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bismark: remove underscores from process names (#303)

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* sanitize process names

no underscores allowed

* remove underscores from process names
This commit is contained in:
Patrick Hüther 2021-03-22 17:46:11 +01:00 committed by GitHub
parent 592002aa23
commit 7fe6f9fab2
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GPG key ID: 4AEE18F83AFDEB23
16 changed files with 70 additions and 70 deletions
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0
software/bismark/genome_preparation/functions.nf → software/bismark/genomepreparation/functions.nf
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2
software/bismark/genome_preparation/main.nf → software/bismark/genomepreparation/main.nf
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@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BISMARK_GENOME_PREPARATION {
process BISMARK_GENOMEPREPARATION {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",

2
software/bismark/genome_preparation/meta.yml → software/bismark/genomepreparation/meta.yml
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@ -1,4 +1,4 @@
name: bismark_genome_preparation
name: bismark_genomepreparation
description: |
Converts a specified reference genome into two different bisulfite
converted versions and indexes them for alignments.

0
software/bismark/methylation_extractor/functions.nf → software/bismark/methylationextractor/functions.nf
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2
software/bismark/methylation_extractor/main.nf → software/bismark/methylationextractor/main.nf
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@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BISMARK_METHYLATION_EXTRACTOR {
process BISMARK_METHYLATIONEXTRACTOR {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",

2
software/bismark/methylation_extractor/meta.yml → software/bismark/methylationextractor/meta.yml
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@ -1,4 +1,4 @@
name: bismark_methylation_extractor
name: bismark_methylationextractor
description: Extracts methylation information for individual cytosines from alignments.
keywords:
- bismark

24
tests/config/pytest_software.yml
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@ -60,21 +60,21 @@ bedtools_sort:
bismark_align:
- software/bismark/align/**
- software/bismark/genome_preparation/**
- software/bismark/genomepreparation/**
- tests/software/bismark/align/**
bismark_deduplicate:
- software/bismark/deduplicate/**
- tests/software/bismark/deduplicate/**
bismark_genome_preparation:
- software/bismark/genome_preparation/**
- tests/software/bismark/genome_preparation/**
bismark_genomepreparation:
- software/bismark/genomepreparation/**
- tests/software/bismark/genomepreparation/**
bismark_methylation_extractor:
- software/bismark/methylation_extractor/**
- software/bismark/genome_preparation/**
- tests/software/bismark/methylation_extractor/**
bismark_methylationextractor:
- software/bismark/methylationextractor/**
- software/bismark/genomepreparation/**
- tests/software/bismark/methylationextractor/**
blast_blastn:
@ -82,18 +82,18 @@ blast_blastn:
- tests/software/blast/blastn/**
bismark_report:
- software/bismark/genome_preparation/**
- software/bismark/genomepreparation/**
- software/bismark/align/**
- software/bismark/deduplicate/**
- software/bismark/methylation_extractor/**
- software/bismark/methylationextractor/**
- software/bismark/report/**
- tests/software/bismark/report/**
bismark_summary:
- software/bismark/genome_preparation/**
- software/bismark/genomepreparation/**
- software/bismark/align/**
- software/bismark/deduplicate/**
- software/bismark/methylation_extractor/**
- software/bismark/methylationextractor/**
- software/bismark/summary/**
- tests/software/bismark/summary/**

10
tests/software/bismark/align/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { BISMARK_GENOME_PREPARATION } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../software/bismark/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../software/bismark/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
@ -16,10 +16,10 @@ workflow test_bismark_align_single_end {
[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ] ]
BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_ALIGN_SE (
input,
BISMARK_GENOME_PREPARATION.out.index
BISMARK_GENOMEPREPARATION.out.index
)
}
@ -34,9 +34,9 @@ workflow test_bismark_align_paired_end {
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_ALIGN_PE (
input,
BISMARK_GENOME_PREPARATION.out.index
BISMARK_GENOMEPREPARATION.out.index
)
}

10
tests/software/bismark/genome_preparation/main.nf
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@ -1,10 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BISMARK_GENOME_PREPARATION } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
workflow test_bismark_genome_preparation {
BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
}

10
tests/software/bismark/genomepreparation/main.nf Normal file
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@ -0,0 +1,10 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
workflow test_bismark_genomepreparation {
BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
}

