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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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6
software/bedtools/genomecov/main.nf
View file

@ -1,4 +1,4 @@
process GENOMECOV {
process BEDTOOLS_GENOMECOV {
tag {bam}
container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
@ -6,13 +6,13 @@ process GENOMECOV {
input:
path (bam)
path (chrom_sizes)
val (genomecov_args)
val (bedtools_genomecov_args)
output:
stdout()
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
View file

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

6
software/bedtools/genomecov/test/main.nf
View file

@ -2,10 +2,10 @@
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 GENOMECOV from '../main.nf' params(params)
include BEDTOOLS_GENOMECOV from '../main.nf' params(params)
// Define input channels
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
workflow {
GENOMECOV(ch_input, chrom_sizes, params.genomecov_args)
BEDTOOLS_GENOMECOV(ch_input, chrom_sizes, params.bedtools_genomecov_args)
// .check_output()
}