g2gtools: caputre stdout sent to stderr...

src/nf_modules/g2gtools/main.nf

@@ -11,6 +11,7 @@ process vci_build {
     tuple val(ref_id), path(fasta)
   output:
     tuple val(file_id), path("*.vci.gz"), emit: vci
+    tuple val(file_id), path("*_report.txt"), emit: report
   script:
 """
 g2gtools vcf2vci \
@@ -18,7 +19,7 @@ g2gtools vcf2vci \
   -f ${fasta} \
   -i ${vcf} \
   -s ${file_id.library} \
-  -o ${file_id.id}.vci.gz > ${file_id.id}
+  -o ${file_id.id}.vci.gz 2> ${file_id.id}_g2gtools_vcf2vci_report.txt
 """
 }
 
@@ -32,13 +33,14 @@ process incorporate_snp {
     tuple val(ref_id), path(fasta)
   output:
     tuple val(file_id), path("${file_id.id}_snp.fasta"), path("${vci}"), emit: fasta
+    tuple val(file_id), path("*_report.txt"), emit: report
   script:
 """
 g2gtools patch \
   -p ${task.cpus} \
   -i ${fasta} \
   -c ${vci} \
-  -o ${file_id.id}_snp.fasta
+  -o ${file_id.id}_snp.fasta 2> ${file_id.id}_g2gtools_path_report.txt
 """
 }
 
@@ -51,13 +53,14 @@ process incorporate_indel {
     tuple val(file_id), path(fasta), path(vci)
   output:
     tuple val(file_id), path("${file_id.id}_snp_indel.fasta"), path("${vci}"), emit: fasta
+    tuple val(file_id), path("*_report.txt"), emit: report
   script:
 """
 g2gtools transform \
   -p ${task.cpus} \
   -i ${fasta} \
   -c ${vci} \
-  -o ${file_id.id}_snp_indel.fasta
+  -o ${file_id.id}_snp_indel.fasta 2> ${file_id.id}_g2gtools_transform_report.txt
 """
 }
 
@@ -71,12 +74,13 @@ process convert_gtf {
     tuple val(annot_id), path(gtf)
   output:
     tuple val(file_id), path("${file_id.id}.gtf"), emit: gtf
+    tuple val(file_id), path("*_report.txt"), emit: report
   script:
 """
 g2gtools convert \
   -i ${gtf} \
   -c ${vci} \
-  -o ${file_id.id}.gtf
+  -o ${file_id.id}.gtf 2> ${file_id.id}_g2gtools_convert_report.txt
 """
 }
 
@@ -90,12 +94,13 @@ process convert_bed {
     tuple val(annot_id), path(bed)
   output:
     tuple val(file_id), path("${file_id.id}.bed"), emit: bed
+    tuple val(file_id), path("*_report.txt"), emit: report
   script:
 """
 g2gtools convert \
   -i ${bed} \
   -c ${vci} \
-  -o ${file_id.id}.bed
+  -o ${file_id.id}.bed 2> ${file_id.id}_g2gtools_convert_report.txt
 """
 }
 
@@ -109,11 +114,12 @@ process convert_bam {
     tuple val(bam_id), path(bam)
   output:
     tuple val(file_id), path("${file_id.id}_${bam_id.baseName}.bam"), emit: bam
+    tuple val(file_id), path("*_report.txt"), emit: report
   script:
 """
 g2gtools convert \
   -i ${bam} \
   -c ${vci} \
-  -o ${file_id.id}_${bam.baseName}.bam
+  -o ${file_id.id}_${bam.baseName}.bam 2> ${file_id.id}_g2gtools_convert_report.txt
 """
 }
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