Make it work without specifying GTF file

nf-core · Apr 30, 2024 · 619d921 · 619d921
1 parent 118d754
commit 619d921
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Showing 3 changed files with 6 additions and 16 deletions.
diff --git a/main.nf b/main.nf
@@ -20,16 +20,13 @@ nextflow.enable.dsl = 2
 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'
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_scrnaseq_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 // we cannot modify params. here, we must load the files
-ch_genome_fasta = params.genome ? file( getGenomeAttribute('fasta'), checkIfExists: true ) : []
-ch_gtf          = params.genome ? file( getGenomeAttribute('gtf'), checkIfExists: true   ) : []
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -44,8 +41,6 @@ workflow NFCORE_SCRNASEQ {
 
     take:
     samplesheet // channel: samplesheet read in from --input
-    ch_genome_fasta
-    ch_gtf
 
     main:
 
@@ -54,8 +49,6 @@ workflow NFCORE_SCRNASEQ {
     //
     SCRNASEQ (
         samplesheet,
-        ch_genome_fasta,
-        ch_gtf
     )
 
     emit:
@@ -90,8 +83,6 @@ workflow {
     //
     NFCORE_SCRNASEQ (
         PIPELINE_INITIALISATION.out.samplesheet,
-        ch_genome_fasta,
-        ch_gtf
     )
 
     //

diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf
@@ -111,7 +111,7 @@ workflow CELLRANGER_MULTI_ALIGN {
         //
         // Prepare GTF
         //
-        if (!cellranger_gex_index || !cellranger_vdj_index) {
+        if ( !cellranger_gex_index || (!cellranger_vdj_index && !params.skip_cellrangermulti_vdjref) ) {
 
             // Filter GTF based on gene biotypes passed in params.modules
             CELLRANGER_MKGTF ( ch_gtf )

diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -16,14 +16,14 @@ include { paramsSummaryMultiqc               } from '../subworkflows/nf-core/uti
 include { softwareVersionsToYAML             } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText             } from '../subworkflows/local/utils_nfcore_scrnaseq_pipeline'
 include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+include { getGenomeAttribute                 } from '../subworkflows/local/utils_nfcore_scrnaseq_pipeline'
+
 
 
 workflow SCRNASEQ {
 
     take:
     ch_fastq
-    ch_genome_fasta
-    ch_gtf
 
     main:
 
@@ -32,9 +32,8 @@ workflow SCRNASEQ {
         error "Only cellranger supports `protocol = 'auto'`. Please specify the protocol manually!"
     }
 
-    // overwrite fasta and gtf if user provide a custom one
-    ch_genome_fasta = Channel.value(params.fasta ? file(params.fasta) : ch_genome_fasta)
-    ch_gtf = Channel.value(params.gtf ? file(params.gtf) : ch_gtf)
+    ch_genome_fasta = params.fasta ? file(params.fasta, checkIfExists: true) : ( params.genome ? file( getGenomeAttribute('fasta'), checkIfExists: true ) : [] )
+    ch_gtf          = params.gtf ? file(params.gtf, checkIfExists: true) : ( params.genome ? file( getGenomeAttribute('gtf'), checkIfExists: true   ) : [] )
 
     // general input and params
     ch_transcript_fasta = params.transcript_fasta ? file(params.transcript_fasta): []
@@ -118,7 +117,7 @@ workflow SCRNASEQ {
     }
 
     // filter gtf
-    ch_filter_gtf = GTF_GENE_FILTER ( ch_genome_fasta, ch_gtf ).gtf
+    ch_filter_gtf = ch_gtf ? GTF_GENE_FILTER ( ch_genome_fasta, ch_gtf ).gtf : []
 
     // Run kallisto bustools pipeline
     if (params.aligner == "kallisto") {