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Merge pull request #85 from nf-core/pytest-workflow-refactor

Browse source 
Refactor all tests to use pytest-workflow
This commit is contained in:
Harshil Patel 2020-12-04 14:30:00 +00:00 committed by GitHub
commit cd2cf9cf2f
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GPG key ID: 4AEE18F83AFDEB23
100 changed files with 543 additions and 2925 deletions
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52
.github/workflows/bwa_index.yml vendored
View file

@ -1,30 +1,36 @@
name: bwa_index
on:
push:
paths:
- software/bwa/index/**
- .github/workflows/bwa_index.yml
- tests
pull_request:
paths:
- software/bwa/index/**
- .github/workflows/bwa_index.yml
- tests
push:
paths:
- software/bwa/index/**
- .github/workflows/bwa_index.yml
- tests/software/bwa/**
pull_request:
paths:
- software/bwa/index/**
- .github/workflows/bwa_index.yml
- tests/software/bwa/**
jobs:
ci_test:
runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps:
ci_test:
runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/bwa/index/test/ -profile docker
# Test the module
- run: pytest --tag bwa_index --symlink --wt 2

26
.github/workflows/bwa_mem.yml vendored
View file

@ -4,12 +4,12 @@ on:
paths:
- software/bwa/mem/**
- .github/workflows/bwa_mem.yml
- tests
- tests/software/bwa/**
pull_request:
paths:
- software/bwa/mem/**
- .github/workflows/bwa_mem.yml
- tests
- tests/software/bwa/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/bwa/mem/test/ -profile docker
# Test the module
- run: pytest --tag bwa_index --symlink --wt 2

54
.github/workflows/docker.yml vendored
View file

@ -1,54 +0,0 @@
name: Build Docker Images
on:
push:
# Only on pushes to master (after PRs are merged)
branches: master
# Only if a conda environment file or a docker build file has been updated
paths:
- software/*/environment.yml
- software/*/Dockerfile
jobs:
build_docker:
runs-on: ubuntu-latest
steps:
# Check out the repo
- uses: actions/checkout@v2
# Find the tool wrappers that changed
# Annoyingly, matrix can't take dynamic variables
- name: Find changed tools
run: |
TOOLS=$( git diff --name-only HEAD~ | egrep -o 'tools\/[^\/]+\/' | sort | uniq | awk NF | tr '\r\n' ' ' )
# Save so that GitHub Actions can see this variable in the next step
echo "::set-env name=TOOLS::$TOOLS"
echo "Tools that appear to have been updated:"
echo $TOOLS
- name: Build images
run: |
echo "Tools that appear to have been updated:"
echo -e $TOOLS
echo '-----'
for TOOL in $TOOLS; do
echo $TOOL
done;
echo '-----'
for d in software/*; do
for TOOL in $TOOLS; do
echo "$d -- $TOOL"
if echo $d/ | grep -q "$TOOL"; then
cd "$GITHUB_WORKSPACE/$d"
TOOLNAME=$(basename `pwd`)
# IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:$GITHUB_SHA
# TODO: How do we have a proper version tag here?
IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:latest
echo "Image name is: $IMGNAME"
echo "${{ secrets.GITHUB_TOKEN }}" | docker login -u ${{ github.actor }} --password-stdin docker.pkg.github.com
docker build -t $IMGNAME .
docker push $IMGNAME
fi;
done;
done;

37
.github/workflows/fastqc.yml vendored
View file

@ -4,34 +4,37 @@ on:
paths:
- software/fastqc/**
- .github/workflows/fastqc.yml
- tests
- tests/software/fastqc/**
pull_request:
paths:
- software/fastqc/**
- .github/workflows/fastqc.yml
- tests
- tests/software/fastqc/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.07.1, '']
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: pytest --tag fastqc --symlink --wt 2
# Test the module
- run: pytest --tag fastqc --symlink --wt 2

26
.github/workflows/picard_collectmultiplemetrics.yml vendored
View file

@ -4,12 +4,12 @@ on:
paths:
- software/picard/collectmultiplemetrics/**
- .github/workflows/picard_collectmultiplemetrics.yml
- tests
- tests/software/picard/**
pull_request:
paths:
- software/picard/collectmultiplemetrics/**
- .github/workflows/picard_collectmultiplemetrics.yml
- tests
- tests/software/picard/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/picard/collectmultiplemetrics/test/ -profile docker
# Test the module
- run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2

26
.github/workflows/picard_markduplicates.yml vendored
View file

@ -4,12 +4,12 @@ on:
paths:
- software/picard/markduplicates/**
- .github/workflows/picard_markduplicates.yml
- tests
- tests/software/picard/**
pull_request:
paths:
- software/picard/markduplicates/**
- .github/workflows/picard_markduplicates.yml
- tests
- tests/software/picard/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/picard/markduplicates/test/ -profile docker
# Test the module
- run: pytest --tag picard_markduplicates --symlink --wt 2

26
.github/workflows/picard_mergesamfiles.yml vendored
View file

@ -4,12 +4,12 @@ on:
paths:
- software/picard/mergesamfiles/**
- .github/workflows/picard_mergesamfiles.yml
- tests
- tests/software/picard/**
pull_request:
paths:
- software/picard/mergesamfiles/**
- .github/workflows/picard_mergesamfiles.yml
- tests
- tests/software/picard/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/picard/mergesamfiles/test/ -profile docker
# Test the module
- run: pytest --tag picard_mergesamfiles --symlink --wt 2

