From 7fe6f9fab290b04096263222c321a6d0194d4b84 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Patrick=20H=C3=BCther?= Date: Mon, 22 Mar 2021 17:46:11 +0100 Subject: [PATCH] bismark: remove underscores from process names (#303) * sanitize process names no underscores allowed * remove underscores from process names --- .../functions.nf | 0 .../main.nf | 2 +- .../meta.yml | 2 +- .../functions.nf | 0 .../main.nf | 2 +- .../meta.yml | 2 +- tests/config/pytest_software.yml | 24 +++++++++---------- tests/software/bismark/align/main.nf | 10 ++++---- .../bismark/genome_preparation/main.nf | 10 -------- .../bismark/genomepreparation/main.nf | 10 ++++++++ .../test.yml | 6 ++--- .../bismark/methylation_extractor/main.nf | 20 ---------------- .../bismark/methylationextractor/main.nf | 20 ++++++++++++++++ .../test.yml | 4 ++-- tests/software/bismark/report/main.nf | 14 +++++------ tests/software/bismark/summary/main.nf | 14 +++++------ 16 files changed, 70 insertions(+), 70 deletions(-) rename software/bismark/{genome_preparation => genomepreparation}/functions.nf (100%) rename software/bismark/{genome_preparation => genomepreparation}/main.nf (96%) rename software/bismark/{genome_preparation => genomepreparation}/meta.yml (96%) rename software/bismark/{methylation_extractor => methylationextractor}/functions.nf (100%) rename software/bismark/{methylation_extractor => methylationextractor}/main.nf (97%) rename software/bismark/{methylation_extractor => methylationextractor}/meta.yml (98%) delete mode 100644 tests/software/bismark/genome_preparation/main.nf create mode 100644 tests/software/bismark/genomepreparation/main.nf rename tests/software/bismark/{genome_preparation => genomepreparation}/test.yml (90%) delete mode 100644 tests/software/bismark/methylation_extractor/main.nf create mode 100644 tests/software/bismark/methylationextractor/main.nf rename tests/software/bismark/{methylation_extractor => methylationextractor}/test.yml (82%) diff --git a/software/bismark/genome_preparation/functions.nf b/software/bismark/genomepreparation/functions.nf similarity index 100% rename from software/bismark/genome_preparation/functions.nf rename to software/bismark/genomepreparation/functions.nf diff --git a/software/bismark/genome_preparation/main.nf b/software/bismark/genomepreparation/main.nf similarity index 96% rename from software/bismark/genome_preparation/main.nf rename to software/bismark/genomepreparation/main.nf index 17f517af..904d9922 100644 --- a/software/bismark/genome_preparation/main.nf +++ b/software/bismark/genomepreparation/main.nf @@ -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}", diff --git a/software/bismark/genome_preparation/meta.yml b/software/bismark/genomepreparation/meta.yml similarity index 96% rename from software/bismark/genome_preparation/meta.yml rename to software/bismark/genomepreparation/meta.yml index f357ffb1..a31add8a 100644 --- a/software/bismark/genome_preparation/meta.yml +++ b/software/bismark/genomepreparation/meta.yml @@ -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. diff --git a/software/bismark/methylation_extractor/functions.nf b/software/bismark/methylationextractor/functions.nf similarity index 100% rename from software/bismark/methylation_extractor/functions.nf rename to software/bismark/methylationextractor/functions.nf diff --git a/software/bismark/methylation_extractor/main.nf b/software/bismark/methylationextractor/main.nf similarity index 97% rename from software/bismark/methylation_extractor/main.nf rename to software/bismark/methylationextractor/main.nf index 238b0220..7ec52d14 100644 --- a/software/bismark/methylation_extractor/main.nf +++ b/software/bismark/methylationextractor/main.nf @@ -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}", diff --git a/software/bismark/methylation_extractor/meta.yml b/software/bismark/methylationextractor/meta.yml similarity index 98% rename from software/bismark/methylation_extractor/meta.yml rename to software/bismark/methylationextractor/meta.yml index aeef7418..a201b586 100644 --- a/software/bismark/methylation_extractor/meta.yml +++ b/software/bismark/methylationextractor/meta.yml @@ -1,4 +1,4 @@ -name: bismark_methylation_extractor +name: bismark_methylationextractor description: Extracts methylation information for individual cytosines from alignments. keywords: - bismark diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml index 19ed2e66..53d70a47 100644 --- a/tests/config/pytest_software.yml +++ b/tests/config/pytest_software.yml @@ -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/** diff --git a/tests/software/bismark/align/main.nf b/tests/software/bismark/align/main.nf index dba06ec1..de25bba1 100644 --- a/tests/software/bismark/align/main.nf +++ b/tests/software/bismark/align/main.nf @@ -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 ) } diff --git a/tests/software/bismark/genome_preparation/main.nf b/tests/software/bismark/genome_preparation/main.nf deleted file mode 100644 index 84ae8cb7..00000000 --- a/tests/software/bismark/genome_preparation/main.nf +++ /dev/null @@ -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("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ) -} diff --git a/tests/software/bismark/genomepreparation/main.nf b/tests/software/bismark/genomepreparation/main.nf new file mode 100644 index 00000000..55da4a65 --- /dev/null +++ b/tests/software/bismark/genomepreparation/main.nf @@ -0,0 +1,10 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] ) + +workflow test_bismark_genomepreparation { + + BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ) +} diff --git a/tests/software/bismark/genome_preparation/test.yml b/tests/software/bismark/genomepreparation/test.yml similarity index 90% rename from tests/software/bismark/genome_preparation/test.yml rename to tests/software/bismark/genomepreparation/test.yml index a0a4f989..b4dd74df 100644 --- a/tests/software/bismark/genome_preparation/test.yml +++ b/tests/software/bismark/genomepreparation/test.yml @@ -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 diff --git a/tests/software/bismark/methylation_extractor/main.nf b/tests/software/bismark/methylation_extractor/main.nf deleted file mode 100644 index 01c51cad..00000000 --- a/tests/software/bismark/methylation_extractor/main.nf +++ /dev/null @@ -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 - ) -} diff --git a/tests/software/bismark/methylationextractor/main.nf b/tests/software/bismark/methylationextractor/main.nf new file mode 100644 index 00000000..3a81f9b4 --- /dev/null +++ b/tests/software/bismark/methylationextractor/main.nf @@ -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 + ) +} diff --git a/tests/software/bismark/methylation_extractor/test.yml b/tests/software/bismark/methylationextractor/test.yml similarity index 82% rename from tests/software/bismark/methylation_extractor/test.yml rename to tests/software/bismark/methylationextractor/test.yml index b351e7a2..8a0d218b 100644 --- a/tests/software/bismark/methylation_extractor/test.yml +++ b/tests/software/bismark/methylationextractor/test.yml @@ -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 diff --git a/tests/software/bismark/report/main.nf b/tests/software/bismark/report/main.nf index 9794b494..e2104be4 100644 --- a/tests/software/bismark/report/main.nf +++ b/tests/software/bismark/report/main.nf @@ -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) ) } diff --git a/tests/software/bismark/summary/main.nf b/tests/software/bismark/summary/main.nf index d866a8a7..155daee7 100644 --- a/tests/software/bismark/summary/main.nf +++ b/tests/software/bismark/summary/main.nf @@ -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 } ) }