mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
Merge pull request #85 from nf-core/pytest-workflow-refactor
Refactor all tests to use pytest-workflow
This commit is contained in:
Harshil Patel
GitHub
commit
cd2cf9cf2f
100 changed files with 543 additions and 2925 deletions
14
.github/workflows/bwa_index.yml
vendored
14
.github/workflows/bwa_index.yml
vendored
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/bwa/index/**
|
- software/bwa/index/**
|
||||||
- .github/workflows/bwa_index.yml
|
- .github/workflows/bwa_index.yml
|
||||||
- tests
|
- tests/software/bwa/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/bwa/index/**
|
- software/bwa/index/**
|
||||||
- .github/workflows/bwa_index.yml
|
- .github/workflows/bwa_index.yml
|
||||||
- tests
|
- tests/software/bwa/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/bwa/index/test/ -profile docker
|
- run: pytest --tag bwa_index --symlink --wt 2
|
||||||
|
|
|
||||||
14
.github/workflows/bwa_mem.yml
vendored
14
.github/workflows/bwa_mem.yml
vendored
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/bwa/mem/**
|
- software/bwa/mem/**
|
||||||
- .github/workflows/bwa_mem.yml
|
- .github/workflows/bwa_mem.yml
|
||||||
- tests
|
- tests/software/bwa/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/bwa/mem/**
|
- software/bwa/mem/**
|
||||||
- .github/workflows/bwa_mem.yml
|
- .github/workflows/bwa_mem.yml
|
||||||
- tests
|
- tests/software/bwa/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/bwa/mem/test/ -profile docker
|
- run: pytest --tag bwa_index --symlink --wt 2
|
||||||
|
|
|
||||||
54
.github/workflows/docker.yml
vendored
54
.github/workflows/docker.yml
vendored
|
|
@ -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;
|
|
||||||
11
.github/workflows/fastqc.yml
vendored
11
.github/workflows/fastqc.yml
vendored
|
|
@ -4,25 +4,28 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/fastqc/**
|
- software/fastqc/**
|
||||||
- .github/workflows/fastqc.yml
|
- .github/workflows/fastqc.yml
|
||||||
- tests
|
- tests/software/fastqc/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/fastqc/**
|
- software/fastqc/**
|
||||||
- .github/workflows/fastqc.yml
|
- .github/workflows/fastqc.yml
|
||||||
- tests
|
- tests/software/fastqc/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
runs-on: ubuntu-latest
|
runs-on: ubuntu-latest
|
||||||
|
strategy:
|
||||||
|
matrix:
|
||||||
|
nxf_version: [20.07.1, '']
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
env:
|
||||||
|
NXF_VER: ${{ matrix.nxf_version }}
|
||||||
run: |
|
run: |
|
||||||
export NXF_VER="20.07.1"
|
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
sudo mv nextflow /usr/local/bin/
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/picard/collectmultiplemetrics/**
|
- software/picard/collectmultiplemetrics/**
|
||||||
- .github/workflows/picard_collectmultiplemetrics.yml
|
- .github/workflows/picard_collectmultiplemetrics.yml
|
||||||
- tests
|
- tests/software/picard/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/picard/collectmultiplemetrics/**
|
- software/picard/collectmultiplemetrics/**
|
||||||
- .github/workflows/picard_collectmultiplemetrics.yml
|
- .github/workflows/picard_collectmultiplemetrics.yml
|
||||||
- tests
|
- tests/software/picard/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/picard/collectmultiplemetrics/test/ -profile docker
|
- run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2
|
||||||
|
|
|
||||||
14
.github/workflows/picard_markduplicates.yml
vendored
14
.github/workflows/picard_markduplicates.yml
vendored
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/picard/markduplicates/**
|
- software/picard/markduplicates/**
|
||||||
- .github/workflows/picard_markduplicates.yml
|
- .github/workflows/picard_markduplicates.yml
|
||||||
- tests
|
- tests/software/picard/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/picard/markduplicates/**
|
- software/picard/markduplicates/**
|
||||||
- .github/workflows/picard_markduplicates.yml
|
- .github/workflows/picard_markduplicates.yml
|
||||||
- tests
|
