessary files from NCBI FTP using `egapx.py` script, and then finally use the path of the downloaded folder in the run command. Here is an example of how to download the files and execute EGAPx in the Biowulf cluster. 
+
+
+- Download the Singularity image:
+```
+rm egap*sif
+singularity cache clean
+singularity pull docker://ncbi/egapx:0.2-alpha
+```
+
+- Clone the repo:
+```
+git clone https://github.com/ncbi/egapx.git
+cd egapx
+```
+
+- Download EGAPx related files from NCBI:
+```
+python3 ui/egapx.py -dl -lc ../local_cache
+```
+
+- Download SRA reads:
+```
+prefetch SRR8506572
+prefetch SRR9005248
+fasterq-dump --skip-technical --threads 6 --split-files --seq-defline ">\$ac.\$si.\$ri" --fasta -O sradir/  ./SRR8506572
+fasterq-dump --skip-technical --threads 6 --split-files --seq-defline ">\$ac.\$si.\$ri" --fasta -O sradir/  ./SRR9005248
+
+```
+You should see downloaded files inside the 'sradir' folder":
+```
+ls  sradir/
+SRR8506572_1.fasta  SRR8506572_2.fasta  SRR9005248_1.fasta  SRR9005248_2.fasta
+```
+Now edit the file paths of SRA reads files in `examples/input_D_farinae_small.yaml` to include the above SRA files. 
+
+- Run `egapx.py` first to edit the `biowulf_cluster.config`:
+```
+ui/egapx.py examples/input_D_farinae_small.yaml -e biowulf_cluster -w dfs_work -o dfs_out -lc ../local_cache
+echo "process.container = '/path_to_/egapx_0.2-alpha.sif'" >> egapx_config/biowulf_cluster.config
+```
+
+- Run `egapx.py`:
+```
+ui/egapx.py examples/input_D_farinae_small.yaml -e biowulf_cluster -w dfs_work -o dfs_out -lc ../local_cache
+
+```
+
+
 ## References
 
-Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics. 2011 Jun 15;27(12):1691-2. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14. PMID: 21493652; PMCID: PMC3106182.
+Buchfink B, Reuter K, Drost HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021 Apr;18(4):366-368. doi: 10.1038/s41592-021-01101-x. Epub 2021 Apr 7. PMID: 33828273; PMCID: PMC8026399.
 
 Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. PMID: 33590861; PMCID: PMC7931819.
 
@@ -280,6 +378,8 @@ Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson
 
 Li H. Protein-to-genome alignment with miniprot. Bioinformatics. 2023 Jan 1;39(1):btad014. doi: 10.1093/bioinformatics/btad014. PMID: 36648328; PMCID: PMC9869432.
 
+Shen W, Le S, Li Y, Hu F. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One. 2016 Oct 5;11(10):e0163962. doi: 10.1371/journal.pone.0163962. PMID: 27706213; PMCID: PMC5051824.
+
 
 
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