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ci: Support multiple nextflow versions

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This commit is contained in:
Edmund Miller 2020-12-09 09:56:40 -06:00
parent f994d55c18
commit 8d27ff53c5
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GPG key ID: BD387FF7BC10AA9D
13 changed files with 61 additions and 13 deletions
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6
.github/workflows/bwa_index.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/bwa_mem.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

2
.github/workflows/fastqc.yml vendored
View file

@ -16,7 +16,7 @@ jobs:
runs-on: ubuntu-latest runs-on: ubuntu-latest
strategy: strategy:
matrix: matrix:
nxf_version: [20.07.1, ''] nxf_version: [20.07.1, ""]
env: env:
NXF_ANSI_LOG: false NXF_ANSI_LOG: false
steps: steps:

6
.github/workflows/multiqc.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/picard_collectmultiplemetrics.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/picard_markduplicates.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/picard_mergesamfiles.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/samtools_flagstat.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/samtools_idxstats.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/samtools_index.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/samtools_sort.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/samtools_stats.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/

6
.github/workflows/trimgalore.yml vendored
View file

@ -14,14 +14,18 @@ on:
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/