- tests/software/picard/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/picard/markduplicates/test/ -profile docker
|
- run: pytest --tag picard_markduplicates --symlink --wt 2
|
||||||
|
|
|
||||||
14
.github/workflows/picard_mergesamfiles.yml
vendored
14
.github/workflows/picard_mergesamfiles.yml
vendored
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/picard/mergesamfiles/**
|
- software/picard/mergesamfiles/**
|
||||||
- .github/workflows/picard_mergesamfiles.yml
|
- .github/workflows/picard_mergesamfiles.yml
|
||||||
- tests
|
- tests/software/picard/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/picard/mergesamfiles/**
|
- software/picard/mergesamfiles/**
|
||||||
- .github/workflows/picard_mergesamfiles.yml
|
- .github/workflows/picard_mergesamfiles.yml
|
||||||
- tests
|
- tests/software/picard/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/picard/mergesamfiles/test/ -profile docker
|
- run: pytest --tag picard_mergesamfiles --symlink --wt 2
|
||||||
|
|
|
||||||
14
.github/workflows/samtools_flagstat.yml
vendored
14
.github/workflows/samtools_flagstat.yml
vendored
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/flagstat/**
|
- software/samtools/flagstat/**
|
||||||
- .github/workflows/samtools_flagstat.yml
|
- .github/workflows/samtools_flagstat.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/flagstat/**
|
- software/samtools/flagstat/**
|
||||||
- .github/workflows/samtools_flagstat.yml
|
- .github/workflows/samtools_flagstat.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/samtools/flagstat/test/ -profile docker
|
- run: pytest --tag samtools_flagstat --symlink --wt 2
|
||||||
|
|
|
||||||
14
.github/workflows/samtools_idxstats.yml
vendored
14
.github/workflows/samtools_idxstats.yml
vendored
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/idxstats/**
|
- software/samtools/idxstats/**
|
||||||
- .github/workflows/samtools_idxstats.yml
|
- .github/workflows/samtools_idxstats.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/idxstats/**
|
- software/samtools/idxstats/**
|
||||||
- .github/workflows/samtools_idxstats.yml
|
- .github/workflows/samtools_idxstats.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/samtools/idxstats/test/ -profile docker
|
- run: pytest --tag samtools_idxstats --symlink --wt 2
|
||||||
|
|
|
||||||
14
.github/workflows/samtools_index.yml
vendored
14
.github/workflows/samtools_index.yml
vendored
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/index/**
|
- software/samtools/index/**
|
||||||
- .github/workflows/samtools_index.yml
|
- .github/workflows/samtools_index.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/index/**
|
- software/samtools/index/**
|
||||||
- .github/workflows/samtools_index.yml
|
- .github/workflows/samtools_index.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/samtools/index/test/ -profile docker
|
- run: pytest --tag samtools_index --symlink --wt 2
|
||||||
|
|
|
||||||
14
.github/workflows/samtools_sort.yml
vendored
14
.github/workflows/samtools_sort.yml
vendored
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/sort/**
|
- software/samtools/sort/**
|
||||||
- .github/workflows/samtools_sort.yml
|
- .github/workflows/samtools_sort.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/sort/**
|
- software/samtools/sort/**
|
||||||
- .github/workflows/samtools_sort.yml
|
- .github/workflows/samtools_sort.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/samtools/sort/test/ -profile docker
|
- run: pytest --tag samtools_sort --symlink --wt 2
|
||||||
|
|
|
||||||
18
.github/workflows/samtools_stats.yml
vendored
18
.github/workflows/samtools_stats.yml
vendored
|
|
@ -3,13 +3,13 @@ on:
|
||||||
push:
|
push:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/stats/**
|
- software/samtools/stats/**
|
||||||
- .github/workflows/samtools_stats.yml
|
- .github/workflows/software/samtools_stats.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/samtools/stats/**
|
- software/samtools/stats/**
|
||||||
- .github/workflows/samtools_stats.yml
|
- .github/workflows/software/samtools_stats.yml
