From 7eb755bcca9be5ea15eb1ce8ec73bb220d2b0c42 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Thu, 2 Nov 2023 12:01:53 +0000
Subject: [PATCH] [skip ci] rewire for updated kallisto modules

---
 conf/modules.config                          | 13 ++++++++++---
 subworkflows/local/prepare_genome/main.nf    |  8 ++++----
 subworkflows/local/quantify_kallisto/main.nf |  8 ++++----
 3 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 52cd65bdf..bcbcbbb5e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -1132,9 +1132,16 @@ if (!params.skip_multiqc) {
 if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') {
     process {
         withName: '.*:QUANTIFY_KALLISTO:KALLISTO_QUANT' {
-            ext.fragment_len = { meta.fragment_len ?: params.kallisto_default_fraglen }
-            ext.sd = { meta.fragment_len ?: params.kallisto_default_fraglen_se }
-            ext.args   = params.extra_kallisto_quant_args ?: ''
+            ext.args = {
+                [
+                    meta.single_end ? 
+                        "--single " + 
+                        "--fragment-length ${meta.fragment_len ?: params.kallisto_default_fraglen} " + 
+                        "--sd ${meta.fraglen_se ?: params.kallisto_default_fraglen_se}" : '',
+                    params.extra_kallisto_quant_args ?: ''
+                ].findAll().join(' ').trim()
+            }           
+
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
                 mode: params.publish_dir_mode,
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index f249ac56c..ca598a199 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -267,14 +267,14 @@ workflow PREPARE_GENOME {
     ch_kallisto_index = Channel.empty()
     if (kallisto_index) {
         if (kallisto_index.endsWith('.tar.gz')) {
-            ch_kallisto_index = UNTAR_KALLISTO_INDEX ( [ [:], kallisto_index ] ).untar.map { it[1] }
+            ch_kallisto_index = UNTAR_KALLISTO_INDEX ( [ [:], kallisto_index ] ).untar
             ch_versions     = ch_versions.mix(UNTAR_KALLISTO_INDEX.out.versions)
         } else {
-            ch_kallisto_index = Channel.value(file(kallisto_index))
+            ch_kallisto_index = Channel.value([[:], file(kallisto_index)])
         }
     } else {
         if ('kallisto' in prepare_tool_indices) {
-            ch_kallisto_index = KALLISTO_INDEX ( ch_transcript_fasta.map{[ [:], it]} ).index.map { it[1] }
+            ch_kallisto_index = KALLISTO_INDEX ( ch_transcript_fasta.map{[ [:], it]} ).index
             ch_versions     = ch_versions.mix(KALLISTO_INDEX.out.versions)
         }
     }
@@ -292,7 +292,7 @@ workflow PREPARE_GENOME {
     rsem_index       = ch_rsem_index             // channel: path(rsem/index/)
     hisat2_index     = ch_hisat2_index           // channel: path(hisat2/index/)
     salmon_index     = ch_salmon_index           // channel: path(salmon/index/)
-    kallisto_index   = ch_kallisto_index         // channel: path(kallisto/index/)
+    kallisto_index   = ch_kallisto_index         // channel: [ meta, path(kallisto/index/) ]
 
     versions         = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/quantify_kallisto/main.nf b/subworkflows/local/quantify_kallisto/main.nf
index 93ef56f9d..843d769fc 100644
--- a/subworkflows/local/quantify_kallisto/main.nf
+++ b/subworkflows/local/quantify_kallisto/main.nf
@@ -14,7 +14,7 @@ include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT         } from '..
 workflow QUANTIFY_KALLISTO {
     take:
     reads            // channel: [ val(meta), [ reads ] ]
-    index            // channel: /path/to/kallisto/index/
+    index            // channel: [ val(meta2), /path/to/kallisto/index/ ]
     transcript_fasta // channel: /path/to/transcript.fasta
     gtf              // channel: /path/to/genome.gtf
     alignment_mode   //    bool: Run Salmon in alignment mode
@@ -31,10 +31,10 @@ workflow QUANTIFY_KALLISTO {
     KALLISTO_QUANT ( reads, index, gtf, [])
     ch_versions = ch_versions.mix(KALLISTO_QUANT.out.versions.first())
 
-    SALMON_TX2GENE ( KALLISTO_QUANT.out.abundance_hdf5.collect{it[1]}, gtf )
+    SALMON_TX2GENE ( KALLISTO_QUANT.out.results.collect{it[1]}, gtf )
     ch_versions = ch_versions.mix(SALMON_TX2GENE.out.versions)
 
-    SALMON_TXIMPORT ( KALLISTO_QUANT.out.abundance_hdf5.collect{it[1]}, SALMON_TX2GENE.out.tsv.collect() )
+    SALMON_TXIMPORT ( KALLISTO_QUANT.out.results.collect{it[1]}, SALMON_TX2GENE.out.tsv.collect() )
     ch_versions = ch_versions.mix(SALMON_TXIMPORT.out.versions)
 
     SALMON_SE_GENE (
@@ -63,7 +63,7 @@ workflow QUANTIFY_KALLISTO {
     )
 
     emit:
-    results                       = KALLISTO_QUANT.out.abundance_hdf5             // channel: [ val(meta), abundances ]
+    results                       = KALLISTO_QUANT.out.results                    // channel: [ val(meta), abundances ]
 
     tpm_gene                      = SALMON_TXIMPORT.out.tpm_gene                  // channel: [ val(meta), counts ]
     counts_gene                   = SALMON_TXIMPORT.out.counts_gene               // channel: [ val(meta), counts ]