From 7619538ae5c11ac55c560ed7130345316fe9d6cd Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 3 Oct 2018 18:34:54 +0200
Subject: [PATCH] SNP_calling.nf: fix collect problem
---
src/SNP_calling.nf | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/SNP_calling.nf b/src/SNP_calling.nf
index 56f0568..bcb8237 100644
--- a/src/SNP_calling.nf
+++ b/src/SNP_calling.nf
@@ -139,19 +139,18 @@ sambamba sort -t ${task.cpus} --tmpdir=./tmp -o ${file_id}_sorted.bam ${bam}
sorted_bam_files.into {
sorted_bam_file_norm;
- sorted_bam_file_tumor
+ sorted_bam_file_tumor;
}
collect_sorted_bam_file_norm = sorted_bam_file_norm
.filter{ normal_sample.contains(it[0]) }
.map { it -> it[1]}
- .collect()
+ .buffer( size: normal_sample.size())
.map { it -> ["normal_sample", it]}
-
collect_sorted_bam_file_tumor = sorted_bam_file_tumor
.filter{ tumor_sample.contains(it[0]) }
.map { it -> it[1]}
- .collect()
+ .buffer( size: tumor_sample.size())
.map { it -> ["tumor_sample", it]}
collect_sorted_bam_file = Channel.create()
@@ -246,7 +245,7 @@ samtools faidx ${fasta}
haplotypecaller_bam_files_norm = haplo_bam_files_norm
.filter{ "normal_sample" == it[0] }
haplotypecaller_bam_files_tumor = haplo_bam_files_tumor
- .filter{ "tumor_sample" == it[0] }
+ .filter{ "tumor_sample" == it[0] }
indexed_bam_files.into {
index_bam_files_norm;
@@ -257,6 +256,7 @@ indexed_bam_files_norm = index_bam_files_norm
indexed_bam_files_tumor = index_bam_files_tumor
.filter{ "tumor_sample" == it[0] }
+/*
process HaplotypeCaller {
tag "$file_id"
cpus 4
--
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