mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
ci: Move all files to filter file and delete old tests
This commit is contained in:
Edmund Miller
parent
b008afe2e6
commit
506ebe515e
20 changed files with 73 additions and 952 deletions
74
.github/filters.yml
vendored
74
.github/filters.yml
vendored
|
|
@ -1,4 +1,76 @@
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bowtie_align:
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- software/bowtie/align/**
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- software/bowtie/index/**
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- tests/software/bowtie/**
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bowtie_index:
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- software/bowtie/index/**
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- tests/software/bowtie/**
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bwa_index:
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- software/bwa/index/**
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- tests/software/bwa/**
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bwa_mem:
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- software/bwa/mem/**
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||||
- tests/software/bwa/**
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|
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fastqc:
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- software/fastqc/**
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- .github/workflows/fastqc.yml
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- tests/software/fastqc/**
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|
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gffread:
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- software/gffread/**
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- tests/software/gffread/**
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multiqc:
|
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- software/multiqc/**
|
||||
- tests/software/multiqc/**
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|
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picard_collectmultiplemetrics:
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- software/picard/collectmultiplemetrics/**
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- tests/software/picard/**
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||||
|
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picard_markduplicates:
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- software/picard/markduplicates/**
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- tests/software/picard/**
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picard_mergesamfiles:
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- software/picard/mergesamfiles/**
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- tests/software/picard/**
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preseq_lcextrap:
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- software/preseq/lcextrap/**
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- tests/software/preseq/**
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|
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samtools_flagstat:
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- software/samtools/flagstat/**
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||||
- tests/software/samtools/**
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samtools_idxstats:
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- software/samtools/idxstats/**
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||||
- tests/software/samtools/**
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samtools_index:
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- software/samtools/index/**
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||||
- tests/software/samtools/**
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samtools_sort:
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- software/samtools/sort/**
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- tests/software/samtools/**
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samtools_stats:
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- software/samtools/stats/**
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- tests/software/samtools/**
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stringtie:
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- software/stringtie/**
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- tests/software/stringtie/**
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trimgalore:
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- software/trimgalore/**
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- tests/software/trimgalore/**
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ucsc_bedgraphtobigwig:
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- software/ucsc/bedgraphtobigwig/**
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- tests/software/ucsc/**
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|
|
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52
.github/workflows/bowtie_align.yml
vendored
52
.github/workflows/bowtie_align.yml
vendored
|
|
@ -1,52 +0,0 @@
|
|||
name: bowtie_align
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on:
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push:
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paths:
|
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- software/bowtie/align/**
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- software/bowtie/index/**
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- .github/workflows/bowtie_align.yml
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- tests/software/bowtie/**
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pull_request:
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paths:
|
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- software/bowtie/align/**
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- software/bowtie/index/**
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- .github/workflows/bowtie_align.yml
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- tests/software/bowtie/**
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|
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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nxf_version: [20.11.0-edge]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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||||
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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- run: pytest --kwdof --tag bowtie_align --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/.nextflow.log
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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||||
50
.github/workflows/bowtie_index.yml
vendored
50
.github/workflows/bowtie_index.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: bowtie_index
|
||||
on:
|
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push:
|
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paths:
|
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- software/bowtie/index/**
|
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- .github/workflows/bowtie_index.yml
|
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- tests/software/bowtie/**
|
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pull_request:
|
||||
paths:
|
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- software/bowtie/index/**
|
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- .github/workflows/bowtie_index.yml
|
||||
- tests/software/bowtie/**
|
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|
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jobs:
|
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ci_test:
|
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runs-on: ubuntu-latest
|
||||
strategy:
|
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matrix:
|
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nxf_version: [20.11.0-edge]
|
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env:
|
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
|
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|
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- name: Install Nextflow
|
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env:
|
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
|
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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|
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- name: Set up Python
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uses: actions/setup-python@v2
|
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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- run: pytest --kwdof --tag bowtie_index --symlink --wt 2
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- name: Upload logs on failure
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if: ${{ failure() }}
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uses: actions/upload-artifact@v2
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with:
|
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name: logs
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path: |
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/tmp/pytest_workflow_*/*/.nextflow.log
|
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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50
.github/workflows/bwa_index.yml
vendored
50
.github/workflows/bwa_index.yml
vendored
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@ -1,50 +0,0 @@
|
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name: bwa_index
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on:
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push:
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paths:
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- software/bwa/index/**
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- .github/workflows/software/bwa_index.yml
|
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- tests/software/bwa/**
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pull_request:
|
||||
paths:
|
||||
- software/bwa/index/**
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- .github/workflows/software/bwa_index.yml
|
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- tests/software/bwa/**
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|
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jobs:
|
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ci_test:
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runs-on: ubuntu-latest
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strategy:
|
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matrix:
|
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nxf_version: [20.11.0-edge]
|
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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|
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- name: Install Nextflow
|
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
|
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
|
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|
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
|
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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- run: pytest --kwdof --tag bwa_index --symlink --wt 2
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|
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- name: Upload logs on failure
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if: ${{ failure() }}
|
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uses: actions/upload-artifact@v2
|
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with:
|
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name: logs
|
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path: |
|
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/tmp/pytest_workflow_*/*/.nextflow.log
|
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/tmp/pytest_workflow_*/*/log.out
|
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/tmp/pytest_workflow_*/*/log.err
|
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50
.github/workflows/bwa_mem.yml
vendored
50
.github/workflows/bwa_mem.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: bwa_mem
|
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on:
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push:
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paths:
|
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- software/bwa/mem/**
|
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- .github/workflows/bwa_mem.yml
|
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- tests/software/bwa/**
|
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pull_request:
|
||||
paths:
|
||||
- software/bwa/mem/**
|
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- .github/workflows/bwa_mem.yml
|
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- tests/software/bwa/**
|
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|
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jobs:
|
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ci_test:
|
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runs-on: ubuntu-latest
|
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strategy:
|
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matrix:
|
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nxf_version: [20.11.0-edge]
|
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env:
|
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NXF_ANSI_LOG: false
|
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steps:
|
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- uses: actions/checkout@v2
|
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|
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- name: Install Nextflow
|
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env:
|
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NXF_VER: ${{ matrix.nxf_version }}
|
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run: |
|
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wget -qO- get.nextflow.io | bash
|
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sudo mv nextflow /usr/local/bin/
|
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|
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- name: Set up Python
|
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uses: actions/setup-python@v2
|
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with:
|
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python-version: "3.x"
|
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- name: Install dependencies
|
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run: python -m pip install --upgrade pip pytest-workflow
|
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|
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# Test the module
|
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- run: pytest --kwdof --tag bwa_index --symlink --wt 2
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|
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- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
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uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/fastqc.yml
vendored
50
.github/workflows/fastqc.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: fastqc
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/fastqc/**
|
||||
- .github/workflows/fastqc.yml
|
||||
- tests/software/fastqc/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/fastqc/**
|
||||
- .github/workflows/fastqc.yml
|
||||
- tests/software/fastqc/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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
|
||||
|
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# Test the module
|
||||
- run: pytest --kwdof --tag fastqc --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/gffread.yml
vendored
50
.github/workflows/gffread.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: gffread
|
||||
on:
|
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push:
|
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paths:
|
||||
