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@peterk87
Last active February 9, 2022 18:24
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Custom Mosdepth modules config for nf-core/viralrecon v2.2 to output `.bed.gz` files. Will not work for v2.3
params {
modules {
'illumina_mosdepth_genome' {
args = '--fast-mode'
publish_files = ['summary.txt':'', 'per-base.bed.gz':'', 'regions.bed.gz':'']
publish_dir = 'variants/bowtie2/mosdepth/genome'
}
'illumina_mosdepth_amplicon' {
args = '--fast-mode --use-median --thresholds 0,1,10,50,100,500'
publish_files = ['summary.txt':'', 'per-base.bed.gz':'', 'regions.bed.gz':'']
publish_dir = 'variants/bowtie2/mosdepth/amplicon'
}
}
}
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