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FriederikeHanssen 2021-02-23 14:58:09 +01:00
parent 13733b2581
commit e251a3bed5
1 changed files with 0 additions and 12 deletions
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software/seqkit/split2/main.nf
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@ -1,16 +1,6 @@
// Import generic module functions // Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions' include { initOptions; saveFiles; getSoftwareName } from './functions'
// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
// All other parameters MUST be provided as a string i.e. "options.args"
// where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
// Any parameters that need to be evaluated in the context of a particular sample
// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
// unless there is a run-time, storage advantage in implementing in this way
// e.g. bwa mem | samtools view -B -T ref.fasta to output BAM instead of SAM.
// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.
params.options = [:] params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
@ -40,8 +30,6 @@ process SEQKIT_SPLIT2 {
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
//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.
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if(meta.single_end){ if(meta.single_end){