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Bedtools complement adapted to the current module standard

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JoseEspinosa 2020-07-15 18:15:16 +02:00
parent 1273c31294
commit 2cbc988d5f
6 changed files with 24 additions and 14 deletions
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4
software/bedtools/complement/Dockerfile
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@ -1,7 +1,7 @@
FROM nfcore/base FROM nfcore/base
LABEL authors="Jose Espinosa-Carrasco" \ LABEL authors="Jose Espinosa-Carrasco" \
description="Docker image containing all requirements for nf-core/modules/bedtools/complementbed" description="Docker image containing all requirements for nf-core/modules/bedtools/complement"
COPY environment.yml / COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nf-core-bedtools-complementbed/bin:$PATH ENV PATH /opt/conda/envs/nf-core-bedtools-complement/bin:$PATH

19
software/bedtools/complement/main.nf
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@ -1,18 +1,33 @@
def MODULE = "bedtools_complement"
params.publish_dir = MODULE
params.publish_results = "default"
process BEDTOOLS_COMPLEMENT { process BEDTOOLS_COMPLEMENT {
tag {input_file} tag {input_file}
publishDir "${params.out_dir}/${params.publish_dir}",
mode: params.publish_dir_mode,
saveAs: { filename ->
if (params.publish_results == "none") null
else filename }
//container "docker.pkg.github.com/nf-core/$MODULE"
container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0' container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
conda "${moduleDir}/environment.yml"
input: input:
path (input_file) path (input_file)
path (fasta_sizes) path (fasta_sizes)
val (bedtools_complement_args) val (bedtools_complement_args)
output: output:
stdout() path "${input_file}.bed", emit: complement
path "*.version.txt", emit: version
script: script:
""" """
bedtools complement -i ${input_file} -g ${fasta_sizes} ${bedtools_complement_args} bedtools complement -i ${input_file} -g ${fasta_sizes} ${bedtools_complement_args} > ${input_file}.bed
bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
""" """
} }

5
software/bedtools/complement/test/input_data/A.bed
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chr1 951 1061
chr1 1300 1420
chr1 1400 1500

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software/bedtools/complement/test/input_data/A.bed Symbolic link
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../../../../../tests/data/bed/A.bed

1
software/bedtools/complement/test/input_data/genome.sizes
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chr1 1780869

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software/bedtools/complement/test/input_data/genome.sizes Symbolic link
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../../../../../tests/data/bed/genome.sizes

5
software/bedtools/complement/test/main.nf
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nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
params.out_dir = "test_output"
params.fastqc_args = ''
params.publish_dir_mode = "copy"
params.bedtools_complement_args = '' params.bedtools_complement_args = ''
include check_output from '../../../../tests/functions/check_process_outputs.nf' // params(params)
include BEDTOOLS_COMPLEMENT from '../main.nf' params(params) include BEDTOOLS_COMPLEMENT from '../main.nf' params(params)
// Define input channels // Define input channels
@ -14,5 +16,4 @@ chrom_sizes = Channel.fromPath('./input_data/genome.sizes')
// Run the workflow // Run the workflow
workflow { workflow {
BEDTOOLS_COMPLEMENT(ch_input, chrom_sizes, params.bedtools_complement_args) BEDTOOLS_COMPLEMENT(ch_input, chrom_sizes, params.bedtools_complement_args)
// .check_output()
} }

2
software/bedtools/complement/test/nextflow.config
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@ -1,2 +0,0 @@
docker.enabled = true
params.outdir = './results'