|
||||||
- tests
|
- tests/software/samtools/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/samtools/stats/test/ -profile docker
|
- run: pytest --tag samtools_stats --symlink --wt 2
|
||||||
|
|
|
||||||
14
.github/workflows/trimgalore.yml
vendored
14
.github/workflows/trimgalore.yml
vendored
|
|
@ -4,12 +4,12 @@ on:
|
||||||
paths:
|
paths:
|
||||||
- software/trimgalore/**
|
- software/trimgalore/**
|
||||||
- .github/workflows/trimgalore.yml
|
- .github/workflows/trimgalore.yml
|
||||||
- tests
|
- tests/software/trimgalore/**
|
||||||
pull_request:
|
pull_request:
|
||||||
paths:
|
paths:
|
||||||
- software/trimgalore/**
|
- software/trimgalore/**
|
||||||
- .github/workflows/trimgalore.yml
|
- .github/workflows/trimgalore.yml
|
||||||
- tests
|
- tests/software/trimgalore/**
|
||||||
|
|
||||||
jobs:
|
jobs:
|
||||||
ci_test:
|
ci_test:
|
||||||
|
|
@ -17,7 +17,6 @@ jobs:
|
||||||
env:
|
env:
|
||||||
NXF_ANSI_LOG: false
|
NXF_ANSI_LOG: false
|
||||||
steps:
|
steps:
|
||||||
|
|
||||||
- uses: actions/checkout@v2
|
- uses: actions/checkout@v2
|
||||||
|
|
||||||
- name: Install Nextflow
|
- name: Install Nextflow
|
||||||
|
|
@ -26,5 +25,12 @@ jobs:
|
||||||
wget -qO- get.nextflow.io | bash
|
wget -qO- get.nextflow.io | bash
|
||||||
sudo mv nextflow /usr/local/bin/
|
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
|
# Test the module
|
||||||
- run: nextflow run ./software/trimgalore/test/ -profile docker
|
- run: pytest --tag trimgalore --symlink --wt 2
|
||||||
|
|
|
||||||
|
|
@ -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()
|
|
||||||
}
|
|
||||||
|
|
@ -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
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/fasta/E_coli/NC_010473.fa
|
|
||||||
|
|
@ -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("${baseDir}/input/NC_010473.fa", checkIfExists: true) )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow {
|
|
||||||
test()
|
|
||||||
}
|
|
||||||
|
|
@ -1,20 +0,0 @@
|
||||||
|
|
||||||
params {
|
|
||||||
outdir = "output/"
|
|
||||||
publish_dir_mode = "copy"
|
|
||||||
enable_conda = false
|
|
||||||
}
|
|
||||||
|
|
||||||
profiles {
|
|
||||||
conda {
|
|
||||||
params.enable_conda = true
|
|
||||||
}
|
|
||||||
docker {
|
|
||||||
docker.enabled = true
|
|
||||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
|
||||||
}
|
|
||||||
singularity {
|
|
||||||
singularity.enabled = true
|
|
||||||
singularity.autoMounts = true
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,3 +0,0 @@
|
||||||
4686137 1 2
|
|
||||||
20895 1 Y
|
|
||||||
142347 1 R
|
|
||||||
|
|
@ -1,3 +0,0 @@
|
||||||
4686137 1 11
|
|
||||||
0 gi|170079663|ref|NC_010473.1| Escherichia coli str. K-12 substr. DH10B, complete genome
|
|
||||||
0 4686137 2
|
|
||||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/fasta/E_coli/NC_010473.fa
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/index/E_coli/bwa/
|
|
||||||
|
|
@ -1,44 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { BWA_MEM as BWA_MEM_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
|
|
||||||
include { BWA_MEM as BWA_MEM_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Test with single-end data
|
|
||||||
*/
|
|
||||||
workflow test_single_end {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:true ], // meta map
|
|
||||||
[ file("${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()
|
|
||||||
}
|
|
||||||
|
|
@ -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
|
|
||||||
}
|
|
||||||
}
|
|
||||||
Binary file not shown.
Binary file not shown.
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/fasta/E_coli/NC_010473.fa
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam
|
|
||||||
|
|
@ -1,21 +0,0 @@
|
||||||
#!/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()
|
|
||||||
}
|
|
||||||
|
|
@ -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
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,12 +0,0 @@
|
||||||
## 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
|
|
||||||
|
|
||||||
|
|
||||||
Binary file not shown.
