split truncate concat into two processes/

naobservatory · Dec 11, 2024 · 7a3a59b · 7a3a59b
1 parent 4b966d8
commit 7a3a59b
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Showing 2 changed files with 30 additions and 22 deletions.
diff --git a/modules/local/truncateConcat/main.nf b/modules/local/truncateConcat/main.nf
@@ -1,34 +1,38 @@
 // Truncate concatenated read files for trial run
-process TRUNCATE_CONCAT {
+process TRUNCATE_CONCAT_PAIRED {
     label "single"
     label "BBTools"
     input:
         tuple val(sample), path(reads)
         val n_reads
-        val single_end
     output:
-
-        tuple val(sample), path({
-            single_end ?
-                    "${sample}_trunc.fastq.gz" :
-                    "${sample}_trunc_{1,2}.fastq.gz"
-            }), emit: reads
+        tuple val(sample), path("${sample}_trunc_{1,2}.fastq.gz"), emit: reads
     shell:
         '''
         echo "Number of output reads: !{n_reads}"
         n_lines=$(expr !{n_reads} \\* 4)
         echo "Number of output lines: ${n_lines}"
-        if [ $(echo "!{reads}" | wc -w) -eq 2 ]; then
-            echo "Processing paired-end reads"
-            o1=!{sample}_trunc_1.fastq.gz
-            o2=!{sample}_trunc_2.fastq.gz
-            zcat !{reads[0]} | head -n ${n_lines} | gzip -c > ${o1}
-            zcat !{reads[1]} | head -n ${n_lines} | gzip -c > ${o2}
-        else
-            echo "Processing single-end reads"
-            o=!{sample}_trunc.fastq.gz
-            zcat !{reads[0]} | head -n ${n_lines} | gzip -c > ${o}
-        fi
-
+        o1=!{sample}_trunc_1.fastq.gz
+        o2=!{sample}_trunc_2.fastq.gz
+        zcat !{reads[0]} | head -n ${n_lines} | gzip -c > ${o1}
+        zcat !{reads[1]} | head -n ${n_lines} | gzip -c > ${o2}
         '''
 }
+
+process TRUNCATE_CONCAT_SINGLE {
+    label "single"
+    label "BBTools"
+    input:
+        tuple val(sample), path(reads)
+        val n_reads
+    output:
+        tuple val(sample), path("${sample}_trunc.fastq.gz"), emit: reads
+    shell:
+        '''
+        echo "Number of output reads: !{n_reads}"
+        n_lines=$(expr !{n_reads} \\* 4)
+        echo "Number of output lines: ${n_lines}"
+        o=!{sample}_trunc.fastq.gz
+        zcat !{reads[0]} | head -n ${n_lines} | gzip -c > ${o}
+        '''
+}
diff --git a/subworkflows/local/raw/main.nf b/subworkflows/local/raw/main.nf
@@ -7,7 +7,11 @@
 ***************************/
 
 include { QC } from "../../../subworkflows/local/qc"
-include { TRUNCATE_CONCAT } from "../../../modules/local/truncateConcat"
+if (params.single_end) {
+    include { TRUNCATE_CONCAT_SINGLE as TRUNCATE_CONCAT } from "../../../modules/local/truncateConcat"
+} else {
+    include { TRUNCATE_CONCAT_PAIRED as TRUNCATE_CONCAT } from "../../../modules/local/truncateConcat"
+}
 
 /***********
 | WORKFLOW |
@@ -23,7 +27,7 @@ workflow RAW {
         single_end
     main:
         if ( n_reads_trunc > 0 ) {
-            out_ch = TRUNCATE_CONCAT(samplesheet_ch, n_reads_trunc, single_end)
+            out_ch = TRUNCATE_CONCAT(samplesheet_ch, n_reads_trunc)
         } else {
             out_ch = samplesheet_ch
         }