26
.github/workflows/samtools_flagstat.yml vendored
View file

@ -4,12 +4,12 @@ on:
paths:
- software/samtools/flagstat/**
- .github/workflows/samtools_flagstat.yml
- tests
- tests/software/samtools/**
pull_request:
paths:
- software/samtools/flagstat/**
- .github/workflows/samtools_flagstat.yml
- tests
- tests/software/samtools/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/samtools/flagstat/test/ -profile docker
# Test the module
- run: pytest --tag samtools_flagstat --symlink --wt 2

26
.github/workflows/samtools_idxstats.yml vendored
View file

@ -4,12 +4,12 @@ on:
paths:
- software/samtools/idxstats/**
- .github/workflows/samtools_idxstats.yml
- tests
- tests/software/samtools/**
pull_request:
paths:
- software/samtools/idxstats/**
- .github/workflows/samtools_idxstats.yml
- tests
- tests/software/samtools/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/samtools/idxstats/test/ -profile docker
# Test the module
- run: pytest --tag samtools_idxstats --symlink --wt 2

26
.github/workflows/samtools_index.yml vendored
View file

@ -4,12 +4,12 @@ on:
paths:
- software/samtools/index/**
- .github/workflows/samtools_index.yml
- tests
- tests/software/samtools/**
pull_request:
paths:
- software/samtools/index/**
- .github/workflows/samtools_index.yml
- tests
- tests/software/samtools/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/samtools/index/test/ -profile docker
# Test the module
- run: pytest --tag samtools_index --symlink --wt 2

26
.github/workflows/samtools_sort.yml vendored
View file

@ -4,12 +4,12 @@ on:
paths:
- software/samtools/sort/**
- .github/workflows/samtools_sort.yml
- tests
- tests/software/samtools/**
pull_request:
paths:
- software/samtools/sort/**
- .github/workflows/samtools_sort.yml
- tests
- tests/software/samtools/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/samtools/sort/test/ -profile docker
# Test the module
- run: pytest --tag samtools_sort --symlink --wt 2

30
.github/workflows/samtools_stats.yml vendored
View file

@ -3,13 +3,13 @@ on:
push:
paths:
- software/samtools/stats/**
- .github/workflows/samtools_stats.yml
- tests
- .github/workflows/software/samtools_stats.yml
- tests/software/samtools/**
pull_request:
paths:
- software/samtools/stats/**
- .github/workflows/samtools_stats.yml
- tests
- .github/workflows/software/samtools_stats.yml
- tests/software/samtools/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/samtools/stats/test/ -profile docker
# Test the module
- run: pytest --tag samtools_stats --symlink --wt 2

26
.github/workflows/trimgalore.yml vendored
View file

@ -4,12 +4,12 @@ on:
paths:
- software/trimgalore/**
- .github/workflows/trimgalore.yml
- tests
- tests/software/trimgalore/**
pull_request:
paths:
- software/trimgalore/**
- .github/workflows/trimgalore.yml
- tests
- tests/software/trimgalore/**
jobs:
ci_test:
@ -17,14 +17,20 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: nextflow run ./software/trimgalore/test/ -profile docker
# Test the module
- run: pytest --tag trimgalore --symlink --wt 2

0
software/SOFTWARE/TOOL/test/input/soflink_test_data_here
View file

36
software/SOFTWARE/TOOL/test/main.nf
View file

@ -1,36 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { FASTQC as FASTQC_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { FASTQC as FASTQC_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/*
* Test with single-end data
*/
workflow test_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
FASTQC_SE ( input )
}
/*
* Test with paired-end data
*/
workflow test_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
FASTQC_PE ( input )
}
workflow {
test_single_end()
test_paired_end()
}

20
software/SOFTWARE/TOOL/test/nextflow.config
View file

@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

0
software/SOFTWARE/TOOL/test/output/upload_test_data_output_here
View file

1
software/bwa/index/test/input/NC_010473.fa
View file

@ -1 +0,0 @@
../../../../../tests/data/fasta/E_coli/NC_010473.fa

13
software/bwa/index/test/main.nf
View file

@ -1,13 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../main.nf' addParams( options: [:] )
workflow test {
BWA_INDEX ( file("${baseDir}/input/NC_010473.fa", checkIfExists: true) )
}
workflow {
test()
}

20
software/bwa/index/test/nextflow.config
View file

@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

3
software/bwa/index/test/output/bwa/NC_010473.fa.amb
View file

@ -1,3 +0,0 @@
4686137 1 2
20895 1 Y
142347 1 R

3
software/bwa/index/test/output/bwa/NC_010473.fa.ann
View file

@ -1,3 +0,0 @@
4686137 1 11
0 gi|170079663|ref|NC_010473.1| Escherichia coli str. K-12 substr. DH10B, complete genome
0 4686137 2

BIN
software/bwa/index/test/output/bwa/NC_010473.fa.bwt
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BIN
software/bwa/index/test/output/bwa/NC_010473.fa.pac
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BIN
software/bwa/index/test/output/bwa/NC_010473.fa.sa
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1
software/bwa/mem/test/input/Ecoli_DNA_R1.fastq.gz
View file

