Merge pull request #132 from drpatelh/bowtie

Rename bowtie_index to bowtie_build
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Kevin Menden 2021-02-02 07:47:37 +01:00 committed by GitHub
commit 4301afb771
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6 changed files with 22 additions and 21 deletions

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@ -1,14 +1,14 @@
name: bowtie_index name: bowtie_build
on: on:
push: push:
paths: paths:
- software/bowtie/index/** - software/bowtie/build/**
- .github/workflows/bowtie_index.yml - .github/workflows/bowtie_build.yml
- tests/software/bowtie/** - tests/software/bowtie/**
pull_request: pull_request:
paths: paths:
- software/bowtie/index/** - software/bowtie/build/**
- .github/workflows/bowtie_index.yml - .github/workflows/bowtie_build.yml
- tests/software/bowtie/** - tests/software/bowtie/**
jobs: jobs:
@ -37,4 +37,4 @@ jobs:
run: python -m pip install --upgrade pip pytest-workflow run: python -m pip install --upgrade pip pytest-workflow
# Test the module # Test the module
- run: pytest --tag bowtie_index --symlink --wt 2 - run: pytest --tag bowtie_build --symlink --wt 2

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@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:] params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
process BOWTIE_INDEX { process BOWTIE_BUILD {
tag "$fasta" tag "$fasta"
label 'process_high' label 'process_high'
publishDir "${params.outdir}", publishDir "${params.outdir}",
@ -22,7 +22,7 @@ process BOWTIE_INDEX {
path fasta path fasta
output: output:
path 'bowtie', emit: index path 'bowtie' , emit: index
path '*.version.txt', emit: version path '*.version.txt', emit: version
script: script:

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@ -1,4 +1,4 @@
name: bowtie_index name: bowtie_build
description: Create bowtie index for reference genome description: Create bowtie index for reference genome
keywords: keywords:
- index - index
@ -49,3 +49,4 @@ output:
pattern: "*.{version.txt}" pattern: "*.{version.txt}"
authors: authors:
- "@kevinmenden" - "@kevinmenden"
- "@drpatelh"

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@ -2,32 +2,32 @@
nextflow.enable.dsl = 2 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: [:] ) include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
workflow test_bowtie_index { workflow test_bowtie_build {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta ) BOWTIE_BUILD ( fasta )
} }
workflow test_bowtie_alignment_single_end { workflow test_bowtie_alignment_single_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta ) BOWTIE_BUILD ( fasta )
def input = [] def input = []
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] [ file("${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 { workflow test_bowtie_alignment_paired_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta ) BOWTIE_BUILD ( fasta )
def input = [] def input = []
input = [ [ id:'test', single_end:false ], // meta map 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_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] file("${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 )
} }

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@ -1,8 +1,8 @@
- name: Run bowtie index - name: Run bowtie build
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_build -c tests/config/nextflow.config
tags: tags:
- bowtie - bowtie
- bowtie_index - bowtie_build
files: files:
- path: output/bowtie/bowtie/NC_010473.1.ebwt - path: output/bowtie/bowtie/NC_010473.1.ebwt
md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
@ -17,7 +17,7 @@
- path: output/bowtie/bowtie/NC_010473.rev.2.ebwt - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051 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 command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
tags: tags:
- bowtie - bowtie