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Link rather than mv
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parent
bdbb111344
commit
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2 changed files with 5 additions and 4 deletions
4
modules/nf-core/porechop/porechop/main.nf
generated
4
modules/nf-core/porechop/porechop/main.nf
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@ -23,10 +23,10 @@ process PORECHOP_PORECHOP {
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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## To ensure ID matches rest of pipeline based on meta.id rather than input file name
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mv $reads ${prefix}.fastq.gz
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ln -s $reads ${prefix}.fastq.gz
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porechop \\
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-i $reads \\
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-i ${prefix}.fastq.gz \\
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-t $task.cpus \\
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$args \\
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-o ${prefix}_porechopped.fastq.gz \\
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@ -6,10 +6,11 @@ Changes in module 'nf-core/porechop/porechop'
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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+ ## To ensure ID matches rest of pipeline based on meta.id rather than input file name
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+ mv $reads ${prefix}.fastq.gz
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+ ln -s $reads ${prefix}.fastq.gz
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+
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porechop \\
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-i $reads \\
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- -i $reads \\
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+ -i ${prefix}.fastq.gz \\
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-t $task.cpus \\
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$args \\
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- -o ${prefix}.fastq.gz \\
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