From 65697532a1b78f8742c23863c0a293945fd499d2 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 1 Dec 2020 11:40:16 -0600 Subject: [PATCH] ci: Get rid of software folder --- .github/workflows/bwa_index.yml | 36 +++++++++++++++++++ .github/workflows/{software => }/bwa_mem.yml | 4 +-- .../picard_collectmultiplemetrics.yml | 4 +-- .../{software => }/picard_markduplicates.yml | 4 +-- .../{software => }/picard_mergesamfiles.yml | 4 +-- .../{software => }/samtools_flagstat.yml | 4 +-- .../{software => }/samtools_idxstats.yml | 4 +-- .../{software => }/samtools_index.yml | 4 +-- .../{software => }/samtools_sort.yml | 4 +-- .../{software => }/samtools_stats.yml | 4 +-- .github/workflows/software/bwa_index.yml | 36 ------------------- .../workflows/{software => }/trimgalore.yml | 4 +-- 12 files changed, 56 insertions(+), 56 deletions(-) create mode 100644 .github/workflows/bwa_index.yml rename .github/workflows/{software => }/bwa_mem.yml (89%) rename .github/workflows/{software => }/picard_collectmultiplemetrics.yml (86%) rename .github/workflows/{software => }/picard_markduplicates.yml (87%) rename .github/workflows/{software => }/picard_mergesamfiles.yml (87%) rename .github/workflows/{software => }/samtools_flagstat.yml (87%) rename .github/workflows/{software => }/samtools_idxstats.yml (87%) rename .github/workflows/{software => }/samtools_index.yml (88%) rename .github/workflows/{software => }/samtools_sort.yml (88%) rename .github/workflows/{software => }/samtools_stats.yml (86%) delete mode 100644 .github/workflows/software/bwa_index.yml rename .github/workflows/{software => }/trimgalore.yml (88%) diff --git a/.github/workflows/bwa_index.yml b/.github/workflows/bwa_index.yml new file mode 100644 index 00000000..609fde64 --- /dev/null +++ b/.github/workflows/bwa_index.yml @@ -0,0 +1,36 @@ +name: bwa_index +on: + push: + paths: + - software/bwa/index/** + - .github/workflows/bwa_index.yml + - tests/software/bwa/** + pull_request: + paths: + - software/bwa/index/** + - .github/workflows/bwa_index.yml + - tests/software/bwa/** + +jobs: + ci_test: + runs-on: ubuntu-latest + env: + NXF_ANSI_LOG: false + steps: + - uses: actions/checkout@v2 + + - name: Install Nextflow + run: | + export NXF_VER="20.07.1" + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow + + # Test the module + - run: pytest --tag bwa_index --symlink --wt 2 diff --git a/.github/workflows/software/bwa_mem.yml b/.github/workflows/bwa_mem.yml similarity index 89% rename from .github/workflows/software/bwa_mem.yml rename to .github/workflows/bwa_mem.yml index 581f8c3d..93f8ea07 100644 --- a/.github/workflows/software/bwa_mem.yml +++ b/.github/workflows/bwa_mem.yml @@ -3,12 +3,12 @@ on: push: paths: - software/bwa/mem/** - - .github/workflows/software/bwa_mem.yml + - .github/workflows/bwa_mem.yml - tests/software/bwa/** pull_request: paths: - software/bwa/mem/** - - .github/workflows/software/bwa_mem.yml + - .github/workflows/bwa_mem.yml - tests/software/bwa/** jobs: diff --git a/.github/workflows/software/picard_collectmultiplemetrics.yml b/.github/workflows/picard_collectmultiplemetrics.yml similarity index 86% rename from .github/workflows/software/picard_collectmultiplemetrics.yml rename to .github/workflows/picard_collectmultiplemetrics.yml index 6c85840d..b9176d72 100644 --- a/.github/workflows/software/picard_collectmultiplemetrics.yml +++ b/.github/workflows/picard_collectmultiplemetrics.yml @@ -3,12 +3,12 @@ on: push: paths: - software/picard/collectmultiplemetrics/** - - .github/workflows/software/picard_collectmultiplemetrics.yml + - .github/workflows/picard_collectmultiplemetrics.yml - tests/software/picard/** pull_request: paths: - software/picard/collectmultiplemetrics/** - - .github/workflows/software/picard_collectmultiplemetrics.yml + - .github/workflows/picard_collectmultiplemetrics.yml - tests/software/picard/** jobs: diff --git a/.github/workflows/software/picard_markduplicates.yml b/.github/workflows/picard_markduplicates.yml similarity index 87% rename from .github/workflows/software/picard_markduplicates.yml rename to .github/workflows/picard_markduplicates.yml index 186bbac9..b6374318 100644 --- a/.github/workflows/software/picard_markduplicates.yml +++ b/.github/workflows/picard_markduplicates.yml @@ -3,12 +3,12 @@ on: push: paths: - software/picard/markduplicates/** - - .github/workflows/software/picard_markduplicates.yml + - .github/workflows/picard_markduplicates.yml - tests/software/picard/** pull_request: paths: - software/picard/markduplicates/** - - .github/workflows/software/picard_markduplicates.yml + - .github/workflows/picard_markduplicates.yml - tests/software/picard/** jobs: diff --git a/.github/workflows/software/picard_mergesamfiles.yml b/.github/workflows/picard_mergesamfiles.yml similarity index 87% rename from .github/workflows/software/picard_mergesamfiles.yml rename to .github/workflows/picard_mergesamfiles.yml index c67e5d42..0d329d8a 100644 --- a/.github/workflows/software/picard_mergesamfiles.yml +++ b/.github/workflows/picard_mergesamfiles.yml @@ -3,12 +3,12 @@ on: push: paths: - software/picard/mergesamfiles/** - - .github/workflows/software/picard_mergesamfiles.yml + - .github/workflows/picard_mergesamfiles.yml - tests/software/picard/** pull_request: paths: - software/picard/mergesamfiles/** - - .github/workflows/software/picard_mergesamfiles.yml + - .github/workflows/picard_mergesamfiles.yml - tests/software/picard/** jobs: diff --git a/.github/workflows/software/samtools_flagstat.yml b/.github/workflows/samtools_flagstat.yml similarity index 87% rename from .github/workflows/software/samtools_flagstat.yml rename to .github/workflows/samtools_flagstat.yml index 2946dfc6..a35dd0ac 100644 --- a/.github/workflows/software/samtools_flagstat.yml +++ b/.github/workflows/samtools_flagstat.yml @@ -3,12 +3,12 @@ on: push: paths: - software/samtools/flagstat/** - - .github/workflows/software/samtools_flagstat.yml + - .github/workflows/samtools_flagstat.yml - tests/software/samtools/** pull_request: paths: - software/samtools/flagstat/** - - .github/workflows/software/samtools_flagstat.yml + - .github/workflows/samtools_flagstat.yml - tests/software/samtools/** jobs: diff --git a/.github/workflows/software/samtools_idxstats.yml b/.github/workflows/samtools_idxstats.yml similarity index 87% rename from .github/workflows/software/samtools_idxstats.yml rename to .github/workflows/samtools_idxstats.yml index c55b7f43..4c01046f 100644 --- a/.github/workflows/software/samtools_idxstats.yml +++ b/.github/workflows/samtools_idxstats.yml @@ -3,12 +3,12 @@ on: push: paths: - software/samtools/idxstats/** - - .github/workflows/software/samtools_idxstats.yml + - .github/workflows/samtools_idxstats.yml - tests/software/samtools/** pull_request: paths: - software/samtools/idxstats/** - - .github/workflows/software/samtools_idxstats.yml + - .github/workflows/samtools_idxstats.yml - tests/software/samtools/** jobs: diff --git a/.github/workflows/software/samtools_index.yml b/.github/workflows/samtools_index.yml similarity index 88% rename from .github/workflows/software/samtools_index.yml