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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:
James Fellows Yates 2022-06-15 15:22:25 +02:00
commit 76b0d1dd85
8 changed files with 135 additions and 14 deletions

55
.github/workflows/fix-linting.yml vendored Normal file
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@ -0,0 +1,55 @@
name: Fix linting from a comment
on:
issue_comment:
types: [created]
jobs:
deploy:
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
if: >
contains(github.event.comment.html_url, '/pull/') &&
contains(github.event.comment.body, '@nf-core-bot fix linting') &&
github.repository == 'nf-core/configs'
runs-on: ubuntu-latest
steps:
# Use the @nf-core-bot token to check out so we can push later
- uses: actions/checkout@v3
with:
token: ${{ secrets.nf_core_bot_auth_token }}
# Action runs on the issue comment, so we don't get the PR by default
# Use the gh cli to check out the PR
- name: Checkout Pull Request
run: gh pr checkout ${{ github.event.issue.number }}
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
- uses: actions/setup-node@v2
- name: Install Prettier
run: npm install -g prettier @prettier/plugin-php
# Check that we actually need to fix something
- name: Run 'prettier --check'
id: prettier_status
run: |
if prettier --check ${GITHUB_WORKSPACE}; then
echo "::set-output name=result::pass"
else
echo "::set-output name=result::fail"
fi
- name: Run 'prettier --write'
if: steps.prettier_status.outputs.result == 'fail'
run: prettier --write ${GITHUB_WORKSPACE}
- name: Commit & push changes
if: steps.prettier_status.outputs.result == 'fail'
run: |
git config user.email "core@nf-co.re"
git config user.name "nf-core-bot"
git config push.default upstream
git add .
git status
git commit -m "[automated] Fix linting with Prettier"
git push

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@ -66,6 +66,7 @@ jobs:
- "jax"
- "lugh"
- "marvin"
- "mjolnir_globe"
- "maestro"
- "mpcdf"
- "munin"

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@ -121,6 +121,7 @@ Currently documentation is available for the following systems:
- [LUGH](docs/lugh.md)
- [MAESTRO](docs/maestro.md)
- [MARVIN](docs/marvin.md)
- [MJOLNIR_GLOBE](docs/mjolnir_globe.md)
- [MPCDF](docs/mpcdf.md)
- [MUNIN](docs/munin.md)
- [NU_GENOMICS](docs/nu_genomics.md)

25
conf/mjolnir_globe.config Normal file
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//Profile config names for nf-core/configs
params {
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.'
config_profile_contact = 'Aashild Vaagene (@ashildv)'
config_profile_url = 'https://globe.ku.dk/research/'
max_memory = 500.GB
max_cpus = 50
max_time = 720.h
}
singularity {
enabled = true
autoMounts = true
cacheDir = '/maps/projects/mjolnir1/data/cache/nf-core/singularity'
}
process {
executor = 'slurm'
}
cleanup = true
executor {
queueSize = 10
}

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@ -196,10 +196,14 @@ process {
withName:get_software_versions {
cache = false
clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}M" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 8)}M" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName:multiqc {
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga() * 2}G" }
}
}
profiles {

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@ -1,8 +1,11 @@
// Define the Scratch directory
def scratch_dir = System.getenv("VSC_SCRATCH_VO_USER") ?: "scratch/"
// Specify the work directory
workDir = "$VSC_SCRATCH_VO_USER/work"
workDir = "$scratch_dir/work"
// Perform work directory cleanup when the run has succesfully completed
cleanup = true
// cleanup = true
// Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
executor {
@ -13,7 +16,7 @@ executor {
singularity {
enabled = true
autoMounts = true
cacheDir = "$VSC_SCRATCH_VO_USER/singularity"
cacheDir = "$scratch_dir/singularity"
}
// Define profiles for each cluster
@ -32,8 +35,8 @@ profiles {
executor = 'slurm'
queue = 'skitty'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
@ -51,8 +54,8 @@ profiles {
executor = 'slurm'
queue = 'swalot'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
@ -70,8 +73,8 @@ profiles {
executor = 'slurm'
queue = 'victini'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
@ -89,8 +92,8 @@ profiles {
executor = 'slurm'
queue = 'kirlia'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
@ -108,8 +111,8 @@ profiles {
executor = 'slurm'
queue = 'doduo'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
}

31
docs/mjolnir_globe.md Normal file
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@ -0,0 +1,31 @@
# nf-core/configs: Section for Hologenomics at GLOBE, University of Copenhagen (Mjolnir server) Configuration
> **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
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).
The contents of the `.tmp_nfcore` directory should be periodically deleted manually to save on space.
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.
The following lines **must** be added by users to their `~/.bash_profile`:
```bash
#re-direct tmp files away from /tmp directories on compute nodes or the headnode
export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_nfcore
# nextflow - limiting memory of virtual java machine
NXF_OPTS='-Xms1g -Xmx4g'
```
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.
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:
```bash
## Load Java and Nextflow environment modules
module purge
module load jdk/1.8.0_291 miniconda singularity/3.8.0 nextflow/21.04.1.5556
```
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.
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 {
lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" }
maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" }
marvin { includeConfig "${params.custom_config_base}/conf/marvin.config" }
mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" }
mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
munin { includeConfig "${params.custom_config_base}/conf/munin.config" }
nihbiowulf { includeConfig "${params.custom_config_base}/conf/nihbiowulf.config" }