mirror of
https://github.com/MillironX/nf-configs.git
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Merge branch 'eva-java-correction' of github.com:jfy133/nf-core-configs into eva-java-correction
This commit is contained in:
commit
76b0d1dd85
8 changed files with 135 additions and 14 deletions
55
.github/workflows/fix-linting.yml
vendored
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55
.github/workflows/fix-linting.yml
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@ -0,0 +1,55 @@
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name: Fix linting from a comment
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on:
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issue_comment:
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types: [created]
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jobs:
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deploy:
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# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
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if: >
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contains(github.event.comment.html_url, '/pull/') &&
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contains(github.event.comment.body, '@nf-core-bot fix linting') &&
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github.repository == 'nf-core/configs'
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runs-on: ubuntu-latest
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steps:
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# Use the @nf-core-bot token to check out so we can push later
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- uses: actions/checkout@v3
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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# Action runs on the issue comment, so we don't get the PR by default
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# Use the gh cli to check out the PR
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- name: Checkout Pull Request
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run: gh pr checkout ${{ github.event.issue.number }}
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env:
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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- uses: actions/setup-node@v2
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- name: Install Prettier
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run: npm install -g prettier @prettier/plugin-php
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# Check that we actually need to fix something
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- name: Run 'prettier --check'
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id: prettier_status
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run: |
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if prettier --check ${GITHUB_WORKSPACE}; then
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echo "::set-output name=result::pass"
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else
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echo "::set-output name=result::fail"
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fi
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- name: Run 'prettier --write'
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if: steps.prettier_status.outputs.result == 'fail'
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run: prettier --write ${GITHUB_WORKSPACE}
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- name: Commit & push changes
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if: steps.prettier_status.outputs.result == 'fail'
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run: |
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git config user.email "core@nf-co.re"
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git config user.name "nf-core-bot"
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git config push.default upstream
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git add .
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git status
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git commit -m "[automated] Fix linting with Prettier"
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git push
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1
.github/workflows/main.yml
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1
.github/workflows/main.yml
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@ -66,6 +66,7 @@ jobs:
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- "jax"
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- "lugh"
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- "marvin"
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- "mjolnir_globe"
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- "maestro"
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- "mpcdf"
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- "munin"
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@ -121,6 +121,7 @@ Currently documentation is available for the following systems:
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- [LUGH](docs/lugh.md)
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- [MAESTRO](docs/maestro.md)
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- [MARVIN](docs/marvin.md)
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- [MJOLNIR_GLOBE](docs/mjolnir_globe.md)
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- [MPCDF](docs/mpcdf.md)
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- [MUNIN](docs/munin.md)
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- [NU_GENOMICS](docs/nu_genomics.md)
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25
conf/mjolnir_globe.config
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conf/mjolnir_globe.config
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//Profile config names for nf-core/configs
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params {
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config_profile_description = 'Section for Hologenomics and Section for Molecular Ecology and Evolution @ Globe Institute, University of Copenhagen - mjolnir_globe profile provided by nf-core/configs.'
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config_profile_contact = 'Aashild Vaagene (@ashildv)'
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config_profile_url = 'https://globe.ku.dk/research/'
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max_memory = 500.GB
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max_cpus = 50
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max_time = 720.h
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}
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singularity {
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enabled = true
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autoMounts = true
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cacheDir = '/maps/projects/mjolnir1/data/cache/nf-core/singularity'
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}
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process {
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executor = 'slurm'
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}
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cleanup = true
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executor {
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queueSize = 10
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}
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@ -196,10 +196,14 @@ process {
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withName:get_software_versions {
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cache = false
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clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}M" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 8)}M" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName:multiqc {
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clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga() * 2}G" }
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}
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}
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profiles {
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// Define the Scratch directory
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def scratch_dir = System.getenv("VSC_SCRATCH_VO_USER") ?: "scratch/"
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// Specify the work directory
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workDir = "$VSC_SCRATCH_VO_USER/work"
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workDir = "$scratch_dir/work"
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// Perform work directory cleanup when the run has succesfully completed
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cleanup = true
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// cleanup = true
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// Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
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executor {
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singularity {
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enabled = true
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autoMounts = true
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cacheDir = "$VSC_SCRATCH_VO_USER/singularity"
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cacheDir = "$scratch_dir/singularity"
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}
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// Define profiles for each cluster
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executor = 'slurm'
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queue = 'skitty'
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maxRetries = 2
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beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
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scratch = "$VSC_SCRATCH_VO_USER"
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beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
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scratch = "$scratch_dir"
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}
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}
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executor = 'slurm'
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queue = 'swalot'
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maxRetries = 2
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beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
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scratch = "$VSC_SCRATCH_VO_USER"
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beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
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scratch = "$scratch_dir"
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}
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}
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executor = 'slurm'
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queue = 'victini'
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maxRetries = 2
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beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
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scratch = "$VSC_SCRATCH_VO_USER"
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beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
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scratch = "$scratch_dir"
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}
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}
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executor = 'slurm'
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queue = 'kirlia'
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maxRetries = 2
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beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
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scratch = "$VSC_SCRATCH_VO_USER"
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beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
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scratch = "$scratch_dir"
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}
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}
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@ -108,8 +111,8 @@ profiles {
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executor = 'slurm'
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queue = 'doduo'
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maxRetries = 2
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beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
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scratch = "$VSC_SCRATCH_VO_USER"
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beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
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scratch = "$scratch_dir"
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}
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}
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}
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31
docs/mjolnir_globe.md
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31
docs/mjolnir_globe.md
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# nf-core/configs: Section for Hologenomics at GLOBE, University of Copenhagen (Mjolnir server) Configuration
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> **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
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Prior to running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_nfcore` in their data/project directory on Mjolnir where the temp files from nf-core pipelines will be re-directed by the `NXF_TEMP` command (see below).
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The contents of the `.tmp_nfcore` directory should be periodically deleted manually to save on space.
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If the `NXF_TEMP` command is not used to properly re-direct temp files the `/tmp` directory on the compute nodes will be used and quickly filled up, which blocks anyone from working on these nodes until the offending user removes their files.
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The following lines **must** be added by users to their `~/.bash_profile`:
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```bash
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#re-direct tmp files away from /tmp directories on compute nodes or the headnode
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export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_nfcore
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# nextflow - limiting memory of virtual java machine
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NXF_OPTS='-Xms1g -Xmx4g'
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```
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Once you have created the `.tmp_nfcore` directory and added the above lines of code to your `.bash_profile` you can run an nf-core pipeline.
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Before running a pipeline you will need to load Java, Miniconda, Singularity and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
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```bash
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## Load Java and Nextflow environment modules
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module purge
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module load jdk/1.8.0_291 miniconda singularity/3.8.0 nextflow/21.04.1.5556
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```
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All of the intermediate output files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
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The `mjolnir_globe` config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space.
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@ -49,6 +49,7 @@ profiles {
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lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" }
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maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" }
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marvin { includeConfig "${params.custom_config_base}/conf/marvin.config" }
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mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" }
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mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
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munin { includeConfig "${params.custom_config_base}/conf/munin.config" }
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nihbiowulf { includeConfig "${params.custom_config_base}/conf/nihbiowulf.config" }
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