6
tests/software/bismark/genome_preparation/test.yml → tests/software/bismark/genomepreparation/test.yml
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@ -1,8 +1,8 @@
- name: Run bismark_genome_preparation test workflow
command: nextflow run ./tests/software/bismark/genome_preparation -entry test_bismark_genome_preparation -c tests/config/nextflow.config
- name: Run bismark_genomepreparation test workflow
command: nextflow run ./tests/software/bismark/genomepreparation -entry test_bismark_genomepreparation -c tests/config/nextflow.config
tags:
- bismark
- bismark_genome_preparation
- bismark_genomepreparation
files:
- path: ./output/bismark/BismarkIndex/test_genome.fasta
md5sum: 6e9fe4042a72f2345f644f239272b7e6

20
tests/software/bismark/methylation_extractor/main.nf
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@ -1,20 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BISMARK_GENOME_PREPARATION } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
include { BISMARK_METHYLATION_EXTRACTOR } from '../../../../software/bismark/methylation_extractor/main.nf' addParams( options: [:] )
workflow test_bismark_methylation_extractor {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam", checkIfExists: true) ] ]
BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_METHYLATION_EXTRACTOR (
input,
BISMARK_GENOME_PREPARATION.out.index
)
}

20
tests/software/bismark/methylationextractor/main.nf Normal file
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@ -0,0 +1,20 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
workflow test_bismark_methylationextractor {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam", checkIfExists: true) ] ]
BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_METHYLATIONEXTRACTOR (
input,
BISMARK_GENOMEPREPARATION.out.index
)
}

4
tests/software/bismark/methylation_extractor/test.yml → tests/software/bismark/methylationextractor/test.yml
View file

@ -1,8 +1,8 @@
- name: Run bismark methylation extractor test workflow
command: nextflow run ./tests/software/bismark/methylation_extractor -entry test_bismark_methylation_extractor -c tests/config/nextflow.config
command: nextflow run ./tests/software/bismark/methylationextractor -entry test_bismark_methylationextractor -c tests/config/nextflow.config
tags:
- bismark
- bismark_methylation_extractor
- bismark_methylationextractor
files:
- path: output/bismark/CHG_OB_test_methylated_paired_end.txt.gz
- path: output/bismark/CHG_OT_test_methylated_paired_end.txt.gz

14
tests/software/bismark/report/main.nf
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@ -2,10 +2,10 @@
nextflow.enable.dsl = 2
include { BISMARK_GENOME_PREPARATION } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
include { BISMARK_ALIGN } from '../../../../software/bismark/align/main.nf' addParams( options: [:] )
include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
include { BISMARK_METHYLATION_EXTRACTOR } from '../../../../software/bismark/methylation_extractor/main.nf' addParams( options: [:] )
include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
include { BISMARK_REPORT } from '../../../../software/bismark/report/main.nf' addParams( options: [:] )
workflow test_bismark_report {
@ -15,15 +15,15 @@ workflow test_bismark_report {
[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_ALIGN ( input, BISMARK_GENOME_PREPARATION.out.index )
BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
BISMARK_METHYLATION_EXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOME_PREPARATION.out.index )
BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
BISMARK_REPORT (
BISMARK_ALIGN.out.report
.join(BISMARK_DEDUPLICATE.out.report)
.join(BISMARK_METHYLATION_EXTRACTOR.out.report)
.join(BISMARK_METHYLATION_EXTRACTOR.out.mbias)
.join(BISMARK_METHYLATIONEXTRACTOR.out.report)
.join(BISMARK_METHYLATIONEXTRACTOR.out.mbias)
)
}

14
tests/software/bismark/summary/main.nf
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@ -2,10 +2,10 @@
nextflow.enable.dsl = 2
include { BISMARK_GENOME_PREPARATION } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
include { BISMARK_ALIGN } from '../../../../software/bismark/align/main.nf' addParams( options: [:] )
include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
include { BISMARK_METHYLATION_EXTRACTOR } from '../../../../software/bismark/methylation_extractor/main.nf' addParams( options: [:] )
include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
include { BISMARK_SUMMARY } from '../../../../software/bismark/summary/main.nf' addParams( options: [:] )
workflow test_bismark_summary {
@ -15,16 +15,16 @@ workflow test_bismark_summary {
[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_ALIGN ( input, BISMARK_GENOME_PREPARATION.out.index )
BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
BISMARK_METHYLATION_EXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOME_PREPARATION.out.index )
BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
BISMARK_SUMMARY (
BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam },
BISMARK_ALIGN.out.report.collect{ meta, report -> report },
BISMARK_DEDUPLICATE.out.report.collect{ meta, bam -> bam },
BISMARK_METHYLATION_EXTRACTOR.out.report.collect{ meta, report -> report },
BISMARK_METHYLATION_EXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report },
BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
)
}