Merge branch 'dev' into anndata-concatenation

nf-core · Jan 15, 2025 · 3fb71b1 · 3fb71b1
2 parents a8e46f2 + 0e282f6
commit 3fb71b1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,9 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## dev
+## [Unreleased]
 
 - Add a checker so that `--fb_reference` does not break the pipeline in case `ab` files are not used in `cellranger multi` sub-workflow.
+- Update example usage command in README with valid reference genome parameter ([#339](https://github.com/nf-core/scrnaseq/issues/339))
 
 ## v3.0.0 - 2024-12-09
 

diff --git a/README.md b/README.md
@@ -62,7 +62,7 @@ Now, you can run the pipeline using:
 nextflow run nf-core/scrnaseq \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
-   --genome_fasta GRCm38.p6.genome.chr19.fa \
+   --fasta GRCm38.p6.genome.chr19.fa \
    --gtf gencode.vM19.annotation.chr19.gtf \
    --protocol 10XV2 \
    --aligner <alevin/kallisto/star/cellranger> \

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/tree/dev" target="_blank">nf-core/scrnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/scrnaseq/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/tree/dev" target="_blank">nf-core/scrnaseq</a>
+  analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/scrnaseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-scrnaseq-methods-description":
     order: -1000

diff --git a/main.nf b/main.nf
@@ -15,6 +15,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_scrnaseq_pipeline'
 include { SCRNASEQ                } from './workflows/scrnaseq'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_scrnaseq_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_scrnaseq_pipeline'
@@ -24,7 +25,16 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_scrn
     GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-// we cannot modify params. here, we must load the files
+
+// Params cannot be changed if they have been set beforehand
+// Thus, manually provided files are not overwritten by the genome attributes
+params.fasta            = getGenomeAttribute('fasta')
+params.gtf              = getGenomeAttribute('gtf')
+params.salmon_index     = getGenomeAttribute('simpleaf')
+params.txp2gene         = getGenomeAttribute('simpleaf_tx2pgene')
+params.cellranger_index = params.aligner == 'cellrangerarc' ?
+                            getGenomeAttribute('cellrangerarc') :
+                            getGenomeAttribute('cellranger')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/nextflow.config b/nextflow.config
@@ -287,7 +287,7 @@ manifest {
     description     = """Pipeline for processing 10x Genomics single cell rnaseq data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = 'dev'
+    version         = '3.1.0dev'
     doi             = '10.5281/zenodo.3568187'
 }
 

diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -23,44 +23,29 @@ include { GUNZIP as GUNZIP_FASTA                            } from '../modules/n
 include { GUNZIP as GUNZIP_GTF                              } from '../modules/nf-core/gunzip/main'
 include { H5AD_CONVERSION                                   } from '../subworkflows/local/h5ad_conversion'
 
+
 workflow SCRNASEQ {
 
     take:
     ch_fastq
 
     main:
+    ch_multiqc_files = Channel.empty()
+    ch_versions      = Channel.empty()
+    ch_mtx_matrices  = Channel.empty()
 
     protocol_config = Utils.getProtocol(workflow, log, params.aligner, params.protocol)
     if (protocol_config['protocol'] == 'auto' && params.aligner !in ["cellranger", "cellrangerarc", "cellrangermulti"]) {
         error "Only cellranger supports `protocol = 'auto'`. Please specify the protocol manually!"
     }
 
-    // collect paths from genome attributes file (e.g. iGenomes.config; optional)
-    // we cannot overwrite params in the workflow (they stay null as coming from the config file)
-    def genome_fasta = params.fasta        ?: getGenomeAttribute('fasta')
-    def gtf          = params.gtf          ?: getGenomeAttribute('gtf')
-    def star_index   = params.star_index   // ?: getGenomeAttribute('star') TODO: Currently not fetching iGenomes star index due version incompatibility
-    def salmon_index = params.salmon_index ?: getGenomeAttribute('simpleaf')
-    def txp2gene     = params.txp2gene     ?: getGenomeAttribute('simpleaf_tx2pgene')
-
-    // Make cellranger or cellranger-arc index conditional
-    def cellranger_index = []
-    if (params.aligner in ["cellranger", "cellrangermulti"]){
-        cellranger_index = params.cellranger_index ?: getGenomeAttribute('cellranger')
-    }
-    else if (params.aligner == "cellrangerarc") {
-        cellranger_index = params.cellranger_index ?: getGenomeAttribute('cellrangerarc')
-    }
-
-    ch_genome_fasta = genome_fasta ? file(genome_fasta, checkIfExists: true) : []
-    ch_gtf = gtf ? file(gtf, checkIfExists: true) : []
-
     // general input and params
-    ch_transcript_fasta = params.transcript_fasta ? file(params.transcript_fasta): []
-    ch_motifs = params.motifs ? file(params.motifs) : []
-    ch_cellrangerarc_config = params.cellrangerarc_config ? file(params.cellrangerarc_config) : []
-    ch_txp2gene = txp2gene ? file(txp2gene, checkIfExists: true) : []
-    ch_multiqc_files = Channel.empty()
+    ch_genome_fasta         = params.fasta                ? file(params.fasta, checkIfExists: true)    : []
+    ch_gtf                  = params.gtf                  ? file(params.gtf, checkIfExists: true)      : []
+    ch_transcript_fasta     = params.transcript_fasta     ? file(params.transcript_fasta)              : []
+    ch_motifs               = params.motifs               ? file(params.motifs)                        : []
+    ch_txp2gene             = params.txp2gene             ? file(params.txp2gene, checkIfExists: true) : []
+
     if (params.barcode_whitelist) {
         ch_barcode_whitelist = file(params.barcode_whitelist, checkIfExists: true)
     } else if (protocol_config.containsKey("whitelist")) {
@@ -75,28 +60,26 @@ workflow SCRNASEQ {
 
