paired.nf files : pass the pair_id information in output

src/nf_modules/BEDtools/bedtools.nf

 /*
 * bedtools :
-* Imputs : fastq files
-* Output : fastq files
+* Imputs : fasta files
+* Imputs : bed files
+* Output : fasta files
 */
 /*                      fasta extraction                                     */
 

src/nf_modules/Bowtie2/bowtie2.nf

@@ -66,7 +66,7 @@ process mapping_fastq {
   file index from index_files.toList()
 
   output:
-  file "*.bam" into bam_files
+  set pair_id, "*.bam" into bam_files
 
   script:
 """

src/nf_modules/Bowtie2/tests/mapping_paired.nf

@@ -23,7 +23,7 @@ process mapping_fastq {
   file index from index_files.toList()
 
   output:
-  file "*.bam" into bam_files
+  set pair_id, "*.bam" into bam_files
 
   script:
 """
@@ -37,3 +37,4 @@ if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
 fi
 """
 }
+

src/nf_modules/Kallisto/kallisto.nf

@@ -58,7 +58,7 @@ process mapping_fastq {
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:
-  file reads from fastq_files
+  set pair_id, file(reads) from fastq_files
   file index from index_files.toList()
 
   output:
@@ -68,8 +68,8 @@ process mapping_fastq {
 """
 mkdir ${reads[0].baseName}
 kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${reads[0].baseName} \
-${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
+--bias --bootstrap-samples 100 -o ${pair_id} \
+${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
 """
 }
 

src/nf_modules/Kallisto/tests/mapping_paired.nf

@@ -14,7 +14,7 @@ Channel
   .set { index_files }
 
 process mapping_fastq {
-  tag "$pair_id"
+  tag "$reads"
   cpus 4
   publishDir "results/mapping/quantification/", mode: 'copy'
 
@@ -27,7 +27,7 @@ process mapping_fastq {
 
   script:
 """
-mkdir ${pair_id}
+mkdir ${reads[0].baseName}
 kallisto quant -i ${index} -t ${task.cpus} \
 --bias --bootstrap-samples 100 -o ${pair_id} \
 ${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt

src/nf_modules/UrQt/tests/trimming_paired.nf

@@ -6,14 +6,15 @@ Channel
   .set { fastq_files }
 
 process trimming {
-  tag "$pair_id"
+  tag "${reads}"
   cpus 4
+  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files
 
   output:
-  file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
+  set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
 
   script:
 """
@@ -23,3 +24,4 @@ UrQt --t 20 --m ${task.cpus} --gz \
 > ${pair_id}_trimming_report.txt
 """
 }
+

src/nf_modules/UrQt/urqt.nf

@@ -24,17 +24,17 @@ process trimming {
   publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
-  file reads from fastq_files
+  set pair_id, file(reads) from fastq_files
 
   output:
-  file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+  set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
 
   script:
 """
 UrQt --t 20 --m ${task.cpus} --gz \
 --in ${reads[0]} --inpair ${reads[1]} \
---out ${reads[0].baseName}_trim_R1.fastq.gz --outpair ${reads[1].baseName}_trim_R2.fastq.gz \
-> ${reads[0].baseName}_trimming_report.txt
+--out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
+> ${pair_id}_trimming_report.txt
 """
 }
 

src/nf_modules/cutadapt/cutadapt.nf

@@ -27,7 +27,7 @@ process adaptor_removal {
   set pair_id, file(reads) from fastq_files
 
   output:
-  file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+  set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
 
   script:
   """
@@ -91,7 +91,7 @@ process trimming {
   set pair_id, file(reads) from fastq_files
 
   output:
-  file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+  set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
 
   script:
   """

src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf

@@ -7,12 +7,13 @@ Channel
 
 process adaptor_removal {
   tag "$pair_id"
+  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files
 
   output:
-  file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+  set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
 
   script:
   """
@@ -21,4 +22,3 @@ process adaptor_removal {
   ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
   """
 }
-

src/nf_modules/cutadapt/tests/trimming_paired.nf

@@ -7,12 +7,13 @@ Channel
 
 process trimming {
   tag "$pair_id"
+  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files
 
   output:
-  file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
+  set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
 
   script:
   """
@@ -21,4 +22,3 @@ process trimming {
   ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
   """
 }
-