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Update main.nf
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// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
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// https://github.com/nf-core/modules/tree/master/modules
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// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
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// https://nf-co.re/join
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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 using the "task.ext" directive, see here:
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// https://www.nextflow.io/docs/latest/process.html#ext
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// where "task.ext" is a string.
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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. it's ok to have a single module for bwa to output BAM instead of SAM:
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// bwa mem | samtools view -B -T ref.fasta
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// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
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// list (`[]`) instealdd of a file can be used to work around this issue.
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process HMTNOTE {
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tag "$meta.id"
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label 'process_low'
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@ -76,7 +59,7 @@ process HMTNOTE {
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touch ${prefix}_annotated.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote //; s/Using.*\$//' ))
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hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
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END_VERSIONS
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"""
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}
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