@ -1 +0,0 @@
../../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz

1
software/bwa/mem/test/input/Ecoli_DNA_R2.fastq.gz
View file

@ -1 +0,0 @@
../../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz

1
software/bwa/mem/test/input/NC_010473.fa
View file

@ -1 +0,0 @@
../../../../../tests/data/fasta/E_coli/NC_010473.fa

1
software/bwa/mem/test/input/index
View file

@ -1 +0,0 @@
../../../../../tests/data/index/E_coli/bwa/

44
software/bwa/mem/test/main.nf
View file

@ -1,44 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWA_MEM as BWA_MEM_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BWA_MEM as BWA_MEM_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/*
* Test with single-end data
*/
workflow test_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
BWA_MEM_SE (
input,
file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
)
}
/*
* Test with paired-end data
*/
workflow test_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${baseDir}/input/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
BWA_MEM_PE (
input,
file("${baseDir}/input/index/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
)
}
workflow {
test_single_end()
test_paired_end()
}

20
software/bwa/mem/test/nextflow.config
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@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

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1
software/picard/collectmultiplemetrics/test/input/NC_010473.fa
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@ -1 +0,0 @@
../../../../../tests/data/fasta/E_coli/NC_010473.fa

1
software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam
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../../../../../tests/data/bam/test.paired_end.sorted.bam

21
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf' addParams( options: [:] )
workflow test {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
PICARD_COLLECTMULTIPLEMETRICS (
input,
file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
)
}
workflow {
test()
}

20
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@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

12
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## htsjdk.samtools.metrics.StringHeader
# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Aug 07 15:24:11 GMT 2020
## METRICS CLASS picard.analysis.AlignmentSummaryMetrics
CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS PF_READS_IMPROPER_PAIRS PCT_PF_READS_IMPROPER_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP
FIRST_OF_PAIR 10000 10000 1 0 10000 1 1000000 9367 936700 936700 0 0 0 0 100 10000 1 0 0 0 0.5078 0 0
SECOND_OF_PAIR 10000 10000 1 0 10000 1 1000000 9366 936600 936600 0 0.000001 0.000001 0 100 10000 1 0 0 0 0.4922 0 0
PAIR 20000 20000 1 0 20000 1 2000000 18733 1873300 1873300 0 0.000001 0.000001 0 100 20000 1 0 0 0 0.5 0 0

