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Patch fastp until I have an OK on the module update

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James Fellows Yates 2022-09-08 14:25:23 +02:00
parent cc5df924e4
commit 60224e9149
3 changed files with 39 additions and 4 deletions
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3
modules.json
View file

@ -43,7 +43,8 @@
}, },
"fastp": { "fastp": {
"branch": "master", "branch": "master",
"git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f" "git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f",
"patch": "modules/nf-core/modules/fastp/fastp.diff"
}, },
"fastqc": { "fastqc": {
"branch": "master", "branch": "master",

33
modules/nf-core/modules/fastp/fastp.diff generated Normal file
View file

@ -0,0 +1,33 @@
Changes in module 'nf-core/modules/fastp'
--- modules/nf-core/modules/fastp/main.nf
+++ modules/nf-core/modules/fastp/main.nf
@@ -33,9 +33,8 @@
def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
"""
[ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
- cat ${prefix}.fastq.gz \\
- | fastp \\
- --stdin \\
+
+ fastp \\
--stdout \\
--in1 ${prefix}.fastq.gz \\
--thread $task.cpus \\
@@ -45,6 +44,7 @@
$args \\
2> ${prefix}.fastp.log \\
| gzip -c > ${prefix}.fastp.fastq.gz
+
cat <<-END_VERSIONS > versions.yml
"${task.process}":
fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
@@ -69,6 +69,7 @@
--detect_adapter_for_pe \\
$args \\
2> ${prefix}.fastp.log
+
cat <<-END_VERSIONS > versions.yml
"${task.process}":
************************************************************

7
modules/nf-core/modules/fastp/main.nf generated
View file

@ -33,9 +33,8 @@ process FASTP {
def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : '' def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
""" """
[ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz [ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
cat ${prefix}.fastq.gz \\
| fastp \\ fastp \\
--stdin \\
--stdout \\ --stdout \\
--in1 ${prefix}.fastq.gz \\ --in1 ${prefix}.fastq.gz \\
--thread $task.cpus \\ --thread $task.cpus \\
@ -45,6 +44,7 @@ process FASTP {
$args \\ $args \\
2> ${prefix}.fastp.log \\ 2> ${prefix}.fastp.log \\
| gzip -c > ${prefix}.fastp.fastq.gz | gzip -c > ${prefix}.fastp.fastq.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g") fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
@ -70,6 +70,7 @@ process FASTP {
$args \\ $args \\
2> ${prefix}.fastp.log 2> ${prefix}.fastp.log
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g") fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")