From aa24c8d175751178844105309cb4f535a375a10d Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 16 Jul 2020 17:11:34 +0200 Subject: [PATCH] Fix a bunch of stuff in GitHub Actions test workflows --- .github/workflows/cutadapt.yml | 12 +++--------- .github/workflows/docker.yml | 2 +- .github/workflows/fastqc.yml | 2 -- .github/workflows/lint-code.yml | 2 +- .github/workflows/samtools_index.yml | 9 ++++----- .github/workflows/samtools_sort.yml | 9 ++++----- .github/workflows/tcoffee.yml | 12 +++--------- .github/workflows/trim_galore.yml | 9 ++++----- 8 files changed, 20 insertions(+), 37 deletions(-) diff --git a/.github/workflows/cutadapt.yml b/.github/workflows/cutadapt.yml index 7092e868..ff1e8a91 100644 --- a/.github/workflows/cutadapt.yml +++ b/.github/workflows/cutadapt.yml @@ -1,8 +1,9 @@ name: cutadapt on: - push: {} + push: + paths: software/cutadapt/** pull_request: - paths: software/cutadapt/* + paths: software/cutadapt/** jobs: run_ci_test: @@ -12,13 +13,6 @@ jobs: steps: - uses: actions/checkout@v2 - - name: Checkout submodules - shell: bash - run: | - auth_header="$(git config --local --get http.https://github.com/.extraheader)" - git submodule sync --recursive - git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1 - - name: Install Nextflow run: | wget -qO- get.nextflow.io | bash diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index d63a83a3..35171a6f 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -14,7 +14,7 @@ jobs: steps: # Check out the repo - - uses: actions/checkout@v1 + - uses: actions/checkout@v2 # Find the tool wrappers that changed # Annoyingly, matrix can't take dynamic variables diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml index 66a14c7c..7589e4b0 100644 --- a/.github/workflows/fastqc.yml +++ b/.github/workflows/fastqc.yml @@ -12,9 +12,7 @@ jobs: NXF_ANSI_LOG: false steps: - # Check out the repository - uses: actions/checkout@v1 - submodules: true - name: Install Nextflow run: | diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml index 7e366a4b..ebbe34cb 100644 --- a/.github/workflows/lint-code.yml +++ b/.github/workflows/lint-code.yml @@ -36,7 +36,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out repository - uses: actions/checkout@v1 + uses: actions/checkout@v2 - name: Install NodeJS uses: actions/setup-node@v1 diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml index 5b7c1cd5..a8ee85fd 100644 --- a/.github/workflows/samtools_index.yml +++ b/.github/workflows/samtools_index.yml @@ -1,8 +1,9 @@ name: samtools index on: - push: {} + push: + paths: software/samtools/index/** pull_request: - paths: software/samtools/index* + paths: software/samtools/index/** jobs: run_ci_test: @@ -11,9 +12,7 @@ jobs: NXF_ANSI_LOG: false steps: - # Check out the repository - - uses: actions/checkout@v1 - submodules: true + - uses: actions/checkout@v2 - name: Install Nextflow run: | diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml index bba7d578..4d6aa099 100644 --- a/.github/workflows/samtools_sort.yml +++ b/.github/workflows/samtools_sort.yml @@ -1,8 +1,9 @@ name: samtools sort on: - push: {} + push: + paths: software/samtools/sort** pull_request: - paths: software/samtools/sort* + paths: software/samtools/sort** jobs: run_ci_test: @@ -11,9 +12,7 @@ jobs: NXF_ANSI_LOG: false steps: - # Check out the repository - - uses: actions/checkout@v1 - submodules: true + - uses: actions/checkout@v2 - name: Install Nextflow run: | diff --git a/.github/workflows/tcoffee.yml b/.github/workflows/tcoffee.yml index 582a1bb7..98f84e95 100644 --- a/.github/workflows/tcoffee.yml +++ b/.github/workflows/tcoffee.yml @@ -1,8 +1,9 @@ name: tcoffee on: - push: {} + push: + paths: software/tcoffee/** pull_request: - paths: software/tcoffee/* + paths: software/tcoffee/** jobs: run_ci_test: @@ -11,14 +12,7 @@ jobs: NXF_ANSI_LOG: false steps: - # Check out the repository - uses: actions/checkout@v2 - - name: Checkout submodules - shell: bash - run: | - auth_header="$(git config --local --get http.https://github.com/.extraheader)" - git submodule sync --recursive - git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1 - name: Install Nextflow run: | diff --git a/.github/workflows/trim_galore.yml b/.github/workflows/trim_galore.yml index b34f2ae6..8812ad87 100644 --- a/.github/workflows/trim_galore.yml +++ b/.github/workflows/trim_galore.yml @@ -1,8 +1,9 @@ name: Trim Galore! on: - push: {} + push: + paths: software/trim_galore/** pull_request: - paths: software/trim_galore/* + paths: software/trim_galore/** jobs: run_ci_test: @@ -11,9 +12,7 @@ jobs: NXF_ANSI_LOG: false steps: - # Check out the repository - - uses: actions/checkout@v1 - submodules: true + - uses: actions/checkout@v2 - name: Install Nextflow run: |