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## htsjdk.samtools.metrics.StringHeader
# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Aug 07 15:24:11 GMT 2020
## METRICS CLASS picard.analysis.BaseDistributionByCycleMetrics
READ_END CYCLE PCT_A PCT_C PCT_G PCT_T PCT_N
1 1 24.74 25.02 25.61 24.63 0
1 2 25.5 23.74 25.96 24.8 0
1 3 24.91 25.4 24.96 24.73 0
1 4 25.44 25.36 24.59 24.61 0
1 5 25.33 25.28 25.04 24.35 0
1 6 24.94 25.83 25.25 23.98 0
1 7 24.26 25.58 26.45 23.71 0
1 8 23.87 26.45 25.17 24.51 0
1 9 24.03 26.08 25.7 24.19 0
1 10 24.8 24.8 25.34 25.06 0
1 11 25.03 25.07 24.86 25.04 0
1 12 24.37 25.97 25.25 24.41 0
1 13 25.16 24.85 25.59 24.4 0
1 14 24.27 25.69 25.79 24.25 0
1 15 24.69 25.93 25.62 23.76 0
1 16 24.86 25.94 24.97 24.23 0
1 17 24.38 25.68 25.18 24.76 0
1 18 24.03 25.63 25.9 24.44 0
1 19 24.48 24.89 25.72 24.91 0
1 20 24.06 25.07 25.75 25.12 0
1 21 24.76 25.39 24.4 25.45 0
1 22 25.18 25.02 24.66 25.14 0
1 23 24.54 25.44 25.83 24.19 0
1 24 23.7 26.35 25.59 24.36 0
1 25 23.81 24.86 25.83 25.5 0
1 26 24.57 25.78 25.11 24.54 0
1 27 24 25.53 25.8 24.67 0
1 28 24.32 25.76 25.36 24.56 0
1 29 24.57 25.03 26.21 24.19 0
1 30 25.44 25.05 24.7 24.81 0
1 31 24.16 25.28 25.86 24.7 0
1 32 24.45 25.24 25.21 25.1 0
1 33 24.47 26.17 24.98 24.38 0
1 34 24.95 24.47 26.38 24.2 0
1 35 24.46 26.59 24.82 24.13 0
1 36 24.35 25.45 25.7 24.5 0
1 37 24.54 25.05 25.9 24.51 0
1 38 24.82 26.59 24.4 24.19 0
1 39 24.37 25.48 25.59 24.56 0
1 40 24.93 25.4 25.17 24.5 0
1 41 24.6 25.51 24.78 25.11 0
1 42 24.33 26.16 25.04 24.47 0
1 43 25.01 25.57 25.51 23.91 0
1 44 24.57 25.52 25.48 24.43 0
1 45 24.62 25.32 25.59 24.47 0
1 46 24.53 25.4 25.15 24.92 0
1 47 24.59 25.66 24.94 24.81 0
1 48 23.81 25.76 25.33 25.1 0
1 49 25.35 25.7 23.8 25.15 0
1 50 24.53 25.21 25.47 24.79 0
1 51 24.03 25.69 25.92 24.36 0
1 52 23.98 25.01 25.99 25.02 0
1 53 24.46 25.5 25.59 24.45 0
1 54 24.41 25.73 25.45 24.41 0
1 55 25.18 25.19 25.45 24.18 0
1 56 24.18 25.49 25.72 24.61 0
1 57 24.08 25.49 25.41 25.02 0
1 58 24.1 25.35 25.38 25.17 0
1 59 24.58 25.58 25.39 24.45 0
1 60 24.67 25.22 25.47 24.64 0
1 61 24.09 25.56 25.36 24.99 0
1 62 25.2 25.47 25.68 23.65 0
1 63 24.47 25.4 25.28 24.85 0
1 64 24.8 25.45 25.4 24.35 0
1 65 25.08 26.2 24.91 23.81 0
1 66 24.89 24.74 25.37 25 0
1 67 25.1 25.13 25.01 24.76 0
1 68 24.73 25.3 25.13 24.84 0
1 69 24.94 25.18 25.2 24.68 0
1 70 24.29 25.21 25.62 24.88 0
1 71 24.21 26.3 25.72 23.77 0
1 72 24.39 25.61 25.34 24.66 0
1 73 25.29 24.55 25.67 24.49 0
1 74 25.66 25.07 24.54 24.73 0
1 75 24.26 26.19 24.81 24.74 0
1 76 24.04 24.89 26.43 24.64 0
1 77 25.01 25.04 25.04 24.91 0
1 78 24.37 26.53 25.05 24.05 0
1 79 24.6 25.35 25.69 24.36 0
1 80 24.9 25.32 25.33 24.45 0
1 81 25.1 26.14 24.64 24.12 0
1 82 23.95 25.9 25.23 24.92 0
1 83 24.73 25.25 25.41 24.61 0
1 84 24.81 25.43 25.68 24.08 0
1 85 24.73 24.72 25.57 24.98 0
1 86 24.12 25.26 25.17 25.45 0
1 87 24.68 25.94 25.17 24.21 0
1 88 24.77 25.11 25.88 24.24 0
1 89 24.09 25.62 25.34 24.95 0
1 90 24.35 25.57 24.76 25.32 0
1 91 25.17 25.07 25.31 24.45 0
1 92 25.65 25.04 25 24.31 0
1 93 25.04 25.51 25.04 24.41 0
1 94 24.85 26.17 25.11 23.87 0
1 95 24.81 25.37 25.5 24.32 0
1 96 24.84 25.25 25.47 24.44 0
1 97 24.61 25.47 25.27 24.65 0
1 98 24.86 25 25.48 24.66 0
1 99 23.74 25.3 25.96 25 0
1 100 23.83 26.06 25.13 24.98 0
2 101 24.05 25.38 26.27 24.3 0
2 102 23.62 25.98 25.49 24.91 0
2 103 23.93 25.62 26.32 24.13 0
2 104 24.94 25.34 25.24 24.48 0
2 105 24.69 25.34 25.35 24.62 0
2 106 24.69 24.97 25.08 25.26 0
2 107 24.1 25.17 26.68 24.05 0
2 108 24.92 25.49 24.96 24.63 0
2 109 24.23 25.94 24.81 25.02 0
2 110 24.38 25.12 25.59 24.91 0
2 111 24.42 25.6 25.75 24.23 0
2 112 25.33 25.73 24.96 23.98 0
2 113 25.35 24.51 26.17 23.97 0
2 114 24.12 25.34 26.17 24.37 0
2 115 24.77 25.23 25.13 24.87 0
2 116 25.36 25.27 25.1 24.27 0
2 117 24.88 24.93 25.68 24.51 0
2 118 23.79 25.75 25.19 25.27 0
2 119 24.43 25.82 24.93 24.82 0
2 120 24.4 25.93 24.62 25.05 0
2 121 25.88 24.75 25.12 24.25 0
2 122 24.27 25.8 24.92 25.01 0
2 123 24.61 25.95 25.28 24.16 0
2 124 24.66 25.46 25.69 24.19 0
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2 126 25.11 24.62 25.34 24.93 0
2 127 24.51 26.23 24.74 24.52 0
2 128 25.39 25.58 24.73 24.3 0
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2 168 24.04 25.06 25.86 25.04 0
2 169 24.44 25.11 25.49 24.95 0.01
2 170 24.47 25.75 25.4 24.38 0
2 171 24.31 25.94 25.55 24.2 0
2 172 25.19 25.19 25.29 24.33 0
2 173 24.78 25.82 25.31 24.09 0
2 174 24.65 25.8 25.01 24.54 0
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2 200 23.53 26.05 26.1 24.32 0