rename to .github/workflows/samtools_index.yml index 9ae9a711..2c680274 100644 --- a/.github/workflows/software/samtools_index.yml +++ b/.github/workflows/samtools_index.yml @@ -3,12 +3,12 @@ on: push: paths: - software/samtools/index/** - - .github/workflows/software/samtools_index.yml + - .github/workflows/samtools_index.yml - tests/software/samtools/** pull_request: paths: - software/samtools/index/** - - .github/workflows/software/samtools_index.yml + - .github/workflows/samtools_index.yml - tests/software/samtools/** jobs: diff --git a/.github/workflows/software/samtools_sort.yml b/.github/workflows/samtools_sort.yml similarity index 88% rename from .github/workflows/software/samtools_sort.yml rename to .github/workflows/samtools_sort.yml index 6edf64f7..2198fac6 100644 --- a/.github/workflows/software/samtools_sort.yml +++ b/.github/workflows/samtools_sort.yml @@ -3,12 +3,12 @@ on: push: paths: - software/samtools/sort/** - - .github/workflows/software/samtools_sort.yml + - .github/workflows/samtools_sort.yml - tests/software/samtools/** pull_request: paths: - software/samtools/sort/** - - .github/workflows/software/samtools_sort.yml + - .github/workflows/samtools_sort.yml - tests/software/samtools/** jobs: diff --git a/.github/workflows/software/samtools_stats.yml b/.github/workflows/samtools_stats.yml similarity index 86% rename from .github/workflows/software/samtools_stats.yml rename to .github/workflows/samtools_stats.yml index d00b1ff3..f147e510 100644 --- a/.github/workflows/software/samtools_stats.yml +++ b/.github/workflows/samtools_stats.yml @@ -3,12 +3,12 @@ on: push: paths: - software/samtools/stats/** - - .github/workflows/software/software/samtools_stats.yml + - .github/workflows/software/samtools_stats.yml - tests/software/samtools/** pull_request: paths: - software/samtools/stats/** - - .github/workflows/software/software/samtools_stats.yml + - .github/workflows/software/samtools_stats.yml - tests/software/samtools/** jobs: diff --git a/.github/workflows/software/bwa_index.yml b/.github/workflows/software/bwa_index.yml deleted file mode 100644 index a2cfe096..00000000 --- a/.github/workflows/software/bwa_index.yml +++ /dev/null @@ -1,36 +0,0 @@ -name: bwa_index -on: - push: - paths: - - software/bwa/index/** - - .github/workflows/software/bwa_index.yml - - tests/software/bwa/** - pull_request: - paths: - - software/bwa/index/** - - .github/workflows/software/bwa_index.yml - - tests/software/bwa/** - -jobs: - ci_test: - runs-on: ubuntu-latest - env: - NXF_ANSI_LOG: false - steps: - - uses: actions/checkout@v2 - - - name: Install Nextflow - run: | - export NXF_VER="20.07.1" - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: "3.x" - - name: Install dependencies - run: python -m pip install --upgrade pip pytest-workflow - - # Test the module - - run: pytest --tag bwa_index --symlink --wt 2 diff --git a/.github/workflows/software/trimgalore.yml b/.github/workflows/trimgalore.yml similarity index 88% rename from .github/workflows/software/trimgalore.yml rename to .github/workflows/trimgalore.yml index b4f09918..dfb081d0 100644 --- a/.github/workflows/software/trimgalore.yml +++ b/.github/workflows/trimgalore.yml @@ -3,12 +3,12 @@ on: push: paths: - software/trimgalore/** - - .github/workflows/software/trimgalore.yml + - .github/workflows/trimgalore.yml - tests/software/trimgalore/** pull_request: paths: - software/trimgalore/** - - .github/workflows/software/trimgalore.yml + - .github/workflows/trimgalore.yml - tests/software/trimgalore/** jobs: