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Triple patch combo!

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This commit is contained in:
James Fellows Yates 2023-01-25 15:02:02 +01:00
parent f63cec3473
commit a77a437313
2 changed files with 5 additions and 3 deletions
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3
modules/nf-core/porechop/porechop/main.nf generated
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@ -23,7 +23,8 @@ 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
ln -s $reads ${prefix}.fastq.gz
[[ -f ${prefix}.fastq.gz ]] || ln -s $reads ${prefix}.fastq.gz
porechop \\ porechop \\
-i ${prefix}.fastq.gz \\ -i ${prefix}.fastq.gz \\

5
modules/nf-core/porechop/porechop/porechop-porechop.diff generated
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@ -10,12 +10,13 @@ Changes in module 'nf-core/porechop/porechop'
tuple val(meta), path("*.log") , emit: log tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
@@ -22,12 +22,16 @@ @@ -22,12 +22,17 @@
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
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
+ ln -s $reads ${prefix}.fastq.gz +
+ [[ -f ${prefix}.fastq.gz ]] || ln -s $reads ${prefix}.fastq.gz
+ +
porechop \\ porechop \\
- -i $reads \\ - -i $reads \\