- software/gffread/**
|
||||
- .github/workflows/gffread.yml
|
||||
- tests/software/gffread/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/gffread/**
|
||||
- .github/workflows/gffread.yml
|
||||
- tests/software/gffread/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag gffread --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/multiqc.yml
vendored
50
.github/workflows/multiqc.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: multiqc
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/multiqc/**
|
||||
- .github/workflows/multiqc.yml
|
||||
- tests
|
||||
pull_request:
|
||||
paths:
|
||||
- software/multiqc/**
|
||||
- .github/workflows/multiqc.yml
|
||||
- tests
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag multiqc --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
|
|
@ -1,50 +0,0 @@
|
|||
name: picard_collectmultiplemetrics
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/picard/collectmultiplemetrics/**
|
||||
- .github/workflows/picard_collectmultiplemetrics.yml
|
||||
- tests/software/picard/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/picard/collectmultiplemetrics/**
|
||||
- .github/workflows/picard_collectmultiplemetrics.yml
|
||||
- tests/software/picard/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag picard_collectmultiplemetrics --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/picard_markduplicates.yml
vendored
50
.github/workflows/picard_markduplicates.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: picard_markduplicates
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/picard/markduplicates/**
|
||||
- .github/workflows/picard_markduplicates.yml
|
||||
- tests/software/picard/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/picard/markduplicates/**
|
||||
- .github/workflows/picard_markduplicates.yml
|
||||
- tests/software/picard/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag picard_markduplicates --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/picard_mergesamfiles.yml
vendored
50
.github/workflows/picard_mergesamfiles.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: picard_mergesamfiles
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/picard/mergesamfiles/**
|
||||
- .github/workflows/picard_mergesamfiles.yml
|
||||
- tests/software/picard/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/picard/mergesamfiles/**
|
||||
- .github/workflows/picard_mergesamfiles.yml
|
||||
- tests/software/picard/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag picard_mergesamfiles --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/preseq_lcextrap.yml
vendored
50
.github/workflows/preseq_lcextrap.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: preseq_lcextrap
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/preseq/lcextrap/**
|
||||
- .github/workflows/preseq_lcextrap.yml
|
||||
- tests/software/preseq/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/preseq/lcextrap/**
|
||||
- .github/workflows/preseq_lcextrap.yml
|
||||
- tests/software/preseq/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag preseq_lcextrap --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/samtools_flagstat.yml
vendored
50
.github/workflows/samtools_flagstat.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: samtools_flagstat
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/samtools/flagstat/**
|
||||
- .github/workflows/samtools_flagstat.yml
|
||||
- tests/software/samtools/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/samtools/flagstat/**
|
||||
- .github/workflows/samtools_flagstat.yml
|
||||
- tests/software/samtools/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag samtools_flagstat --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/samtools_idxstats.yml
vendored
50
.github/workflows/samtools_idxstats.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: samtools_idxstats
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/samtools/idxstats/**
|
||||
- .github/workflows/samtools_idxstats.yml
|
||||
- tests/software/samtools/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/samtools/idxstats/**
|
||||
- .github/workflows/samtools_idxstats.yml
|
||||
- tests/software/samtools/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag samtools_idxstats --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/samtools_index.yml
vendored
50
.github/workflows/samtools_index.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: samtools_index
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/samtools/index/**
|
||||
- .github/workflows/samtools_index.yml
|
||||
- tests/software/samtools/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/samtools/index/**
|
||||
- .github/workflows/samtools_index.yml
|
||||
- tests/software/samtools/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag samtools_index --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/samtools_sort.yml
vendored
50
.github/workflows/samtools_sort.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: samtools_sort
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/samtools/sort/**
|
||||
- .github/workflows/samtools_sort.yml
|
||||
- tests/software/samtools/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/samtools/sort/**
|
||||
- .github/workflows/samtools_sort.yml
|
||||
- tests/software/samtools/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag samtools_sort --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/samtools_stats.yml
vendored
50
.github/workflows/samtools_stats.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: samtools_stats
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/samtools/stats/**
|
||||
- .github/workflows/software/samtools_stats.yml
|
||||
- tests/software/samtools/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/samtools/stats/**
|
||||
- .github/workflows/software/samtools_stats.yml
|
||||
- tests/software/samtools/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag samtools_stats --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/stringtie.yml
vendored
50
.github/workflows/stringtie.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: stringtie
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/stringtie/**
|
||||
- .github/workflows/stringtie.yml
|
||||
- tests/software/stringtie/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/stringtie/**
|
||||
- .github/workflows/stringtie.yml
|
||||
- tests/software/stringtie/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag stringtie --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
50
.github/workflows/trimgalore.yml
vendored
50
.github/workflows/trimgalore.yml
vendored
|
|
@ -1,50 +0,0 @@
|
|||
name: trimgalore
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/trimgalore/**
|
||||
- .github/workflows/trimgalore.yml
|
||||
- tests/software/trimgalore/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/trimgalore/**
|
||||
- .github/workflows/trimgalore.yml
|
||||
- tests/software/trimgalore/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag trimgalore --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
49
.github/workflows/ucsc_bedgraphtobigwig.yml
vendored
49
.github/workflows/ucsc_bedgraphtobigwig.yml
vendored
|
|
@ -1,49 +0,0 @@
|
|||
name: ucsc_bedgraphtobigwig
|
||||
on:
|
||||
push:
|
||||
paths:
|
||||
- software/ucsc/bedgraphtobigwig/**
|
||||
- .github/workflows/ucsc_bedgraphtobigwig.yml
|
||||
- tests/software/ucsc/**
|
||||
pull_request:
|
||||
paths:
|
||||
- software/ucsc/bedgraphtobigwig/**
|
||||
- .github/workflows/ucsc_bedgraphtobigwig.yml
|
||||
- tests/software/ucsc/**
|
||||
|
||||
jobs:
|
||||
ci_test:
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
nxf_version: [20.11.0-edge]
|
||||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- 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: 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 --kwdof --tag ucsc_bedgraphtobigwig --symlink --wt 2
|
||||
|
||||
- name: Upload logs on failure
|
||||
if: ${{ failure() }}
|
||||
uses: actions/upload-artifact@v2
|
||||
with:
|
||||
name: logs
|
||||
path: |
|
||||
/tmp/pytest_workflow_*/*/.nextflow.log
|
||||
/tmp/pytest_workflow_*/*/log.out
|
||||
/tmp/pytest_workflow_*/*/log.err
|
||||
Loading…
Reference in a new issue