Fix #907

Author: drpatelh

CHANGELOG.md

@@ -11,12 +11,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updated pipeline template to [nf-core/tools 2.7.1](https://github.com/nf-core/tools/releases/tag/2.7.1)
 - [[#896](https://github.com/nf-core/rnaseq/issues/896)] - Remove `copyTo` call for iGenomes README
 - [[#897](https://github.com/nf-core/rnaseq/issues/897)] - Use `--skip_preseq` by default
+- [[#907](https://github.com/nf-core/rnaseq/issues/907)] - Add `--extra_star_align_args` and `--extra_salmon_quant_args` parameter
 
 ### Parameters
 
-| Old parameter    | New parameter |
-| ---------------- | ------------- |
-| `--enable_conda` |               |
+| Old parameter    | New parameter               |
+| ---------------- | --------------------------- |
+| `--enable_conda` |                             |
+|                  | `--extra_star_align_args`   |
+|                  | `--extra_salmon_quant_args` |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.

conf/modules.config

@@ -517,7 +517,8 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 '--outSAMattributes NH HI AS NM MD',
                 '--quantTranscriptomeBan Singleend',
                 '--outSAMstrandField intronMotif',
-                params.save_unaligned ? '--outReadsUnmapped Fastx' : ''
+                params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
+                params.extra_star_align_args ?: ''
             ].join(' ').trim()
             publishDir = [
                 [
@@ -541,6 +542,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
         }
 
         withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
+            ext.args   = params.extra_salmon_quant_args ?: ''
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
                 mode: params.publish_dir_mode,
@@ -1045,6 +1047,7 @@ if (!params.skip_multiqc) {
 if (params.pseudo_aligner == 'salmon') {
     process {
         withName: '.*:QUANTIFY_SALMON:SALMON_QUANT' {
+            ext.args   = params.extra_salmon_quant_args ?: ''
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
                 mode: params.publish_dir_mode,

nextflow.config

@@ -68,6 +68,8 @@ params {
     hisat2_build_memory        = '200.GB'  // Amount of memory required to build HISAT2 index with splice sites
     stringtie_ignore_gtf       = false
     min_mapped_reads           = 5
+    extra_star_args            = null
+    extra_salmon_args          = null
     save_merged_fastq          = false
     save_unaligned             = false
     save_align_intermeds       = false

nextflow_schema.json

@@ -424,6 +424,16 @@
                     "description": "Perform reference-guided de novo assembly of transcripts using StringTie i.e. dont restrict to those in GTF file.",
                     "fa_icon": "fas fa-ban"
                 },
+                "extra_star_align_args": {
+                    "type": "string",
+                    "description": "Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline.",
+                    "fa_icon": "fas fa-plus"
+                },
+                "extra_salmon_quant_args": {
+                    "type": "string",
+                    "description": "Extra arguments to pass to Salmon quant command in addition to defaults defined by the pipeline.",
+                    "fa_icon": "fas fa-plus"
+                },
                 "save_unaligned": {
                     "type": "boolean",
                     "fa_icon": "fas fa-save",