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Using bedtools{_,-}genomecov instead of genomecov alone

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This commit is contained in:
JoseEspinosa 2020-07-14 17:31:40 +02:00
parent 71eaa83bf6
commit c059a485b9
3 changed files with 10 additions and 10 deletions
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12
software/bedtools/genomecov/main.nf
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@ -1,18 +1,18 @@
process GENOMECOV { process BEDTOOLS_GENOMECOV {
tag {bam} tag {bam}
container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0' container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
input: input:
path (bam) path (bam)
path (chrom_sizes) path (chrom_sizes)
val (genomecov_args) val (bedtools_genomecov_args)
output: output:
stdout() stdout()
script: script:
""" """
bedtools genomecov -ibam ${bam} -g ${chrom_sizes} ${genomecov_args} bedtools genomecov -ibam ${bam} -g ${chrom_sizes} ${bedtools_genomecov_args}
""" """
} }

2
software/bedtools/genomecov/meta.yml
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@ -1,7 +1,7 @@
name: bedtools genomecov name: bedtools genomecov
description: Returns feature coverage for a given genome in different formats description: Returns feature coverage for a given genome in different formats
keywords: keywords:
- complement - genomecov
tools: tools:
- bedtools: - bedtools:
description: | description: |

6
software/bedtools/genomecov/test/main.nf
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@ -2,10 +2,10 @@
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
params.genomecov_args = '' //'-bg' params.bedtools_genomecov_args = '' //'-bg'
include check_output from '../../../../tests/functions/check_process_outputs.nf' // params(params) include check_output from '../../../../tests/functions/check_process_outputs.nf' // params(params)
include GENOMECOV from '../main.nf' params(params) include BEDTOOLS_GENOMECOV from '../main.nf' params(params)
// Define input channels // Define input channels
ch_input = Channel.fromPath('./input_data/JK2067_downsampled_s0.1.bam') ch_input = Channel.fromPath('./input_data/JK2067_downsampled_s0.1.bam')
@ -13,6 +13,6 @@ chrom_sizes = Channel.fromPath('./input_data/genome.sizes')
// Run the workflow // Run the workflow
workflow { workflow {
GENOMECOV(ch_input, chrom_sizes, params.genomecov_args) BEDTOOLS_GENOMECOV(ch_input, chrom_sizes, params.bedtools_genomecov_args)
// .check_output() // .check_output()
} }