Sortmerna: index once

CHANGELOG.md

@@ -13,7 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#9](https://github.com/nf-core/riboseq/pull/9)] - Important! Template update for nf-core/tools v2.12 ([nf-core-bot](https://github.com/nf-core-bot), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#12](https://github.com/nf-core/riboseq/pull/12) - Add alignment via STAR + postprocessing (([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
 - [[#32](https://github.com/nf-core/riboseq/pull/32) - Nf core template merge 2.13 (manual) ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse), [@adamrtalbot](https://github.com/adamrtalbot))
-- [[#34](https://github.com/nf-core/riboseq/pull/34) - Fix order of preprocessing steps ([@pinin4fjords](https://github.com/pinin4fjords), review by )
+- [[#34](https://github.com/nf-core/riboseq/pull/34) - Fix order of preprocessing steps ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
+- [[#35](https://github.com/nf-core/riboseq/pull/35) - Sortmerna: index once ([@pinin4fjords](https://github.com/pinin4fjords), review by )
 
 Initial release of nf-core/riboseq, created with the [nf-core](https://nf-co.re/) template.
 

conf/modules.config

@@ -151,6 +151,19 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
     }
 }
 
+if (params.remove_ribo_rna && params.ribo_database_manifest) {
+    process {
+        withName: 'SORTMERNA_INDEX' {
+            ext.args   = '--index 1'
+            publishDir = [
+                path: { "${params.outdir}/genome/sortmerna" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            ]
+        }
+    }
+}
+
 //
 // Read subsampling and strand inferring options
 //
@@ -315,8 +328,8 @@ if (!params.skip_bbsplit) {
 
 if (params.remove_ribo_rna) {
     process {
-        withName: 'SORTMERNA' {
-            ext.args   = '--num_alignments 1 -v'
+        withName: '.*:PREPROCESS_RNASEQ:SORTMERNA' {
+            ext.args   = '--num_alignments 1 -v --index 0'
             publishDir = [
                 [
                     path: { "${params.outdir}/sortmerna" },

main.nf

@@ -42,6 +42,7 @@ params.star_index       = getGenomeAttribute('star')
 params.hisat2_index     = getGenomeAttribute('hisat2')
 params.rsem_index       = getGenomeAttribute('rsem')
 params.salmon_index     = getGenomeAttribute('salmon')
+params.sortmerna_index  = getGenomeAttribute('sortmerna')
 params.kallisto_index   = getGenomeAttribute('kallisto')
 
 /*
@@ -71,18 +72,21 @@ workflow NFCORE_RIBOSEQ {
         params.gene_bed,
         params.splicesites,
         params.bbsplit_fasta_list,
+        params.ribo_database_manifest,
         params.star_index,
         params.rsem_index,
         params.salmon_index,
         params.kallisto_index,
         params.hisat2_index,
         params.bbsplit_index,
+        params.sortmerna_index,
         params.gencode,
         params.featurecounts_group_type,
         params.aligner,
         params.pseudo_aligner,
         params.skip_gtf_filter,
         params.skip_bbsplit,
+        ! params.remove_ribo_rna,
         params.skip_alignment,
         params.skip_pseudo_alignment
     )
@@ -115,6 +119,7 @@ workflow NFCORE_RIBOSEQ {
         PREPARE_GENOME.out.salmon_index,
         PREPARE_GENOME.out.kallisto_index,
         PREPARE_GENOME.out.bbsplit_index,
+        PREPARE_GENOME.out.sortmerna_index,
         PREPARE_GENOME.out.splicesites
     )
     ch_versions = ch_versions.mix(RIBOSEQ.out.versions)

modules.json

@@ -117,7 +117,7 @@
                     },
                     "sortmerna": {
                         "branch": "master",
-                        "git_sha": "ad22467dff16284093e7335d5e77964e9bbc510b",
+                        "git_sha": "df05c8db5195867c0bc7b92c1788115b66f0d17d",
                         "installed_by": ["preprocess_rnaseq"]
                     },
                     "star/align": {
@@ -196,7 +196,7 @@
                     },
                     "preprocess_rnaseq": {
                         "branch": "master",
-                        "git_sha": "53a97948affb07725328a1bba2fec79b331374a6",
+                        "git_sha": "8aa7040ca55a511ee4bc079803a8446db00f34c8",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {