From 533fa476e94943387c146605094d1acc5710d02a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 5 Oct 2018 23:38:32 +0200
Subject: [PATCH] SNP_calling.nf: add sample_name info for mapping_fastq
---
src/SNP_calling.nf | 18 +++++++++++++++++-
1 file changed, 17 insertions(+), 1 deletion(-)
diff --git a/src/SNP_calling.nf b/src/SNP_calling.nf
index 84027a8d..9fd40b14 100644
--- a/src/SNP_calling.nf
+++ b/src/SNP_calling.nf
@@ -107,13 +107,29 @@ fi
"""
}
+fastq_files_trim.into{
+ fastq_files_trim_norm;
+ fastq_files_trim_tumor
+}
+
+collect_fastq_files_trim_norm = fastq_files_trim_norm
+ .filter{ normal_sample.contains(it[0]) }
+ .map { it -> ["normal_sample", it[0], it[1]]}
+
+collect_fastq_files_trim_tumor = fastq_files_trim_tumor
+ .filter{ tumor_sample.contains(it[0]) }
+ .map { it -> ["tumor_sample", it[0], it[1]]}
+
+collect_fastq_files_trim = Channel.create()
+ .mix(collect_fastq_files_trim_norm, collect_fastq_files_trim_tumor)
+
process mapping_fastq {
tag "$pair_id"
cpus 12
publishDir "results/mapping/bam/", mode: 'copy'
input:
- set pair_id, file(reads) from fastq_files_trim
+ set sample_name, pair_id, file(reads) from collect_fastq_files_trim
file index from index_files.collect()
output:
--
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