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Merge pull request #132 from drpatelh/bowtie
Rename bowtie_index to bowtie_build
This commit is contained in:
commit
4301afb771
6 changed files with 22 additions and 21 deletions
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@ -1,14 +1,14 @@
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name: bowtie_index
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name: bowtie_build
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on:
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on:
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push:
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push:
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paths:
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paths:
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- software/bowtie/index/**
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- software/bowtie/build/**
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- .github/workflows/bowtie_index.yml
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- .github/workflows/bowtie_build.yml
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- tests/software/bowtie/**
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- tests/software/bowtie/**
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pull_request:
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pull_request:
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paths:
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paths:
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- software/bowtie/index/**
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- software/bowtie/build/**
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- .github/workflows/bowtie_index.yml
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- .github/workflows/bowtie_build.yml
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- tests/software/bowtie/**
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- tests/software/bowtie/**
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jobs:
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jobs:
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@ -37,4 +37,4 @@ jobs:
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run: python -m pip install --upgrade pip pytest-workflow
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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# Test the module
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- run: pytest --tag bowtie_index --symlink --wt 2
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- run: pytest --tag bowtie_build --symlink --wt 2
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@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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params.options = [:]
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def options = initOptions(params.options)
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def options = initOptions(params.options)
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process BOWTIE_INDEX {
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process BOWTIE_BUILD {
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tag "$fasta"
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tag "$fasta"
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label 'process_high'
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label 'process_high'
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publishDir "${params.outdir}",
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publishDir "${params.outdir}",
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@ -1,4 +1,4 @@
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name: bowtie_index
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name: bowtie_build
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description: Create bowtie index for reference genome
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description: Create bowtie index for reference genome
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keywords:
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keywords:
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- index
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- index
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@ -49,3 +49,4 @@ output:
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pattern: "*.{version.txt}"
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pattern: "*.{version.txt}"
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authors:
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authors:
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- "@kevinmenden"
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- "@kevinmenden"
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- "@drpatelh"
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@ -2,32 +2,32 @@
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nextflow.enable.dsl = 2
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nextflow.enable.dsl = 2
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include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
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include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] )
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include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
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include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
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workflow test_bowtie_index {
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workflow test_bowtie_build {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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BOWTIE_INDEX ( fasta )
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BOWTIE_BUILD ( fasta )
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}
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}
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workflow test_bowtie_alignment_single_end {
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workflow test_bowtie_alignment_single_end {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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BOWTIE_INDEX ( fasta )
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BOWTIE_BUILD ( fasta )
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def input = []
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
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BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
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BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
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}
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}
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workflow test_bowtie_alignment_paired_end {
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workflow test_bowtie_alignment_paired_end {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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BOWTIE_INDEX ( fasta )
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BOWTIE_BUILD ( fasta )
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def input = []
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
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file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
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BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
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BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
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}
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}
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@ -1,8 +1,8 @@
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- name: Run bowtie index
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- name: Run bowtie build
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command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_build -c tests/config/nextflow.config
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tags:
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tags:
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- bowtie
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- bowtie
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- bowtie_index
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- bowtie_build
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files:
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files:
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- path: output/bowtie/bowtie/NC_010473.1.ebwt
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- path: output/bowtie/bowtie/NC_010473.1.ebwt
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md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
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md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
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@ -17,7 +17,7 @@
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- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
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- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
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md5sum: f3c398bba5158f4039334a932d79c051
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md5sum: f3c398bba5158f4039334a932d79c051
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- name: Run bowtie index and align single-end
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- name: Run bowtie build and align single-end
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command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
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tags:
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tags:
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- bowtie
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- bowtie
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