mirror of
https://github.com/MillironX/nf-core_modules.git
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test(bwa): Refactor to use pytest-workflow
This commit is contained in:
Edmund Miller
parent
dfc8528df9
commit
016d8684f3
21 changed files with 106 additions and 124 deletions
22
.github/workflows/software/bwa_index.yml
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22
.github/workflows/software/bwa_index.yml
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@ -17,14 +17,20 @@ jobs:
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v2
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- name: Install Nextflow
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run: |
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export NXF_VER="20.07.1"
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Install Nextflow
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run: |
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export NXF_VER="20.07.1"
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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- run: nextflow run ./software/bwa/index/test/ -profile docker
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# Test the module
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- run: pytest --tag bwa_index --symlink --wt 2
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22
.github/workflows/software/bwa_mem.yml
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22
.github/workflows/software/bwa_mem.yml
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@ -17,14 +17,20 @@ jobs:
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v2
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- name: Install Nextflow
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run: |
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export NXF_VER="20.07.1"
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Install Nextflow
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run: |
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export NXF_VER="20.07.1"
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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- run: nextflow run ./software/bwa/mem/test/ -profile docker
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# Test the module
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- run: pytest --tag bwa_index --symlink --wt 2
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@ -1 +0,0 @@
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../../../../../tests/data/fasta/E_coli/NC_010473.fa
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@ -1,13 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../main.nf' addParams( options: [:] )
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workflow test {
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BWA_INDEX ( file("${baseDir}/input/NC_010473.fa", checkIfExists: true) )
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}
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workflow {
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test()
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}
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@ -1,20 +0,0 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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enable_conda = false
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}
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profiles {
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conda {
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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@ -1,3 +0,0 @@
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4686137 1 2
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20895 1 Y
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142347 1 R
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@ -1,3 +0,0 @@
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4686137 1 11
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0 gi|170079663|ref|NC_010473.1| Escherichia coli str. K-12 substr. DH10B, complete genome
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0 4686137 2
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@ -1 +0,0 @@
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../../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz
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@ -1 +0,0 @@
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../../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz
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@ -1 +0,0 @@
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../../../../../tests/data/fasta/E_coli/NC_010473.fa
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@ -1 +0,0 @@
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../../../../../tests/data/index/E_coli/bwa/
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@ -1,44 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWA_MEM as BWA_MEM_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { BWA_MEM as BWA_MEM_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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/*
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* Test with single-end data
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*/
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workflow test_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
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BWA_MEM_SE (
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input,
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file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
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file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
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)
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}
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/*
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* Test with paired-end data
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*/
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workflow test_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
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file("${baseDir}/input/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
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BWA_MEM_PE (
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input,
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file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
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file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
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)
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}
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workflow {
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test_single_end()
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test_paired_end()
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}
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@ -1,20 +0,0 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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enable_conda = false
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}
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profiles {
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conda {
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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44
tests/software/bwa/main.nf
Normal file
44
tests/software/bwa/main.nf
Normal file
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@ -0,0 +1,44 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] )
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include { BWA_MEM as BWA_MEM_SE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { BWA_MEM as BWA_MEM_PE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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workflow test_bwa_index {
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BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
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}
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/*
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* Test with single-end data
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*/
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workflow test_bwa_mem_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
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BWA_MEM_SE (
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input,
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file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
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file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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)
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}
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/*
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* Test with paired-end data
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*/
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workflow test_bwa_mem_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
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BWA_MEM_PE (
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input,
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file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
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file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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)
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}
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32
tests/software/bwa/test.yml
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32
tests/software/bwa/test.yml
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@ -0,0 +1,32 @@
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- name: Run bwa index
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command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config
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tags:
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- bwa
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- bwa_index
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files:
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- path: output/bwa/NC_010473.fa.amb
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md5sum: 942a990ae872f1c0b8d72dda2db405d5
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- path: output/bwa/NC_010473.fa.bwt
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md5sum: 7301b52e2ecb893d429a49fa692447ae
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- path: output/bwa/NC_010473.fa.pac
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md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
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- path: output/bwa/NC_010473.fa.sa
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md5sum: a47dcc92e750e2f16fbd979b8ff9538e
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- name: Run bwa mem single-end
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command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config
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tags:
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- bwa
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- bwa_mem
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files:
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- path: output/test_single_end/test.bam
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md5sum: 3ee21210bac387e0335008146e4728bc
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- name: Run bwa mem paired-end
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command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
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tags:
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- bwa
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- bwa_mem
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files:
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- path: output/test_paired_end/test.bam
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md5sum: 510d8acc6448c07cdacce8e64ec0904c
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@ -29,3 +29,5 @@ workflow test_paired_end {
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FASTQC_PE ( input )
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}
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// TODO Test e2e
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