|
|
@ -1,209 +0,0 @@
|
||||||
## 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
|
|
||||||
2 125 24.09 25.61 25.73 24.57 0
|
|
||||||
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
|
|
||||||
2 129 24.85 25.62 24.9 24.63 0
|
|
||||||
2 130 24.43 25.89 25.15 24.53 0
|
|
||||||
2 131 24.7 25.53 25.58 24.19 0
|
|
||||||
2 132 24.5 26.2 25.01 24.29 0
|
|
||||||
2 133 23.88 25.74 25.43 24.95 0
|
|
||||||
2 134 24.9 25.2 25.18 24.72 0
|
|
||||||
2 135 24.16 25.63 25.75 24.46 0
|
|
||||||
2 136 23.8 25.87 25.42 24.91 0
|
|
||||||
2 137 24.96 25.03 26.27 23.74 0
|
|
||||||
2 138 24.53 25.69 24.99 24.79 0
|
|
||||||
2 139 23.96 25.89 24.7 25.45 0
|
|
||||||
2 140 24.13 24.91 25.68 25.28 0
|
|
||||||
2 141 24.32 25.44 25.03 25.21 0
|
|
||||||
2 142 24.23 25.86 24.69 25.22 0
|
|
||||||
2 143 24.44 25.74 24.6 25.22 0
|
|
||||||
2 144 25.39 24.13 25.44 25.04 0
|
|
||||||
2 145 24.68 25.9 25.28 24.14 0
|
|
||||||
2 146 23.85 25.25 25.61 25.29 0
|
|
||||||
2 147 25.2 23.57 26.09 25.14 0
|
|
||||||
2 148 25.49 25.2 25.07 24.24 0
|
|
||||||
2 149 25.12 25.47 25.15 24.26 0
|
|
||||||
2 150 24.73 25.26 25.44 24.57 0
|
|
||||||
2 151 25.43 25.54 24.96 24.07 0
|
|
||||||
2 152 25.03 25.6 24.97 24.4 0
|
|
||||||
2 153 25.63 25.45 24.67 24.25 0
|
|
||||||
2 154 24.32 25.73 25.33 24.62 0
|
|
||||||
2 155 23.73 25.22 25.57 25.48 0
|
|
||||||
2 156 23.82 25.86 26.08 24.24 0
|
|
||||||
2 157 24.82 24.65 25.22 25.31 0
|
|
||||||
2 158 24.96 25.77 24.82 24.45 0
|
|
||||||
2 159 24.16 26.01 25.42 24.41 0
|
|
||||||
2 160 24.57 25.49 25.27 24.67 0
|
|
||||||
2 161 24.56 25.46 25.66 24.32 0
|
|
||||||
2 162 24.85 24.93 25.01 25.21 0
|
|
||||||
2 163 24.54 24.82 25.87 24.77 0
|
|
||||||
2 164 24.88 25.37 25.67 24.08 0
|
|
||||||
2 165 24.49 25.02 26.39 24.1 0
|
|
||||||
2 166 24.03 25.21 25.87 24.89 0
|
|
||||||
2 167 24.37 24.94 25.79 24.9 0
|
|
||||||
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
|
|
||||||
2 175 24.7 25.09 25.57 24.64 0
|
|
||||||
2 176 24.75 25 24.93 25.32 0
|
|
||||||
2 177 24.61 25.39 25.07 24.93 0
|
|
||||||
2 178 24.64 25.38 25.92 24.06 0
|
|
||||||
2 179 25.21 25.97 24.86 23.96 0
|
|
||||||
2 180 23.95 26.44 25.54 24.07 0
|
|
||||||
2 181 25.06 25.25 26.07 23.62 0
|
|
||||||
2 182 23.91 26.04 25.25 24.8 0
|
|
||||||
2 183 25.01 25.52 25.44 24.03 0
|
|
||||||
2 184 25.19 25.68 24.67 24.46 0
|
|
||||||
2 185 24.81 25.27 24.82 25.1 0
|
|
||||||
2 186 24.31 25.78 24.9 25.01 0
|
|
||||||
2 187 24.94 24.98 25.55 24.53 0
|
|
||||||
2 188 25.25 25.77 25.32 23.66 0
|
|
||||||
2 189 25.07 25.91 24.94 24.08 0
|
|
||||||
2 190 24.64 25.42 26.18 23.76 0
|
|
||||||
2 191 24.92 25.38 25.24 24.46 0
|
|
||||||
2 192 24.47 25.18 25.08 25.27 0
|
|
||||||
2 193 25.02 25.58 24.58 24.82 0
|
|
||||||
2 194 24.05 25.41 24.94 25.6 0
|
|
||||||
2 195 24.91 25.05 25.08 24.96 0
|
|
||||||
2 196 24.1 25.22 25.74 24.94 0
|
|
||||||
2 197 24.56 24.56 25.68 25.2 0
|
|
||||||
2 198 25.34 25.16 25.36 24.14 0
|
|
||||||
2 199 24.8 25.47 25.7 24.03 0
|
|
||||||
2 200 23.53 26.05 26.1 24.32 0
|
|
||||||
|
|
||||||
|
|
||||||
Binary file not shown.