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## htsjdk.samtools.metrics.StringHeader
# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Aug 07 15:24:11 GMT 2020
## METRICS CLASS picard.analysis.InsertSizeMetrics
MEDIAN_INSERT_SIZE MODE_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_95_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP
236 117 82 69 404 234.8136 94.885497 10000 FR 35 67 99 133 165 199 231 263 295 313 329
## HISTOGRAM java.lang.Integer
insert_size All_Reads.fr_count
69 36
70 11
71 30
72 24
73 34
74 25
75 30
76 22
77 26
78 24
79 30
80 25
81 33
82 33
83 27
84 26
85 36
86 26
87 26
88 34
89 24
90 33
91 35
92 40
93 37
94 20
95 30
96 26
97 33
98 29
99 30
100 33
101 27
102 29
103 37
104 32
105 26
106 38
107 26
108 32
109 26
110 29
111 43
112 26
113 20
114 34
115 32
116 32
117 52
118 30
119 29
120 28
121 35
122 25
123 34
124 22
125 20
126 38
127 30
128 32
129 31
130 33
131 32
132 22
133 35
134 30
135 28
136 33
137 28
138 29
139 31
140 34
141 37
142 30
143 30
144 27
145 24
146 26
147 33
148 33
149 28
150 25
151 25
152 24
153 24
154 33
155 36
156 21
157 26
158 26
159 27
160 27
161 34
162 28
163 27
164 28
165 25
166 34
167 24
168 41
169 26
170 34
171 28
172 30
173 28
174 26
175 29
176 37
177 35
178 28
179 25
180 25
181 36
182 31
183 25
184 29
185 32
186 24
187 27
188 31
189 34
190 45
191 32
192 20
193 41
194 30
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196 24
197 36
198 27
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201 26
202 40
203 37
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205 28
206 33
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208 31
209 37
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215 29
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217 33
218 27
219 22
220 31
221 38
222 29
223 41
224 22
225 28
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227 26
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229 33
230 21
231 24
232 31
233 33
234 23
235 29
236 30
237 31
238 33
239 31
240 25
241 29
242 40
243 24
244 29
245 39
246 32
247 40
248 30
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250 32
251 22
252 33
253 33
254 27
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256 19
257 39
258 27
259 34
260 30
261 36
262 34
263 32
264 34
265 19
266 45
267 29
268 38
269 28
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272 35
273 31
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275 25
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278 31
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280 27
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284 19
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286 31
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289 42
290 34
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292 36
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295 29
296 26
297 19
298 37
299 24
300 29
301 25
302 26
303 43
304 31
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306 28
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308 35
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310 29
311 35
312 30
313 48
314 17
315 26
316 25
317 28
318 31
319 33
320 36
321 30
322 34
323 30
324 38
325 34
326 23
327 28
328 37
329 26
330 30
331 37
332 33
333 28
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335 37
336 42
337 30
338 33
339 32
340 37
341 26
342 37
343 29
344 23
345 35
346 25
347 33
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349 37
350 30
351 23
352 30
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355 30
356 28
357 26
358 31
359 28
360 27
361 32
362 30
363 26
364 29
365 40
366 33
367 38
368 27
369 34
370 43
371 27
372 35
373 27
374 24
375 30
376 36
377 24
378 30
379 35
380 26
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382 34
383 34
384 34
385 21
386 34
387 35
388 29
389 25
390 24
391 25
392 29
393 32
394 33
395 27
396 22
397 36
398 28
404 1

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## htsjdk.samtools.metrics.StringHeader
# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Aug 07 15:24:11 GMT 2020
## HISTOGRAM java.lang.Integer
CYCLE MEAN_QUALITY
1 40
2 40
3 40
4 40
5 40
6 40
7 40
8 40
9 40
10 40
11 40
12 40
13 40
14 40
15 40
16 40
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187 40
188 40
189 40
190 40
191 40
192 40
193 40
194 40
195 40
196 40
197 40
198 40
199 40
200 40

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software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
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software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
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## htsjdk.samtools.metrics.StringHeader
# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Aug 07 15:24:11 GMT 2020
## HISTOGRAM java.lang.Byte
QUALITY COUNT_OF_Q
40 1999999

1
software/picard/markduplicates/test/input/test.paired_end.sorted.bam
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../../../../../tests/data/bam/test.paired_end.sorted.bam

18
software/picard/markduplicates/test/main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_MARKDUPLICATES } from '../main.nf' addParams( options: [:] )
workflow test {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}
workflow {
test()
}

20
software/picard/markduplicates/test/nextflow.config
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params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

13
software/picard/markduplicates/test/output/picard/test.MarkDuplicates.metrics.txt
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@ -1,13 +0,0 @@
## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[test.paired_end.sorted.bam] OUTPUT=test.bam METRICS_FILE=test.MarkDuplicates.metrics.txt MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Aug 07 15:11:32 GMT 2020
## METRICS CLASS picard.sam.DuplicationMetrics
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
Unknown Library 0 10000 0 0 0 0 0 0
## HISTOGRAM java.lang.Double
set_size all_sets non_optical_sets
1.0 10000 10000

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1
software/picard/mergesamfiles/test/input/test.paired_end.COPY.sorted.bam
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../../../../../tests/data/bam/test.paired_end.sorted.bam

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../../../../../tests/data/bam/test.paired_end.sorted.bam

19
software/picard/mergesamfiles/test/main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_MERGESAMFILES } from '../main.nf' addParams( options: [:] )
workflow test {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
file("${baseDir}/input/test.paired_end.COPY.sorted.bam", checkIfExists: true), ] ]
PICARD_MERGESAMFILES ( input )
}
workflow {
test()
}

20
software/picard/mergesamfiles/test/nextflow.config
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params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

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../../../../../tests/data/bam/test.paired_end.sorted.bam

1
software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai
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../../../../../tests/data/bam/test.paired_end.sorted.bam.bai

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software/samtools/flagstat/test/main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_FLAGSTAT } from '../main.nf' addParams( options: [:] )
workflow test {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_FLAGSTAT ( input )
}
workflow {
test()
}

20
software/samtools/flagstat/test/nextflow.config
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@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

