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Merge pull request #165 from ewels/fix-show-profiles
Set params.custom_config_base in nextflow.config
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commit
d510cb254e
3 changed files with 31 additions and 7 deletions
17
.github/workflows/main.yml
vendored
17
.github/workflows/main.yml
vendored
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@ -1,15 +1,28 @@
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name: Configs tests
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on: [pull_request, push]
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jobs:
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test_all_profiles:
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runs-on: ubuntu-latest
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name: Check if all profiles are tested
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steps:
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- uses: actions/checkout@v1
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- name: Check whether profiles are all tested
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run: python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
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check_nextflow_config:
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runs-on: ubuntu-latest
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name: Check if nextflow config runs in repository root
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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run: |
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python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- run: nextflow config -show-profiles ${GITHUB_WORKSPACE}
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profile_test:
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runs-on: ubuntu-latest
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name: Run ${{ matrix.profile }} profile
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@ -82,4 +95,4 @@ jobs:
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env:
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SCRATCH: "~"
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NXF_GLOBAL_CONFIG: awsbatch.config
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run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}
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run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf -profile ${{ matrix.profile }}
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@ -1,6 +1,6 @@
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singularityDir = "$SCRATCH/singularity_images_nextflow"
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singularityModule = "singularity/3.2.1"
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squashfsModule = "squashfs/4.3"
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def singularityDir = set_singularity_path()
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def singularityModule = "singularity/3.2.1"
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def squashfsModule = "squashfs/4.3"
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params {
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config_profile_description = """
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@ -13,11 +13,21 @@ params {
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}
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singularity {
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enabled = true
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cacheDir = singularityDir
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enabled = true
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cacheDir = singularityDir
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}
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process {
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beforeScript = "module load $singularityModule $squashfsModule"
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executor = 'slurm'
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}
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def set_singularity_path() {
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def scratch = System.getenv('SCRATCH')
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if(scratch == null){
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System.err.println("WARNING: prince.config requires the SCRATCH env var to be set.")
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return null
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} else {
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return "$SCRATCH/singularity_images_nextflow"
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}
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}
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@ -1 +1,2 @@
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params.custom_config_base = "."
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includeConfig("nfcore_custom.config")
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