|
|
@ -1,343 +0,0 @@
|
||||||
## 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
|
|
||||||
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404 1
|
|
||||||
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|
||||||
Binary file not shown.
|
|
@ -1,209 +0,0 @@
|
||||||
## 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
|
|
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1 40
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|
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|
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|
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|
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|
|
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|
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|
|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
|
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|
|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
|
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|
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|
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|
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|
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|
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|
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|
|
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|
|
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|
|
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|
|
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|
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|
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|
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|
|
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|
|
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|
|
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|
|
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|
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|
|
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|
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|
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|
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|
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|
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|
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|
|
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|
|
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|
|
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|
|
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|
|
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|
|
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164 40
|
|
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|
|
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|
|
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167 40
|
|
||||||
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|
|
||||||
169 40
|
|
||||||
170 40
|
|
||||||
171 40
|
|
||||||
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|
|
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|
|
||||||
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|
|
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
182 40
|
|
||||||
183 40
|
|
||||||
184 40
|
|
||||||
185 40
|
|
||||||
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|
|
||||||
187 40
|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
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|
|
||||||
195 40
|
|
||||||
196 40
|
|
||||||
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|
|
||||||
198 40
|
|
||||||
199 40
|
|
||||||
200 40
|
|
||||||
|
|
||||||
Binary file not shown.
|
|
@ -1,10 +0,0 @@
|
||||||
## 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 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam
|
|
||||||
|
|
@ -1,18 +0,0 @@
|
||||||
#!/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()
|
|
||||||
}
|
|
||||||
|
|
@ -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
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -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
|
|
||||||
|
|
||||||
Binary file not shown.
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam
|
|
||||||
|
|
@ -1,19 +0,0 @@
|
||||||
#!/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("${baseDir}/input/test.paired_end.COPY.sorted.bam", checkIfExists: true), ] ]
|
|
||||||
|
|
||||||
PICARD_MERGESAMFILES ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow {
|
|
||||||
test()
|
|
||||||
}
|
|
||||||
|
|
@ -1,20 +0,0 @@
|
||||||
|
|
||||||
params {
|
|
||||||
outdir = "output/"
|
|
||||||
publish_dir_mode = "copy"
|
|
||||||
enable_conda = false
|
|
||||||
}
|
|
||||||
|
|
||||||
profiles {
|
|
||||||
conda {
|
|
||||||
params.enable_conda = true
|
|
||||||
}
|
|
||||||
docker {
|
|
||||||
docker.enabled = true
|
|
||||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
|
||||||
}
|
|
||||||
singularity {
|
|
||||||
singularity.enabled = true
|
|
||||||
singularity.autoMounts = true
|
|
||||||
}
|
|
||||||
}
|
|
||||||
Binary file not shown.
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam.bai
|
|
||||||
|
|
@ -1,19 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { SAMTOOLS_FLAGSTAT } from '../main.nf' addParams( options: [:] )
|
|
||||||
|
|
||||||
workflow test {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
|
|
||||||
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_FLAGSTAT ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow {
|
|
||||||
test()
|
|
||||||
}
|
|
||||||
|
|
@ -1,20 +0,0 @@
|
||||||
|
|
||||||
params {
|
|
||||||
outdir = "output/"
|
|
||||||
publish_dir_mode = "copy"
