From f84e5b59ca97ef04551c6134cae023164501137c Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 1 Feb 2021 17:53:31 +0000 Subject: [PATCH] Rename bowtie_index to bowtie_build --- .../{bowtie_index.yml => bowtie_build.yml} | 12 ++++++------ software/bowtie/{index => build}/functions.nf | 0 software/bowtie/{index => build}/main.nf | 6 +++--- software/bowtie/{index => build}/meta.yml | 3 ++- tests/software/bowtie/main.nf | 14 +++++++------- tests/software/bowtie/test.yml | 8 ++++---- 6 files changed, 22 insertions(+), 21 deletions(-) rename .github/workflows/{bowtie_index.yml => bowtie_build.yml} (76%) rename software/bowtie/{index => build}/functions.nf (100%) rename software/bowtie/{index => build}/main.nf (90%) rename software/bowtie/{index => build}/meta.yml (97%) diff --git a/.github/workflows/bowtie_index.yml b/.github/workflows/bowtie_build.yml similarity index 76% rename from .github/workflows/bowtie_index.yml rename to .github/workflows/bowtie_build.yml index 291d04f5..1a02341e 100644 --- a/.github/workflows/bowtie_index.yml +++ b/.github/workflows/bowtie_build.yml @@ -1,14 +1,14 @@ -name: bowtie_index +name: bowtie_build on: push: paths: - - software/bowtie/index/** - - .github/workflows/bowtie_index.yml + - software/bowtie/build/** + - .github/workflows/bowtie_build.yml - tests/software/bowtie/** pull_request: paths: - - software/bowtie/index/** - - .github/workflows/bowtie_index.yml + - software/bowtie/build/** + - .github/workflows/bowtie_build.yml - tests/software/bowtie/** jobs: @@ -37,4 +37,4 @@ jobs: run: python -m pip install --upgrade pip pytest-workflow # Test the module - - run: pytest --tag bowtie_index --symlink --wt 2 + - run: pytest --tag bowtie_build --symlink --wt 2 diff --git a/software/bowtie/index/functions.nf b/software/bowtie/build/functions.nf similarity index 100% rename from software/bowtie/index/functions.nf rename to software/bowtie/build/functions.nf diff --git a/software/bowtie/index/main.nf b/software/bowtie/build/main.nf similarity index 90% rename from software/bowtie/index/main.nf rename to software/bowtie/build/main.nf index 8b982bcf..4dd20b85 100644 --- a/software/bowtie/index/main.nf +++ b/software/bowtie/build/main.nf @@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] def options = initOptions(params.options) -process BOWTIE_INDEX { +process BOWTIE_BUILD { tag "$fasta" label 'process_high' publishDir "${params.outdir}", @@ -22,11 +22,11 @@ process BOWTIE_INDEX { path fasta output: - path 'bowtie', emit: index + path 'bowtie' , emit: index path '*.version.txt', emit: version script: - def software = getSoftwareName(task.process) + def software = getSoftwareName(task.process) """ mkdir bowtie bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName} diff --git a/software/bowtie/index/meta.yml b/software/bowtie/build/meta.yml similarity index 97% rename from software/bowtie/index/meta.yml rename to software/bowtie/build/meta.yml index e5296b05..f9a8f1c9 100644 --- a/software/bowtie/index/meta.yml +++ b/software/bowtie/build/meta.yml @@ -1,4 +1,4 @@ -name: bowtie_index +name: bowtie_build description: Create bowtie index for reference genome keywords: - index @@ -49,3 +49,4 @@ output: pattern: "*.{version.txt}" authors: - "@kevinmenden" + - "@drpatelh" diff --git a/tests/software/bowtie/main.nf b/tests/software/bowtie/main.nf index c496a619..1073195d 100644 --- a/tests/software/bowtie/main.nf +++ b/tests/software/bowtie/main.nf @@ -2,32 +2,32 @@ nextflow.enable.dsl = 2 -include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] ) +include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] ) include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] ) -workflow test_bowtie_index { +workflow test_bowtie_build { fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE_INDEX ( fasta ) + BOWTIE_BUILD ( fasta ) } workflow test_bowtie_alignment_single_end { fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE_INDEX ( fasta ) + BOWTIE_BUILD ( fasta ) def input = [] input = [ [ id:'test', single_end:true ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] - BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index ) + BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) } workflow test_bowtie_alignment_paired_end { fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) - BOWTIE_INDEX ( fasta ) + BOWTIE_BUILD ( fasta ) def input = [] input = [ [ id:'test', single_end:false ], // meta map [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] - BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index ) + BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) } diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml index 229165ac..96037548 100644 --- a/tests/software/bowtie/test.yml +++ b/tests/software/bowtie/test.yml @@ -1,8 +1,8 @@ -- name: Run bowtie index - command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config +- name: Run bowtie build + command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_build -c tests/config/nextflow.config tags: - bowtie - - bowtie_index + - bowtie_build files: - path: output/bowtie/bowtie/NC_010473.1.ebwt md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c @@ -17,7 +17,7 @@ - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt md5sum: f3c398bba5158f4039334a932d79c051 -- name: Run bowtie index and align single-end +- name: Run bowtie build and align single-end command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config tags: - bowtie