From ea9751264a74d8aa96e86b19a097c4968c12e6d9 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 6 May 2022 18:06:53 +0200
Subject: [PATCH] update split_fastq
---
subworkflows/local/input_check.nf | 14 +++++++++-----
1 file changed, 9 insertions(+), 5 deletions(-)
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index d5cf6b2..004062c 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -17,11 +17,15 @@ workflow INPUT_CHECK {
.splitCsv ( header:true, sep:',' )
.map { create_fastq_channels(it) }
.splitFastq( by: params.fastq_chunks_size, pe:true, file: true, compress:true)
- .map { it ->
- def meta = it[0].clone()
- meta.chunk = it[1].baseName - ~/.fastq(.gz)?/
- return [meta, [it[1], it[2]]]
- }
+ .map { it -> [it[0], [it[1], it[2]]]}
+ .groupTuple(by: [0])
+ .flatMap { it -> setMetaChunk(it) }
+ .collate(2)
+ //.map { it ->
+ // def meta = it[0].clone()
+ // meta.chunk = it[1].baseName - ~/.fastq(.gz)?/
+ // return [meta, [it[1], it[2]]]
+ //}
.set { reads }
}else{
--
GitLab