From d7fb6ef992b2c4e6aabc2cdd2b15cfecd1bc55af Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 29 Sep 2021 10:27:48 +0200
Subject: [PATCH] rasusa: fix multiple bug
---
src/nf_modules/rasusa/main.nf | 6 +++---
src/nf_modules/rasusa/test.nf | 4 ++--
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/rasusa/main.nf b/src/nf_modules/rasusa/main.nf
index c530af43..e1aefc58 100644
--- a/src/nf_modules/rasusa/main.nf
+++ b/src/nf_modules/rasusa/main.nf
@@ -1,5 +1,5 @@
version = "0.6.0"
-container_url = "quay.io/mbhall88/rasusa:${version}"
+container_url = "lbmc/rasusa:${version}"
include { index_fasta } from "./../samtools/main.nf"
@@ -26,7 +26,7 @@ process sub_sample_fastq {
label "small_mem_multi_cpus"
tag "$file_id"
if (params.index_fasta_out != "") {
- publishDir "results/${params.sample_fastq}", mode: 'copy'
+ publishDir "results/${params.sample_fastq_out}", mode: 'copy'
}
input:
@@ -66,7 +66,7 @@ rasusa \
else
"""
rasusa \
- -i ${fastq} ${fastq} \
+ -i ${fastq} \
-g ${idx} \
${sample_option} \
-o sub_${fastq.simpleName}.fastq.gz
diff --git a/src/nf_modules/rasusa/test.nf b/src/nf_modules/rasusa/test.nf
index 0ee8e599..d505124f 100644
--- a/src/nf_modules/rasusa/test.nf
+++ b/src/nf_modules/rasusa/test.nf
@@ -5,13 +5,13 @@ nextflow.enable.dsl=2
./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq" --size "1Mb"
*/
-include { sample_fastq } from "./main.nf" addParams(sample_fastq_coverage: params.coverage, sample_fastq_size: "")
-
params.fastq = "data/fastq/*R{1,2}*"
params.fasta = "data/fasta/*.fasta"
params.coverage = "2.0"
params.size = ""
+include { sample_fastq } from "./main.nf" addParams(sample_fastq_coverage: params.coverage, sample_fastq_size: params.size, sample_fastq_out: "sample/")
+
channel
.fromFilePairs( params.fastq, size: -1)
.set { fastq_files }
--
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