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Patch fastp until I have an OK on the module update
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parent
cc5df924e4
commit
60224e9149
3 changed files with 39 additions and 4 deletions
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@ -43,7 +43,8 @@
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},
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"fastp": {
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"branch": "master",
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"git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f"
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"git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f",
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"patch": "modules/nf-core/modules/fastp/fastp.diff"
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},
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"fastqc": {
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"branch": "master",
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33
modules/nf-core/modules/fastp/fastp.diff
generated
Normal file
33
modules/nf-core/modules/fastp/fastp.diff
generated
Normal file
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@ -0,0 +1,33 @@
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Changes in module 'nf-core/modules/fastp'
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--- modules/nf-core/modules/fastp/main.nf
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+++ modules/nf-core/modules/fastp/main.nf
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@@ -33,9 +33,8 @@
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def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
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"""
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[ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
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- cat ${prefix}.fastq.gz \\
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- | fastp \\
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- --stdin \\
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+
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+ fastp \\
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--stdout \\
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--in1 ${prefix}.fastq.gz \\
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--thread $task.cpus \\
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@@ -45,6 +44,7 @@
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$args \\
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2> ${prefix}.fastp.log \\
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| gzip -c > ${prefix}.fastp.fastq.gz
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+
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
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@@ -69,6 +69,7 @@
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--detect_adapter_for_pe \\
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$args \\
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2> ${prefix}.fastp.log
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+
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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************************************************************
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7
modules/nf-core/modules/fastp/main.nf
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7
modules/nf-core/modules/fastp/main.nf
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@ -33,9 +33,8 @@ process FASTP {
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def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
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"""
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[ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
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cat ${prefix}.fastq.gz \\
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| fastp \\
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--stdin \\
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fastp \\
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--stdout \\
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--in1 ${prefix}.fastq.gz \\
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--thread $task.cpus \\
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@ -45,6 +44,7 @@ process FASTP {
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$args \\
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2> ${prefix}.fastp.log \\
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| gzip -c > ${prefix}.fastp.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
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@ -69,6 +69,7 @@ process FASTP {
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--detect_adapter_for_pe \\
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$args \\
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2> ${prefix}.fastp.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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