|
|
||||||
enable_conda = false
|
|
||||||
}
|
|
||||||
|
|
||||||
profiles {
|
|
||||||
conda {
|
|
||||||
params.enable_conda = true
|
|
||||||
}
|
|
||||||
docker {
|
|
||||||
docker.enabled = true
|
|
||||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
|
||||||
}
|
|
||||||
singularity {
|
|
||||||
singularity.enabled = true
|
|
||||||
singularity.autoMounts = true
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,13 +0,0 @@
|
||||||
20000 + 0 in total (QC-passed reads + QC-failed reads)
|
|
||||||
0 + 0 secondary
|
|
||||||
0 + 0 supplementary
|
|
||||||
0 + 0 duplicates
|
|
||||||
20000 + 0 mapped (100.00% : N/A)
|
|
||||||
20000 + 0 paired in sequencing
|
|
||||||
10000 + 0 read1
|
|
||||||
10000 + 0 read2
|
|
||||||
20000 + 0 properly paired (100.00% : N/A)
|
|
||||||
20000 + 0 with itself and mate mapped
|
|
||||||
0 + 0 singletons (0.00% : N/A)
|
|
||||||
0 + 0 with mate mapped to a different chr
|
|
||||||
0 + 0 with mate mapped to a different chr (mapQ>=5)
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam.bai
|
|
||||||
|
|
@ -1,19 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { SAMTOOLS_IDXSTATS } from '../main.nf' addParams( options: [:] )
|
|
||||||
|
|
||||||
workflow test {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
|
|
||||||
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_IDXSTATS ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow {
|
|
||||||
test()
|
|
||||||
}
|
|
||||||
|
|
@ -1,20 +0,0 @@
|
||||||
|
|
||||||
params {
|
|
||||||
outdir = "output/"
|
|
||||||
publish_dir_mode = "copy"
|
|
||||||
enable_conda = false
|
|
||||||
}
|
|
||||||
|
|
||||||
profiles {
|
|
||||||
conda {
|
|
||||||
params.enable_conda = true
|
|
||||||
}
|
|
||||||
docker {
|
|
||||||
docker.enabled = true
|
|
||||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
|
||||||
}
|
|
||||||
singularity {
|
|
||||||
singularity.enabled = true
|
|
||||||
singularity.autoMounts = true
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,2 +0,0 @@
|
||||||
gi|170079663|ref|NC_010473.1| 4686137 20000 0
|
|
||||||
* 0 0 0
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam
|
|
||||||
|
|
@ -1,18 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { SAMTOOLS_INDEX } from '../main.nf' addParams( options: [:] )
|
|
||||||
|
|
||||||
workflow test {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_INDEX ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow {
|
|
||||||
test()
|
|
||||||
}
|
|
||||||
|
|
@ -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
|
|
||||||
}
|
|
||||||
}
|
|
||||||
Binary file not shown.
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.name.sorted.bam
|
|
||||||
|
|
@ -1,18 +0,0 @@
|
||||||
#!/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("${baseDir}/input/test.paired_end.name.sorted.bam", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_SORT ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow {
|
|
||||||
test()
|
|
||||||
}
|
|
||||||
|
|
@ -1,20 +0,0 @@
|
||||||
|
|
||||||
params {
|
|
||||||
outdir = "output/"
|
|
||||||
publish_dir_mode = "copy"
|
|
||||||
enable_conda = false
|
|
||||||
}
|
|
||||||
|
|
||||||
profiles {
|
|
||||||
conda {
|
|
||||||
params.enable_conda = true
|
|
||||||
}
|
|
||||||
docker {
|
|
||||||
docker.enabled = true
|
|
||||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
|
||||||
}
|
|
||||||
singularity {
|
|
||||||
singularity.enabled = true
|
|
||||||
singularity.autoMounts = true
|
|
||||||
}
|
|
||||||
}
|
|
||||||
Binary file not shown.
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../../tests/data/bam/test.paired_end.sorted.bam.bai
|
|
||||||
|
|
@ -1,19 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { SAMTOOLS_STATS } from '../main.nf' addParams( options: [:] )
|
|
||||||
|
|
||||||
workflow test {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
|
|
||||||
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
|
|
||||||
|
|
||||||
SAMTOOLS_STATS ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow {
|
|
||||||
test()
|
|
||||||
}
|
|
||||||
|
|
@ -1,20 +0,0 @@
|
||||||
|
|
||||||
params {
|
|
||||||
outdir = "output/"
|
|
||||||
publish_dir_mode = "copy"
|
|
||||||
enable_conda = false
|
|
||||||
}
|
|
||||||
|
|
||||||
profiles {
|
|
||||||
conda {
|
|
||||||
params.enable_conda = true
|
|
||||||
}
|
|
||||||
docker {
|
|
||||||
docker.enabled = true
|
|
||||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
|
||||||
}
|
|
||||||
singularity {
|
|
||||||
singularity.enabled = true
|
|
||||||
singularity.autoMounts = true
|
|
||||||
}
|
|
||||||
}
|
|
||||||
File diff suppressed because it is too large
Load diff
|
|
@ -1 +0,0 @@
|
||||||
../../../../tests/data/fastq/rna/test_R1.fastq.gz
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../tests/data/fastq/rna/test_R2.fastq.gz
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../tests/data/fastq/rna/test_single_end.fastq.gz
|
|
||||||
|
|
@ -1,36 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { TRIMGALORE as TRIMGALORE_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
|
|
||||||
include { TRIMGALORE as TRIMGALORE_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Test with single-end data
|
|
||||||
*/
|
|
||||||
workflow test_single_end {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:true ], // meta map
|
|
||||||
[ file("${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()
|
|
||||||
}
|
|
||||||
|
|
@ -1,25 +0,0 @@
|
||||||
|
|
||||||
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
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,97 +0,0 @@
|
||||||
|
|
||||||
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
|
|
||||||
|
|
||||||
Binary file not shown.
