Merge pull request #1144 from nf-core/interface_to_kmer

Interface to kmer size for pseudoaligners

Author: pinin4fjords

CHANGELOG.md

@@ -17,10 +17,22 @@ Special thanks to the following for their contributions to the release:
 - [Phil Ewels](https://github.com/ewels)
 - [Vlad Savelyev](https://github.com/vladsavelyev)
 
+### Parameters
+
+| Old parameter | New parameter                |
+| ------------- | ---------------------------- |
+|               | `--pseudo_aligner_kmer_size` |
+
+> **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.
+> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
 ### Enhancements & fixes
 
 - [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling
+- [PR #1141](https://github.com/nf-core/rnaseq/pull/1141) - Important! Template update for nf-core/tools v2.11
 - [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Fix and patch version commands for Fastp, FastQC and UMI-tools modules ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
+- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners
 
 ## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21
 

conf/modules.config

@@ -75,7 +75,10 @@ process {
     }
 
     withName: 'SALMON_INDEX' {
-        ext.args   = params.gencode ? '--gencode' : ''
+        ext.args   = { [
+                params.gencode ? '--gencode' : '',
+                params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}": ''
+        ].join(' ').trim() }
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
@@ -84,7 +87,7 @@ process {
     }
 
     withName: 'KALLISTO_INDEX' {
-        ext.args   = { params.gencode ? '--gencode' : '' }
+        ext.args   = params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}" : ''
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,

nextflow.config

@@ -59,6 +59,7 @@ params {
     // Alignment
     aligner                    = 'star_salmon'
     pseudo_aligner             = null
+    pseudo_aligner_kmer_size   = 31
     seq_center                 = null
     bam_csi_index              = false
     star_ignore_sjdbgtf        = false

nextflow_schema.json

@@ -361,6 +361,13 @@
                     "fa_icon": "fas fa-hamburger",
                     "enum": ["salmon", "kallisto"]
                 },
+                "pseudo_aligner_kmer_size": {
+                    "type": "integer",
+                    "default": 31,
+                    "description": "Kmer length passed to indexing step of pseudoaligners",
+                    "help_text": "Failure to set a good kmer size could cause issues with quantification with Kallisto or Salmon. This is mostly an issue for short reads (<50bp), where the default kmer size of 31 is an problem.",
+                    "fa_icon": "fas fa-ruler-horizontal"
+                },
                 "bam_csi_index": {
                     "type": "boolean",
                     "description": "Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.",
@@ -397,7 +404,7 @@
                 },
                 "min_mapped_reads": {
                     "type": "number",
-                    "default": 5.0,
+                    "default": 5,
                     "fa_icon": "fas fa-percentage",
                     "description": "Minimum percentage of uniquely mapped reads below which samples are removed from further processing.",
                     "help_text": "Some downstream steps in the pipeline will fail if this threshold is too low."