13
software/samtools/flagstat/test/output/samtools/test.paired_end.sorted.bam.flagstat
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20000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
20000 + 0 mapped (100.00% : N/A)
20000 + 0 paired in sequencing
10000 + 0 read1
10000 + 0 read2
20000 + 0 properly paired (100.00% : N/A)
20000 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

1
software/samtools/idxstats/test/input/test.paired_end.sorted.bam
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../../../../../tests/data/bam/test.paired_end.sorted.bam

1
software/samtools/idxstats/test/input/test.paired_end.sorted.bam.bai
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../../../../../tests/data/bam/test.paired_end.sorted.bam.bai

19
software/samtools/idxstats/test/main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_IDXSTATS } from '../main.nf' addParams( options: [:] )
workflow test {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_IDXSTATS ( input )
}
workflow {
test()
}

20
software/samtools/idxstats/test/nextflow.config
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@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

2
software/samtools/idxstats/test/output/samtools/test.paired_end.sorted.bam.idxstats
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@ -1,2 +0,0 @@
gi|170079663|ref|NC_010473.1| 4686137 20000 0
* 0 0 0

1
software/samtools/index/test/input/test.paired_end.sorted.bam
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../../../../../tests/data/bam/test.paired_end.sorted.bam

18
software/samtools/index/test/main.nf
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@ -1,18 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_INDEX } from '../main.nf' addParams( options: [:] )
workflow test {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_INDEX ( input )
}
workflow {
test()
}

20
software/samtools/index/test/nextflow.config
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@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

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1
software/samtools/sort/test/input/test.paired_end.name.sorted.bam
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../../../../../tests/data/bam/test.paired_end.name.sorted.bam

18
software/samtools/sort/test/main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_SORT } from '../main.nf' addParams( options: [:] )
workflow test {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.name.sorted.bam", checkIfExists: true) ]
SAMTOOLS_SORT ( input )
}
workflow {
test()
}

20
software/samtools/sort/test/nextflow.config
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@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

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software/samtools/stats/test/input/test.paired_end.sorted.bam
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../../../../../tests/data/bam/test.paired_end.sorted.bam

1
software/samtools/stats/test/input/test.paired_end.sorted.bam.bai
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../../../../../tests/data/bam/test.paired_end.sorted.bam.bai

19
software/samtools/stats/test/main.nf
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@ -1,19 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_STATS } from '../main.nf' addParams( options: [:] )
workflow test {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_STATS ( input )
}
workflow {
test()
}

20
software/samtools/stats/test/nextflow.config
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@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

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1
software/trimgalore/test/input/test_R1.fastq.gz
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../../../../tests/data/fastq/rna/test_R1.fastq.gz

1
software/trimgalore/test/input/test_R2.fastq.gz
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../../../../tests/data/fastq/rna/test_R2.fastq.gz

1
software/trimgalore/test/input/test_single_end.fastq.gz
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../../../../tests/data/fastq/rna/test_single_end.fastq.gz

36
software/trimgalore/test/main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { TRIMGALORE as TRIMGALORE_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { TRIMGALORE as TRIMGALORE_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/*
* Test with single-end data
*/
workflow test_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE_SE ( input )
}
/*
* Test with paired-end data
*/
workflow test_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE_PE ( input )
}
workflow {
test_single_end()
test_paired_end()
}

25
software/trimgalore/test/nextflow.config
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params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
clip_r1 = 0
clip_r2 = 0
three_prime_clip_r1 = 0
three_prime_clip_r2 = 0
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

97
software/trimgalore/test/output/test_paired_end/test_1.fastq.gz_trimming_report.txt
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SUMMARISING RUN PARAMETERS
==========================
Input filename: test_1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.4_dev
Cutadapt version: 2.6
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Nextera adapter for trimming (count: 83). Second best hit was Illumina (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file will be GZIP compressed
This is cutadapt 2.6 with Python 3.7.3
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_1.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.64 s (64 us/read; 0.94 M reads/minute).
=== Summary ===
Total reads processed: 10,000
Reads with adapters: 3,225 (32.2%)
Reads written (passing filters): 10,000 (100.0%)
Total basepairs processed: 760,000 bp
Quality-trimmed: 4,492 bp (0.6%)
Total written (filtered): 748,403 bp (98.5%)
=== Adapter 1 ===
Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3225 times.
No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1
Bases preceding removed adapters:
A: 23.8%
C: 28.2%
G: 22.7%
T: 25.3%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
1 2170 2500.0 0 2170
2 622 625.0 0 622
3 223 156.2 0 223
4 64 39.1 0 64
5 14 9.8 0 14
6 9 2.4 0 9
7 8 0.6 0 8
8 5 0.2 0 5
9 4 0.0 0 4
10 8 0.0 1 7 1
11 3 0.0 1 3
12 4 0.0 1 4
13 6 0.0 1 6
14 5 0.0 1 4 1
15 5 0.0 1 5
16 6 0.0 1 5 1
17 3 0.0 1 3
18 3 0.0 1 3
19 1 0.0 1 1
20 3 0.0 1 3
21 7 0.0 1 7
22 7 0.0 1 7
23 3 0.0 1 3
24 6 0.0 1 6
25 4 0.0 1 4
26 2 0.0 1 2
27 4 0.0 1 4
28 1 0.0 1 1
29 3 0.0 1 3
30 4 0.0 1 4
32 3 0.0 1 3
33 2 0.0 1 1 1
34 1 0.0 1 1
35 1 0.0 1 1
40 1 0.0 1 1
42 1 0.0 1 0 1
45 1 0.0 1 0 1
49 1 0.0 1 0 1
52 1 0.0 1 0 1
56 2 0.0 1 0 2
59 1 0.0 1 0 1
67 1 0.0 1 0 1
70 2 0.0 1 0 2
RUN STATISTICS FOR INPUT FILE: test_1.fastq.gz
=============================================
10000 sequences processed in total

