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Include falco patch

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James Fellows Yates 2022-12-15 13:27:41 +01:00
parent 9e6a91aff9
commit 0bdc119f9c
2 changed files with 18 additions and 1 deletions
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3
modules.json
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@ -73,7 +73,8 @@
"falco": {
"branch": "master",
"git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
"installed_by": ["modules"]
"installed_by": ["modules"],
"patch": "modules/nf-core/falco/falco.diff"
},
"fastp": {
"branch": "master",

16
modules/nf-core/falco/falco.diff generated Normal file
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@ -0,0 +1,16 @@
Changes in module 'nf-core/falco'
--- modules/nf-core/falco/main.nf
+++ modules/nf-core/falco/main.nf
@@ -33,7 +33,9 @@
"""
} else {
"""
- falco $args --threads $task.cpus ${reads}
+ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+ [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+ falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
************************************************************