     //kallisto params
     ch_kallisto_index = params.kallisto_index ? file(params.kallisto_index, checkIfExists: true) : []
-    kb_workflow = params.kb_workflow
-    kb_t1c = params.kb_t1c ? file(params.kb_t1c, checkIfExists: true) : []
-    kb_t2c = params.kb_t2c ? file(params.kb_t2c, checkIfExists: true) : []
+    kb_t1c            = params.kb_t1c         ? file(params.kb_t1c, checkIfExists: true) : []
+    kb_t2c            = params.kb_t2c         ? file(params.kb_t2c, checkIfExists: true) : []
 
     //salmon params
-    ch_salmon_index = salmon_index ? file(salmon_index, checkIfExists: true) : []
+    ch_salmon_index   = params.salmon_index ? file(params.salmon_index, checkIfExists: true) : []
 
     //star params
-    star_index = star_index ? file(star_index, checkIfExists: true) : null
-    ch_star_index = star_index ? Channel.value( [[id: star_index.baseName], star_index] ) : []
-    star_feature = params.star_feature
+    star_index        = params.star_index ? file(params.star_index, checkIfExists: true) : null
+    ch_star_index     = star_index ? Channel.value( [[id: star_index.baseName], star_index] ) : []
 
     //cellranger params
-    ch_cellranger_index = cellranger_index ? file(cellranger_index, checkIfExists: true) : []
+    ch_cellranger_index = params.cellranger_index ? file(params.cellranger_index, checkIfExists: true) : []
 
     //cellrangermulti params
-    cellranger_vdj_index              = params.cellranger_vdj_index      ? file(params.cellranger_vdj_index, checkIfExists: true)      : []
-    ch_multi_samplesheet              = params.cellranger_multi_barcodes ? file(params.cellranger_multi_barcodes, checkIfExists: true) : []
-    empty_file                        = file("$projectDir/assets/EMPTY", checkIfExists: true)
+    cellranger_vdj_index = params.cellranger_vdj_index      ? file(params.cellranger_vdj_index, checkIfExists: true)      : []
+    ch_multi_samplesheet = params.cellranger_multi_barcodes ? file(params.cellranger_multi_barcodes, checkIfExists: true) : []
+    empty_file           = file("$projectDir/assets/EMPTY", checkIfExists: true)
 
-    ch_versions      = Channel.empty()
-    ch_mtx_matrices = Channel.empty()
+    // cellrangerarc params
+    ch_cellrangerarc_config = params.cellrangerarc_config ? file(params.cellrangerarc_config)          : []
 
     // Run FastQC
     if (!params.skip_fastqc) {
@@ -108,8 +91,8 @@ workflow SCRNASEQ {
     //
     // Uncompress genome fasta file if required
     //
-    if (genome_fasta) {
-        if (genome_fasta.endsWith('.gz')) {
+    if (params.fasta) {
+        if (params.fasta.endsWith('.gz')) {
             ch_genome_fasta    = GUNZIP_FASTA ( [ [:], ch_genome_fasta ] ).gunzip.map { it[1] }
             ch_versions        = ch_versions.mix(GUNZIP_FASTA.out.versions)
         } else {
@@ -120,8 +103,8 @@ workflow SCRNASEQ {
     //
     // Uncompress GTF annotation file or create from GFF3 if required
     //
-    if (gtf) {
-        if (gtf.endsWith('.gz')) {
+    if (params.gtf) {
+        if (params.gtf.endsWith('.gz')) {
             ch_gtf      = GUNZIP_GTF ( [ [:], ch_gtf ] ).gunzip.map { it[1] }
             ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions)
         } else {
@@ -142,7 +125,7 @@ workflow SCRNASEQ {
             kb_t1c,
             kb_t2c,
             protocol_config['protocol'],
-            kb_workflow,
+            params.kb_workflow,
             ch_fastq
         )
         ch_versions = ch_versions.mix(KALLISTO_BUSTOOLS.out.ch_versions)
@@ -176,7 +159,7 @@ workflow SCRNASEQ {
             protocol_config['protocol'],
             ch_barcode_whitelist,
             ch_fastq,
-            star_feature,
+            params.star_feature,
             protocol_config.get('extra_args', ""),
         )
         ch_versions = ch_versions.mix(STARSOLO.out.ch_versions)