From 3cf74222a252a16a385f23d970e67cb74a31dc16 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 30 Nov 2020 18:30:02 +0100
Subject: [PATCH] [MODIF] update test profile
---
main.nf | 17 ++++++++++++-----
1 file changed, 12 insertions(+), 5 deletions(-)
diff --git a/main.nf b/main.nf
index d5c43a2..ef10335 100644
--- a/main.nf
+++ b/main.nf
@@ -153,11 +153,18 @@ if (params.input_paths){
raw_reads = Channel.create()
raw_reads_2 = Channel.create()
- Channel
- .from( params.input_paths )
- .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
- .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1][0]), tuple(a[0], a[1][1])] }
-
+ if ( params.split_fastq ){
+ Channel
+ .from( params.input_paths )
+ .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
+ .splitFastq( by: params.fastq_chunks_size, pe:true, file: true, compress:true)
+ .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1]), tuple(a[0], a[1])] }
+ }else{
+ Channel
+ .from( params.input_paths )
+ .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
+ .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0] + "_R1", a[1][0]), tuple(a[0] + "_R2", a[1][1])] }
+ }
}else{
raw_reads = Channel.create()
raw_reads_2 = Channel.create()
--
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