src/RibosomeProfiling.nf : don't save intermediaire fastq

src/RibosomeProfiling.nf

@@ -127,7 +127,7 @@ process fastqc_raw {
 
 process trimming {
   tag "$file_id"
-  publishDir "${params.output}/01_cutadapt/", mode: 'copy'
+  //publishDir "${params.output}/01_cutadapt/", mode: 'copy'
   echo true
 
   input:
@@ -179,7 +179,7 @@ process fastqc_cut {
 
 process rRNA_removal {
   tag "$file_id"
-  publishDir "${params.output}/02_rRNA_depletion/", mode: 'copy'
+  //publishDir "${params.output}/02_rRNA_depletion/", mode: 'copy'
 
   input:
   set file_id, file(reads) from CUTADAPT_OUTPUT_FILTER
@@ -660,7 +660,7 @@ process multiqc {
 
   input:
 //  file ('fastqc/*') from OUTPUT_FASTQC_RAW.collect().ifEmpty([])
-  file ('*') from CUTADAPT_LOG.collect().ifEmpty([])
+//  file ('*') from CUTADAPT_LOG.collect().ifEmpty([])
   file ('fastqc/*') from OUTPUT_FASTQC_CUT.collect().ifEmpty([])
   file ('*') from FILTER_LOG.collect().ifEmpty([])
 //  file ('fastqc/*') from OUTPUT_FASTQC_FILTER.collect().ifEmpty([])
@@ -669,7 +669,7 @@ process multiqc {
   file ('*') from HTSEQ_COUNT.collect().ifEmpty([])
   file ('*') from POSTGENOME_LOG.collect().ifEmpty([])
 //  file ('fastqc/*') from OUTPUT_FASTQC_POSTGENOME.collect().ifEmpty([])
-  file ('*') from RNASEQC_OUTPUT.collect().ifEmpty([])
+//  file ('*') from RNASEQC_OUTPUT.collect().ifEmpty([])
 
   output:
   file "multiqc_report.html" into multiqc_report