From 40a1988572c317af63e8a5ad7f2116410993978f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 5 Oct 2018 17:32:30 +0200
Subject: [PATCH] SNP_calling.nf: working pipeline with BWA MEM
---
src/SNP_calling.nf | 23 ++++++++++++++++++-----
1 file changed, 18 insertions(+), 5 deletions(-)
diff --git a/src/SNP_calling.nf b/src/SNP_calling.nf
index eead408..2c44436 100644
--- a/src/SNP_calling.nf
+++ b/src/SNP_calling.nf
@@ -183,6 +183,7 @@ collect_sorted_bam_file = Channel.create()
process merge_bam {
tag "$file_id"
cpus 4
+ publishDir "results/mapping/bam/", mode: 'copy'
input:
set file_id, file(bam) from collect_sorted_bam_file
@@ -297,16 +298,19 @@ final_indexed_bam_files_tumor.into{
pileup_index_bam_files_tumor
}
final_fasta_file.into{
- haplo_fasta_file
- artifact_fasta_file
+ haplo_fasta_file;
+ artifact_fasta_file;
+ filter_fasta_file
}
indexed2_fasta_file.into{
- haplo_indexed2_fasta_file
- artifact_indexed2_fasta_file
+ haplo_indexed2_fasta_file;
+ artifact_indexed2_fasta_file;
+ filter_indexed2_fasta_file
}
indexed3_fasta_file.into{
haplo_indexed3_fasta_file;
- artifact_indexed3_fasta_file
+ artifact_indexed3_fasta_file;
+ filter_indexed3_fasta_file
}
process HaplotypeCaller {
@@ -428,6 +432,9 @@ process filter_SNP {
input:
set file_id_norm, file(vcf) from filter_vcf_files
set fileidx_id_norm, file(vcfid) from filter_index_vcf_files
+ set genome_id, file(fasta) from filter_fasta_file
+ set genome2_idx, file(fasta2idx) from filter_indexed2_fasta_file
+ set genome3_idx, file(fasta3idx) from filter_indexed3_fasta_file
output:
set file_id_norm, "*.vcf" into vcf_files_filtered
@@ -439,6 +446,12 @@ gatk FilterMutectCalls \
-V ${vcf} \
-O ${file_id_norm}_filtered.vcf \
2> ${file_id_norm}_filter_report.txt
+gatk SelectVariants \
+-R ${fasta} \
+--variant ${file_id_norm}_filtered.vcf \
+--exclude-filtered \
+-O ${file_id_norm}_filtered_pass.vcf \
+2>> ${file_id_norm}_filter_report.txt
"""
}
--
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