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Code Issues Releases Packages Activity

Link rather than mv

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This commit is contained in:
James Fellows Yates 2023-01-24 15:32:49 +01:00
parent bdbb111344
commit 7843665544
2 changed files with 5 additions and 4 deletions
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4
modules/nf-core/porechop/porechop/main.nf generated
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@ -23,10 +23,10 @@ process PORECHOP_PORECHOP {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
## To ensure ID matches rest of pipeline based on meta.id rather than input file name ## To ensure ID matches rest of pipeline based on meta.id rather than input file name
mv $reads ${prefix}.fastq.gz ln -s $reads ${prefix}.fastq.gz
porechop \\ porechop \\
-i $reads \\ -i ${prefix}.fastq.gz \\
-t $task.cpus \\ -t $task.cpus \\
$args \\ $args \\
-o ${prefix}_porechopped.fastq.gz \\ -o ${prefix}_porechopped.fastq.gz \\

5
modules/nf-core/porechop/porechop/porechop-porechop.diff generated
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@ -6,10 +6,11 @@ Changes in module 'nf-core/porechop/porechop'
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
+ ## To ensure ID matches rest of pipeline based on meta.id rather than input file name + ## To ensure ID matches rest of pipeline based on meta.id rather than input file name
+ mv $reads ${prefix}.fastq.gz + ln -s $reads ${prefix}.fastq.gz
+ +
porechop \\ porechop \\
-i $reads \\ - -i $reads \\
+ -i ${prefix}.fastq.gz \\
-t $task.cpus \\ -t $task.cpus \\
$args \\ $args \\
- -o ${prefix}.fastq.gz \\ - -o ${prefix}.fastq.gz \\