From 17d3a31fab2eadc82d40a51a6b599330e9ef6f13 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Mar 2021 16:56:21 +0100
Subject: [PATCH] g2gtools: simpler file_id structure

---
 src/nf_modules/g2gtools/main.nf | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/nf_modules/g2gtools/main.nf b/src/nf_modules/g2gtools/main.nf
index 6aef9c31..ae4b108e 100644
--- a/src/nf_modules/g2gtools/main.nf
+++ b/src/nf_modules/g2gtools/main.nf
@@ -18,8 +18,8 @@ g2gtools vcf2vci \
   -p ${task.cpus} \
   -f ${fasta} \
   -i ${vcf} \
-  -s ${file_id.library} \
-  -o ${file_id.id}.vci.gz 2> ${file_id.id}_g2gtools_vcf2vci_report.txt
+  -s ${file_id} \
+  -o ${file_id}.vci.gz 2> ${file_id}_g2gtools_vcf2vci_report.txt
 """
 }
 
@@ -32,7 +32,7 @@ process incorporate_snp {
     tuple val(file_id), path(vci)
     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("${file_id}_snp.fasta"), path("${vci}"), emit: fasta
     tuple val(file_id), path("*_report.txt"), emit: report
   script:
 """
@@ -40,7 +40,7 @@ g2gtools patch \
   -p ${task.cpus} \
   -i ${fasta} \
   -c ${vci} \
-  -o ${file_id.id}_snp.fasta 2> ${file_id.id}_g2gtools_path_report.txt
+  -o ${file_id}_snp.fasta 2> ${file_id}_g2gtools_path_report.txt
 """
 }
 
@@ -52,7 +52,7 @@ process incorporate_indel {
   input:
     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("${file_id}_snp_indel.fasta"), path("${vci}"), emit: fasta
     tuple val(file_id), path("*_report.txt"), emit: report
   script:
 """
@@ -60,7 +60,7 @@ g2gtools transform \
   -p ${task.cpus} \
   -i ${fasta} \
   -c ${vci} \
-  -o ${file_id.id}_snp_indel.fasta 2> ${file_id.id}_g2gtools_transform_report.txt
+  -o ${file_id}_snp_indel.fasta 2> ${file_id}_g2gtools_transform_report.txt
 """
 }
 
@@ -73,14 +73,14 @@ process convert_gtf {
     tuple val(file_id), path(vci)
     tuple val(annot_id), path(gtf)
   output:
-    tuple val(file_id), path("${file_id.id}.gtf"), emit: gtf
+    tuple val(file_id), path("${file_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 2> ${file_id.id}_g2gtools_convert_report.txt
+  -o ${file_id}.gtf 2> ${file_id}_g2gtools_convert_report.txt
 """
 }
 
@@ -93,14 +93,14 @@ process convert_bed {
     tuple val(file_id), path(vci)
     tuple val(annot_id), path(bed)
   output:
-    tuple val(file_id), path("${file_id.id}.bed"), emit: bed
+    tuple val(file_id), path("${file_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 2> ${file_id.id}_g2gtools_convert_report.txt
+  -o ${file_id}.bed 2> ${file_id}_g2gtools_convert_report.txt
 """
 }
 
@@ -113,13 +113,13 @@ process convert_bam {
     tuple val(file_id), path(vci)
     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("${file_id}_${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 2> ${file_id.id}_g2gtools_convert_report.txt
+  -o ${file_id}_${bam.baseName}.bam 2> ${file_id}_g2gtools_convert_report.txt
 """
 }
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-- 
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