From 8d27ff53c588eb232d6160d186289f477a39ded1 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 9 Dec 2020 09:56:40 -0600 Subject: [PATCH] ci: Support multiple nextflow versions --- .github/workflows/bwa_index.yml | 6 +++++- .github/workflows/bwa_mem.yml | 6 +++++- .github/workflows/fastqc.yml | 2 +- .github/workflows/multiqc.yml | 6 +++++- .github/workflows/picard_collectmultiplemetrics.yml | 6 +++++- .github/workflows/picard_markduplicates.yml | 6 +++++- .github/workflows/picard_mergesamfiles.yml | 6 +++++- .github/workflows/samtools_flagstat.yml | 6 +++++- .github/workflows/samtools_idxstats.yml | 6 +++++- .github/workflows/samtools_index.yml | 6 +++++- .github/workflows/samtools_sort.yml | 6 +++++- .github/workflows/samtools_stats.yml | 6 +++++- .github/workflows/trimgalore.yml | 6 +++++- 13 files changed, 61 insertions(+), 13 deletions(-) diff --git a/.github/workflows/bwa_index.yml b/.github/workflows/bwa_index.yml index a2cfe096..aa0c3ba3 100644 --- a/.github/workflows/bwa_index.yml +++ b/.github/workflows/bwa_index.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/bwa_mem.yml b/.github/workflows/bwa_mem.yml index 93f8ea07..d24b3fce 100644 --- a/.github/workflows/bwa_mem.yml +++ b/.github/workflows/bwa_mem.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml index c668adb2..6e98cb9c 100644 --- a/.github/workflows/fastqc.yml +++ b/.github/workflows/fastqc.yml @@ -16,7 +16,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - nxf_version: [20.07.1, ''] + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: diff --git a/.github/workflows/multiqc.yml b/.github/workflows/multiqc.yml index 49f39d2e..3ddc4be3 100644 --- a/.github/workflows/multiqc.yml +++ b/.github/workflows/multiqc.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/picard_collectmultiplemetrics.yml b/.github/workflows/picard_collectmultiplemetrics.yml index 945f7cfc..871e9937 100644 --- a/.github/workflows/picard_collectmultiplemetrics.yml +++ b/.github/workflows/picard_collectmultiplemetrics.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/picard_markduplicates.yml b/.github/workflows/picard_markduplicates.yml index b6374318..ef95a19c 100644 --- a/.github/workflows/picard_markduplicates.yml +++ b/.github/workflows/picard_markduplicates.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/picard_mergesamfiles.yml b/.github/workflows/picard_mergesamfiles.yml index 0d329d8a..3a2cdaa8 100644 --- a/.github/workflows/picard_mergesamfiles.yml +++ b/.github/workflows/picard_mergesamfiles.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/samtools_flagstat.yml b/.github/workflows/samtools_flagstat.yml index a35dd0ac..3c9a25da 100644 --- a/.github/workflows/samtools_flagstat.yml +++ b/.github/workflows/samtools_flagstat.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/samtools_idxstats.yml b/.github/workflows/samtools_idxstats.yml index 4c01046f..7b3c7922 100644 --- a/.github/workflows/samtools_idxstats.yml +++ b/.github/workflows/samtools_idxstats.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml index 2c680274..80fbdd2d 100644 --- a/.github/workflows/samtools_index.yml +++ b/.github/workflows/samtools_index.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml index 2198fac6..eaa98eff 100644 --- a/.github/workflows/samtools_sort.yml +++ b/.github/workflows/samtools_sort.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/samtools_stats.yml b/.github/workflows/samtools_stats.yml index f147e510..5b28725e 100644 --- a/.github/workflows/samtools_stats.yml +++ b/.github/workflows/samtools_stats.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ diff --git a/.github/workflows/trimgalore.yml b/.github/workflows/trimgalore.yml index dfb081d0..c33ecbc1 100644 --- a/.github/workflows/trimgalore.yml +++ b/.github/workflows/trimgalore.yml @@ -14,14 +14,18 @@ on: jobs: ci_test: runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.07.1, ""] env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} run: | - export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/