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software/trimgalore/test/output/test_paired_end/test_2.fastq.gz_trimming_report.txt
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SUMMARISING RUN PARAMETERS
==========================
Input filename: test_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.4_dev
Cutadapt version: 2.6
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Nextera adapter for trimming (count: 83). Second best hit was Illumina (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file will be GZIP compressed
This is cutadapt 2.6 with Python 3.7.3
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_2.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.70 s (70 us/read; 0.86 M reads/minute).
=== Summary ===
Total reads processed: 10,000
Reads with adapters: 3,295 (33.0%)
Reads written (passing filters): 10,000 (100.0%)
Total basepairs processed: 760,000 bp
Quality-trimmed: 7,096 bp (0.9%)
Total written (filtered): 745,649 bp (98.1%)
=== Adapter 1 ===
Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3295 times.
No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1
Bases preceding removed adapters:
A: 22.6%
C: 28.2%
G: 23.6%
T: 25.6%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
1 2213 2500.0 0 2213
2 647 625.0 0 647
3 239 156.2 0 239
4 53 39.1 0 53
5 10 9.8 0 10
6 7 2.4 0 7
7 8 0.6 0 8
8 5 0.2 0 5
9 5 0.0 0 5
10 10 0.0 1 8 2
11 2 0.0 1 2
12 4 0.0 1 4
13 7 0.0 1 7
14 3 0.0 1 3
15 4 0.0 1 4
16 5 0.0 1 5
17 3 0.0 1 3
18 5 0.0 1 4 1
19 2 0.0 1 1 1
20 3 0.0 1 3
21 7 0.0 1 7
22 6 0.0 1 6
23 3 0.0 1 3
24 7 0.0 1 7
25 4 0.0 1 4
26 2 0.0 1 2
27 4 0.0 1 4
28 1 0.0 1 1
29 3 0.0 1 3
30 4 0.0 1 4
32 3 0.0 1 3
33 1 0.0 1 1
34 1 0.0 1 1
35 2 0.0 1 1 1
40 1 0.0 1 0 1
41 1 0.0 1 1
46 1 0.0 1 0 1
48 1 0.0 1 0 1
49 2 0.0 1 0 2
56 2 0.0 1 0 2
59 1 0.0 1 0 1
70 1 0.0 1 0 1
73 2 0.0 1 0 2
RUN STATISTICS FOR INPUT FILE: test_2.fastq.gz
=============================================
10000 sequences processed in total
Total number of sequences analysed for the sequence pair length validation: 10000
Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21 (0.21%)

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61
software/trimgalore/test/output/test_single_end/test.fastq.gz_trimming_report.txt
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SUMMARISING RUN PARAMETERS
==========================
Input filename: test.fastq.gz
Trimming mode: single-end
Trim Galore version: 0.6.4_dev
Cutadapt version: 2.6
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count smallRNA: 0, count Nextera: 0)
Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp
Output file will be GZIP compressed
This is cutadapt 2.6 with Python 3.7.3
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.06 s (28 us/read; 2.13 M reads/minute).
=== Summary ===
Total reads processed: 2,052
Reads with adapters: 223 (10.9%)
Reads written (passing filters): 2,052 (100.0%)
Total basepairs processed: 103,432 bp
Quality-trimmed: 11 bp (0.0%)
Total written (filtered): 103,117 bp (99.7%)
=== Adapter 1 ===
Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 223 times.
No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1
Bases preceding removed adapters:
A: 31.8%
C: 37.7%
G: 16.1%
T: 14.3%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
1 190 513.0 0 190
2 3 128.2 0 3
3 16 32.1 0 16
4 10 8.0 0 10
5 4 2.0 0 4
RUN STATISTICS FOR INPUT FILE: test.fastq.gz
=============================================
2052 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%)

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software/trimgalore/test/output/test_single_end/test_trimmed.fq.gz
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tests/software/bwa/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] )
include { BWA_MEM as BWA_MEM_SE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BWA_MEM as BWA_MEM_PE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
workflow test_bwa_index {
BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
}
/*
* Test with single-end data
*/
workflow test_bwa_mem_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
BWA_MEM_SE (
input,
file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
)
}
/*
* Test with paired-end data
*/
workflow test_bwa_mem_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
BWA_MEM_PE (
input,
file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
)
}

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tests/software/bwa/test.yml Normal file
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- name: Run bwa index
command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config
tags:
- bwa
- bwa_index
files:
- path: output/bwa/NC_010473.fa.amb
md5sum: 942a990ae872f1c0b8d72dda2db405d5
- path: output/bwa/NC_010473.fa.bwt
md5sum: 7301b52e2ecb893d429a49fa692447ae
- path: output/bwa/NC_010473.fa.pac
md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
- path: output/bwa/NC_010473.fa.sa
md5sum: a47dcc92e750e2f16fbd979b8ff9538e
- name: Run bwa mem single-end
command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config
tags:
- bwa
- bwa_mem
files:
- path: output/test_single_end/test.bam
md5sum: 3ee21210bac387e0335008146e4728bc
- name: Run bwa mem paired-end
command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
tags:
- bwa
- bwa_mem
files:
- path: output/test_paired_end/test.bam
md5sum: 510d8acc6448c07cdacce8e64ec0904c