|
|
@ -1,100 +0,0 @@
|
||||||
|
|
||||||
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%)
|
|
||||||
Binary file not shown.
|
|
@ -1,61 +0,0 @@
|
||||||
|
|
||||||
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%)
|
|
||||||
|
|
||||||
Binary file not shown.
44
tests/software/bwa/main.nf
Normal file
44
tests/software/bwa/main.nf
Normal file
|
|
@ -0,0 +1,44 @@
|
||||||
|
#!/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)
|
||||||
|
)
|
||||||
|
}
|
||||||
32
tests/software/bwa/test.yml
Normal file
32
tests/software/bwa/test.yml
Normal file
|
|
@ -0,0 +1,32 @@
|
||||||
|
- 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
|
||||||
|
|
@ -29,3 +29,5 @@ workflow test_paired_end {
|
||||||
|
|
||||||
FASTQC_PE ( input )
|
FASTQC_PE ( input )
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// TODO Test e2e
|
||||||
|
|
|
||||||
|
|
@ -4,7 +4,6 @@
|
||||||
- fastqc
|
- fastqc
|
||||||
files:
|
files:
|
||||||
- path: output/test_single_end/test_fastqc.html
|
- path: output/test_single_end/test_fastqc.html
|
||||||
md5sum: 7027e72c3e55292c1567f12e02565e3b
|
|
||||||
- path: output/test_single_end/test_fastqc.zip
|
- path: output/test_single_end/test_fastqc.zip
|
||||||
|
|
||||||
- name: Run fastqc paired-end test workflow
|
- name: Run fastqc paired-end test workflow
|
||||||
|
|
@ -13,8 +12,6 @@
|
||||||
- fastqc
|
- fastqc
|
||||||
files:
|
files:
|
||||||
- path: output/test_paired_end/test_1_fastqc.html
|
- path: output/test_paired_end/test_1_fastqc.html
|
||||||
md5sum: b3796b4323dc34970b7461f813135254
|
|
||||||
- path: output/test_paired_end/test_2_fastqc.html
|
- 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_1_fastqc.zip
|
||||||
- path: output/test_paired_end/test_2_fastqc.zip
|
- path: output/test_paired_end/test_2_fastqc.zip
|
||||||
|
|
|
||||||
48
tests/software/picard/main.nf
Normal file
48
tests/software/picard/main.nf
Normal file
|
|
@ -0,0 +1,48 @@
|
||||||
|
#!/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 )
|
||||||
|
}
|
||||||
43
tests/software/picard/test.yml
Normal file
43
tests/software/picard/test.yml
Normal file
|
|
@ -0,0 +1,43 @@
|
||||||
|
- 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
|
||||||
58
tests/software/samtools/main.nf
Normal file
58
tests/software/samtools/main.nf
Normal file
|
|
@ -0,0 +1,58 @@
|
||||||
|
#!/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 )
|
||||||
|
}
|
||||||
44
tests/software/samtools/test.yml
Normal file
44
tests/software/samtools/test.yml
Normal file
|
|
@ -0,0 +1,44 @@
|
||||||
|
- 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
|
||||||
40
tests/software/trimgalore/main.nf
Normal file
40
tests/software/trimgalore/main.nf
Normal file
|
|
@ -0,0 +1,40 @@
|
||||||
|
#!/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 )
|
||||||
|
}
|
||||||
21
tests/software/trimgalore/test.yml
Normal file
21
tests/software/trimgalore/test.yml
Normal file
|
|
@ -0,0 +1,21 @@
|
||||||
|
- 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
|
||||||
Loading…
Reference in a new issue