change prefix for decontaminated reads

EBI-Metagenomics · May 20, 2024 · e0db239 · e0db239
1 parent ba1d0e7
commit e0db239
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 27 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -85,6 +85,7 @@ process {
         cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
         memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        ext.prefix = "decontaminated"
     }
 
     withName: 'SPADES' {

diff --git a/modules/ebi-metagenomics/samtools/bam2fq/main.nf b/modules/ebi-metagenomics/samtools/bam2fq/main.nf
@@ -21,7 +21,7 @@ process SAMTOOLS_BAM2FQ {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ? "decontaminated_${meta.id}": "${meta.id}"
 
     if (split) {
         """

diff --git a/modules/local/compress_pigz.nf b/modules/local/compress_pigz.nf
diff --git a/workflows/miassembler.nf b/workflows/miassembler.nf
@@ -119,6 +119,10 @@ workflow MIASSEMBLER {
         isMetatranscriptomic
     )
 
+    FASTQC_AFTER (
+        READS_QC.out.qc_reads
+    )
+
     /*
     Single end reads // paired end reads distinction
         We need to split single-end and paired-end reads.
@@ -134,10 +138,6 @@ workflow MIASSEMBLER {
     print(qc_reads)
     ch_versions = ch_versions.mix(READS_QC.out.versions)
 
-    FASTQC_AFTER (
-        READS_QC.out.qc_reads
-    )
-
     /* Assembly */
     /* -- Clarification --
         At the moment, the pipeline only processes one set of reads at a time.