2
tests/software/fastqc/main.nf
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@ -29,3 +29,5 @@ workflow test_paired_end {
FASTQC_PE ( input )
}
// TODO Test e2e

3
tests/software/fastqc/test.yml
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@ -4,7 +4,6 @@
- fastqc
files:
- path: output/test_single_end/test_fastqc.html
md5sum: 7027e72c3e55292c1567f12e02565e3b
- path: output/test_single_end/test_fastqc.zip
- name: Run fastqc paired-end test workflow
@ -13,8 +12,6 @@
- fastqc
files:
- path: output/test_paired_end/test_1_fastqc.html
md5sum: b3796b4323dc34970b7461f813135254
- path: output/test_paired_end/test_2_fastqc.html
md5sum: 55182467f48ca5ed88a2608ea57a1afc
- path: output/test_paired_end/test_1_fastqc.zip
- path: output/test_paired_end/test_2_fastqc.zip

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] )
workflow test_picard_mergesamfiles {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true), ] ]
PICARD_MERGESAMFILES ( input )
}
workflow test_picard_collectmultiplemetrics {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
PICARD_COLLECTMULTIPLEMETRICS (
input,
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
)
}
workflow test_picard_markduplicates {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}
workflow test_picard_markduplicates_not_sorted {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}

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- name: Run picard mergesamfiles
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_mergesamfiles -c tests/config/nextflow.config
tags:
- picard
- picard_mergesamfiles
files:
- path: output/picard/test.bam
md5sum: a9c8a28d1aac362df5973ba2d9923f86
- name: Run picard collectmultiplemetrics
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
tags:
- picard
- picard_collectmultiplemetrics
files:
# These can't be md5'd consistently
- path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
- name: Run picard MarkDuplicates
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates -c tests/config/nextflow.config
tags:
- picard
- picard_markduplicates
files:
- path: output/picard/test.MarkDuplicates.metrics.txt
- path: output/picard/test.bam
md5sum: 50407a1ee722f2bf6a20471c8a7fd6b0
- name: Run picard MarkDuplicates without a sorted bam file so it fails
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
tags:
- picard
- picard_markduplicates
- should fail
exit_code: 1

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] )
include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] )
workflow test_samtools_flagstat {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_FLAGSTAT ( input )
}
workflow test_samtools_idxstats {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_IDXSTATS ( input )
}
workflow test_samtools_index {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_INDEX ( input )
}
// FIXME Why is this passing it an already sorted bam?
workflow test_samtools_sort {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
SAMTOOLS_SORT ( input )
}
workflow test_samtools_stats {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_STATS ( input )
}

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- name: Run samtools flagstat test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config
tags:
- samtools
- samtools_flagstat
files:
- path: output/samtools/test.paired_end.sorted.bam.flagstat
md5sum: 80590621c74f5ee43ada20d010a3837f
- name: Run samtools idxstats test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config
tags:
- samtools
- samtools_idxstats
files:
- path: output/samtools/test.paired_end.sorted.bam.idxstats
md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
- name: Run samtools index test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config
tags:
- samtools
- samtools_index
files:
- path: output/samtools/test.paired_end.sorted.bam.bai
md5sum: 67338c2995eae82c849830ca55aa7bd1
- name: Run samtools sort test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config
tags:
- samtools
- samtools_sort
files:
- path: output/samtools/test.bam
md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
- name: Run samtools stats test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config
tags:
- samtools
- samtools_stats
files:
- path: output/samtools/test.paired_end.sorted.bam.stats
md5sum: 06c183864d6e47ab89b0650cae831a93

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tests/software/trimgalore/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { TRIMGALORE as TRIMGALORE_SE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { TRIMGALORE as TRIMGALORE_PE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/*
* Test with single-end data
*/
workflow test_trimgalore_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
TRIMGALORE_SE ( input )
}
// workflow test_trimgalore_single_end {
// def input = []
// input = [ [ id:'test', single_end:false ], // meta map
// [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
// TRIMGALORE_SE ( input )
// }
/*
* Test with paired-end data
*/
workflow test_trimgalore_paired_end {
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) ] ]
TRIMGALORE_PE ( input )
}

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tests/software/trimgalore/test.yml Normal file
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- name: Run trimgalore single-end test workflow
command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_single_end -c tests/config/nextflow.config
tags:
- trimgalore
files:
# These can't be md5'd reliably
# TODO Test for includes
- path: output/test_single_end/test.fastq.gz_trimming_report.txt
- path: output/test_single_end/test_trimmed.fq.gz
- name: Run trimgalore paired-end test workflow
command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_paired_end -c tests/config/nextflow.config
tags:
- trimgalore
files:
# These can't be md5'd reliably
# TODO Test for includes
- path: output/test_paired_end/test_1.fastq.gz_trimming_report.txt
- path: output/test_paired_end/test_1_val_1.fq.gz
- path: output/test_paired_end/test_2.fastq.gz_trimming_report.txt
- path: output/test_paired_end/test_2_val_2.fq.gz