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Remove todos
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@ -1,16 +1,6 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
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// All other parameters MUST be provided as a string i.e. "options.args"
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// where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
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// Any parameters that need to be evaluated in the context of a particular sample
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// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
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// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
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// unless there is a run-time, storage advantage in implementing in this way
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// e.g. bwa mem | samtools view -B -T ref.fasta to output BAM instead of SAM.
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// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.
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params.options = [:]
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def options = initOptions(params.options)
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@ -40,8 +30,6 @@ process SEQKIT_SPLIT2 {
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script:
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def software = getSoftwareName(task.process)
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//TODO not sure if this is useful here, as the splits need to be named individually, and this would make the prefix the same and the outputname I am afraid.
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if(meta.single_end){
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