mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
7daba6a13f
* add unzip alleles + loci * fix the partial absolute prefix path * exchanged deprecated function + added metrics * updated meta * tested logRCorrection + cram input * added BED for WES * added outputs + alleleCounter version * test samtools chr operations, fixed cancerit conda * ch formatting, fasta, bed input * comment out local tests * added metrics, bed, ref_fasta * rm print statement * added stub outputs * rm versions.yml * fix linting * rm fictitious md5sums for stub-run * try fixing top-level of stub versions.yml * ordered inputs alphabetically, ref_fasta -> fasta * rm R system command, adjust meta.yml * prettier yml
40 lines
848 B
Text
40 lines
848 B
Text
process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: ASCAT_SIMPLE {
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ext.args = [
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gender : 'XY',
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genomeVersion : 'hg19',
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minCounts : '1',
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min_base_qual : '1',
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min_map_qual : '1',
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chrom_names : 'c("21","22")'
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]
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}
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withName: ASCAT_PLOIDY_AND_PURITY {
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ext.args = [
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gender : 'XX',
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genomeVersion : 'hg19',
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ploidy : '1.7',
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purity : '0.24',
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chrom_names : 'c("21","22")',
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]
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}
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withName: ASCAT_CRAM {
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ext.args = [
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gender : 'XX',
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genomeVersion : 'hg19',
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ref_fasta : '/mnt/volume/ascat/human_g1k_v37.fasta',
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chrom_names : 'c("21","22")'
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]
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}
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}
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