added parameter to output 10x counts

nf-core · Oct 12, 2022 · 080c258 · 080c258
1 parent 7f7d69e
commit 080c258
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Showing 5 changed files with 23 additions and 12 deletions.
diff --git a/docs/usage.md b/docs/usage.md
@@ -1,4 +1,4 @@
-# nf-core/scrnaseq: Usage
+3# nf-core/scrnaseq: Usage
 
 > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
 

diff --git a/nextflow.config b/nextflow.config
@@ -12,6 +12,7 @@ params {
     // generic options
     aligner           = 'alevin'
     bustools_correct  = true
+    output_10x        = false
     outdir            = null
     input             = null
     save_reference    = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -37,6 +37,10 @@
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
+                },
+                "output_10x": {
+                    "type": "boolean",
+                    "description": "Generate 10x counts"
                 }
             }
         },

diff --git a/subworkflows/local/mtx_conversion.nf b/subworkflows/local/mtx_conversion.nf
@@ -14,6 +14,7 @@ workflow MTX_CONVERSION {
     gtf
     txp2gene
     genome_fasta
+    output_10x
 
 
     main:
@@ -25,17 +26,19 @@ workflow MTX_CONVERSION {
             mtx_matrices
         )
 
-        // Generate the t2g file to enrich the 10x files with gene names
-        KALLISTOBUSTOOLS_REF( genome_fasta, gtf, 'standard' )
-        txp2gene = KALLISTOBUSTOOLS_REF.out.t2g.collect()
+        if (output_10x) {
+            // Generate the t2g file to enrich the 10x files with gene names
+            KALLISTOBUSTOOLS_REF( genome_fasta, gtf, 'standard' )
+            txp2gene = KALLISTOBUSTOOLS_REF.out.t2g.collect()
 
-        //
-        // Convert h5ad files to 10x counts format
-        //
-        H5AD_TO_10X (
-            MTX_TO_H5AD.out.h5ad, // gather all sample-specific files
-            txp2gene
-        )
+            //
+            // Convert h5ad files to 10x counts format
+            //
+            H5AD_TO_10X (
+                MTX_TO_H5AD.out.h5ad, // gather all sample-specific files
+                txp2gene
+            )
+        }
 
         //
         // Concat sample-specific h5ad in one

diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -71,12 +71,14 @@ ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
 
 // general input and params
 ch_input = file(params.input)
+ch_output_10x = params.output_10x
 ch_genome_fasta = params.fasta ? file(params.fasta) : []
 ch_gtf = params.gtf ? file(params.gtf) : []
 ch_transcript_fasta = params.transcript_fasta ? file(params.transcript_fasta): []
 ch_txp2gene = params.txp2gene ? file(params.txp2gene) : []
 ch_multiqc_alevin = Channel.empty()
 ch_multiqc_star = Channel.empty()
+
 if (params.barcode_whitelist) {
     ch_barcode_whitelist = file(params.barcode_whitelist)
 } else if (params.protocol.contains("10X")) {
@@ -188,7 +190,8 @@ workflow SCRNASEQ {
         ch_input,
         ch_gtf,
         ch_txp2gene,
-        ch_genome_fasta
+        ch_genome_fasta,
+        ch_output_10x,
 
     )