From d8a29f6080eeb4fbc3eb19f6356b7ca1207fa73d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 3 Oct 2018 18:42:19 +0200
Subject: [PATCH] SNP_calling.nf: fix Mutect2 variables
---
src/SNP_calling.nf | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/src/SNP_calling.nf b/src/SNP_calling.nf
index bcb8237..e52db59 100644
--- a/src/SNP_calling.nf
+++ b/src/SNP_calling.nf
@@ -256,32 +256,32 @@ indexed_bam_files_norm = index_bam_files_norm
indexed_bam_files_tumor = index_bam_files_tumor
.filter{ "tumor_sample" == it[0] }
-/*
process HaplotypeCaller {
- tag "$file_id"
- cpus 4
+ tag "$file_id_norm"
+ cpus 10
publishDir "results/SNP/vcf/", mode: 'copy'
input:
- set file_id_norm, file(bam_norm) from haplotypecaller_bam_files_norm.collect()
- set file_ididx_norm, file(bamidx_norm) from indexed_bam_files_norm.collect()
- set file_id_tumor, file(bam_tumor) from haplotypecaller_bam_files_tumor.collect()
- set file_ididx_tumor, file(bamidx_tumor) from indexed_bam_files_tumor.collect()
- set genome_id, file(fasta) from haplo_fasta_file.collect()
- set genome2_idx, file(fasta2idx) from indexed2_fasta_file.collect()
- set genome3_idx, file(fasta3idx) from indexed3_fasta_file.collect()
+ set file_id_norm, file(bam_norm) from haplotypecaller_bam_files_norm
+ set file_ididx_norm, file(bamidx_norm) from indexed_bam_files_norm
+ set file_id_tumor, file(bam_tumor) from haplotypecaller_bam_files_tumor
+ set file_ididx_tumor, file(bamidx_tumor) from indexed_bam_files_tumor
+ set genome_id, file(fasta) from haplo_fasta_file
+ set genome2_idx, file(fasta2idx) from indexed2_fasta_file
+ set genome3_idx, file(fasta3idx) from indexed3_fasta_file
output:
- set file_id, "*.vcf" into vcf_files
- set file_id, "*.bam" into realigned_bams_files
+ set file_id_norm, "*.vcf" into vcf_files
+ set file_id_norm, "*.bam" into realigned_bams_files
+ set "*_mutect2_report.txt" into mutect2_report
script:
"""
gatk Mutect2 --native-pair-hmm-threads ${task.cpus} -R ${fasta} \
-I ${bam_tumor} -tumor ${file_id_tumor} \
-I ${bam_norm} -normal ${file_id_norm} \
--O ${file_id}_raw_calls.g.vcf \
--bamout ${file_id}_realigned.bam
+-O ${file_id_norm}_raw_calls.g.vcf \
+-bamout ${file_id_norm}_realigned.bam 2> ${file_id_norm}_mutect2_report.txt
"""
}
--
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