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Standardizing process names to BEDTOOLS_FOO and same with some variables

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This commit is contained in:
JoseEspinosa 2020-07-14 17:25:32 +02:00
parent 99a8196776
commit 8c3d7aa2d8
3 changed files with 10 additions and 10 deletions
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2
software/bedtools/complementbed/environment.yml
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@ -1,6 +1,6 @@
# You can use this file to create a conda environment for this pipeline: # You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml # conda env create -f environment.yml
name: nf-core-bedtools-complementbed name: nf-core-bedtools-complement
channels: channels:
- conda-forge - conda-forge
- bioconda - bioconda

6
software/bedtools/complementbed/main.nf
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@ -1,4 +1,4 @@
process COMPLEMENT_BED { process BEDTOOLS_COMPLEMENT {
tag {input_file} tag {input_file}
container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0' container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
@ -6,13 +6,13 @@ process COMPLEMENT_BED {
input: input:
path (input_file) path (input_file)
path (fasta_sizes) path (fasta_sizes)
val (complementbed_args) val (bedtools_complement_args)
output: output:
stdout() stdout()
script: script:
""" """
bedtools complement -i ${input_file} -g ${fasta_sizes} ${complementbed_args} bedtools complement -i ${input_file} -g ${fasta_sizes} ${bedtools_complement_args}
""" """
} }

6
software/bedtools/complementbed/test/main.nf
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@ -2,10 +2,10 @@
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
params.complementbed_args = '' params.bedtools_complement_args = ''
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 COMPLEMENT_BED from '../main.nf' params(params) include BEDTOOLS_COMPLEMENT from '../main.nf' params(params)
// Define input channels // Define input channels
ch_input = Channel.fromPath('./input_data/A.bed') ch_input = Channel.fromPath('./input_data/A.bed')
@ -13,6 +13,6 @@ chrom_sizes = Channel.fromPath('./input_data/genome.sizes')
// Run the workflow // Run the workflow
workflow { workflow {
COMPLEMENT_BED(ch_input, chrom_sizes, params.complementbed_args) BEDTOOLS_COMPLEMENT(ch_input, chrom_sizes, params.bedtools_complement_args)
// .check_output() // .check_output()
} }