mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-10 20:13:09 +00:00
Merge branch 'nf-core:master' into feat/hasta_java_memory_fix
This commit is contained in:
commit
c8c795595a
22 changed files with 434 additions and 13 deletions
55
.github/workflows/fix-linting.yml
vendored
Normal file
55
.github/workflows/fix-linting.yml
vendored
Normal file
|
@ -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
|
2
.github/workflows/main.yml
vendored
2
.github/workflows/main.yml
vendored
|
@ -66,6 +66,7 @@ jobs:
|
|||
- "jax"
|
||||
- "lugh"
|
||||
- "marvin"
|
||||
- "mjolnir_globe"
|
||||
- "maestro"
|
||||
- "mpcdf"
|
||||
- "munin"
|
||||
|
@ -86,6 +87,7 @@ jobs:
|
|||
- "utd_sysbio"
|
||||
- "uzh"
|
||||
- "vai"
|
||||
- "vsc_ugent"
|
||||
steps:
|
||||
- uses: actions/checkout@v1
|
||||
- name: Install Nextflow
|
||||
|
|
11
README.md
11
README.md
|
@ -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)
|
||||
|
@ -139,6 +140,7 @@ Currently documentation is available for the following systems:
|
|||
- [UTD_SYSBIO](docs/utd_sysbio.md)
|
||||
- [UZH](docs/uzh.md)
|
||||
- [VAI](docs/vai.md)
|
||||
- [VSC_UGENT](docs/vsc_ugent.md)
|
||||
|
||||
### Uploading to `nf-core/configs`
|
||||
|
||||
|
@ -192,13 +194,18 @@ Currently documentation is available for the following pipelines within specific
|
|||
- [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
|
||||
- eager
|
||||
- [EVA](docs/pipeline/eager/eva.md)
|
||||
- mag
|
||||
- [EVA](docs/pipeline/mag/eva.md)
|
||||
- rnafusion
|
||||
- [MUNIN](docs/pipeline/rnafusion/munin.md)
|
||||
- rnavar
|
||||
- [MUNIN](docs/pipeline/rnavar/munin.md)
|
||||
- sarek
|
||||
- [MUNIN](docs/pipeline/sarek/munin.md)
|
||||
- [UPPMAX](docs/pipeline/sarek/uppmax.md)
|
||||
- rnavar
|
||||
- [MUNIN](docs/pipeline/rnavar/munin.md)
|
||||
- taxprofiler
|
||||
- [EVA](docs/pipeline/taxprofiler/eva.md)
|
||||
- [hasta](docs/pipeline/taxprofiler/hasta.md)
|
||||
|
||||
### Pipeline-specific documentation
|
||||
|
||||
|
|
|
@ -17,7 +17,7 @@ process {
|
|||
executor = 'sge'
|
||||
penv = 'smp'
|
||||
queue = 'all.q'
|
||||
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -j y -o output.sge -l h_vmem=${task.memory.toGiga()}G" }
|
||||
}
|
||||
|
||||
executor {
|
||||
|
@ -37,7 +37,7 @@ profiles {
|
|||
|
||||
process {
|
||||
queue = { task.memory > 700.GB ? 'bigmem.q' : 'archgen.q' }
|
||||
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
|
||||
clusterOptions = { "-S /bin/bash -V -j y -o output.sge -l h_vmem=${task.memory.toGiga()}G" }
|
||||
}
|
||||
|
||||
singularity {
|
||||
|
|
|
@ -15,7 +15,8 @@ google.zone = params.google_zone
|
|||
google.lifeSciences.debug = params.google_debug
|
||||
workDir = params.google_bucket
|
||||
google.lifeSciences.preemptible = params.google_preemptible
|
||||
|
||||
if (google.lifeSciences.preemptible) {
|
||||
process.errorStrategy = { task.exitStatus==14 ? 'retry' : 'terminate' }
|
||||
process.errorStrategy = { task.exitStatus in [8,10,14] ? 'retry' : 'terminate' }
|
||||
process.maxRetries = 5
|
||||
}
|
|
@ -2,23 +2,22 @@
|
|||
params {
|
||||
config_profile_description = 'The IFB core cluster profile'
|
||||
config_profile_contact = 'https://community.france-bioinformatique.fr'
|
||||
config_profile_url = 'https://www.france-bioinformatique.fr/'
|
||||
config_profile_url = 'https://ifb-elixirfr.gitlab.io/cluster/doc/cluster-desc/'
|
||||
}
|
||||
|
||||
singularity {
|
||||
// need one image per execution
|
||||
enabled = true
|
||||
runOptions = '-B /shared'
|
||||
}
|
||||
|
||||
process {
|
||||
executor = 'slurm'
|
||||
queue = { task.time <= 24.h ? 'fast' : 'long' }
|
||||
}
|
||||
|
||||
params {
|
||||
igenomes_ignore = true
|
||||
// Max resources requested by a normal node on genotoul.
|
||||
max_memory = 240.GB
|
||||
max_cpus = 28
|
||||
max_time = 96.h
|
||||
max_memory = 252.GB
|
||||
max_cpus = 56
|
||||
max_time = 720.h
|
||||
}
|
||||
|
|
25
conf/mjolnir_globe.config
Normal file
25
conf/mjolnir_globe.config
Normal file
|
@ -0,0 +1,25 @@
|
|||
//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
|
||||
}
|
|
@ -197,6 +197,10 @@ process {
|
|||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName:eigenstrat_snp_coverage {
|
||||
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
|
||||
}
|
||||
|
||||
withName:kraken_merge {
|
||||
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
|
||||
}
|
||||
|
|
14
conf/pipeline/mag/eva.config
Normal file
14
conf/pipeline/mag/eva.config
Normal file
|
@ -0,0 +1,14 @@
|
|||
params {
|
||||
// Specific nf-core/configs params
|
||||
config_profile_contact = 'James Fellows Yates (@jfy133)'
|
||||
config_profile_description = 'nf-core/mag EVA profile provided by nf-core/configs'
|
||||
}
|
||||
|
||||
process {
|
||||
|
||||
withName: FASTQC {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
}
|
29
conf/pipeline/taxprofiler/eva.config
Normal file
29
conf/pipeline/taxprofiler/eva.config
Normal file
|
@ -0,0 +1,29 @@
|
|||
params {
|
||||
// Specific nf-core/configs params
|
||||
config_profile_contact = 'James Fellows Yates (@jfy133)'
|
||||
config_profile_description = 'nf-core/taxprofiler EVA profile provided by nf-core/configs'
|
||||
}
|
||||
|
||||
process {
|
||||
|
||||
withName: BBMAP_BBDUK {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: MALT_RUN {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: METAPHLAN3 {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: MEGAN_RMA2INFO {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
}
|
16
conf/pipeline/taxprofiler/hasta.config
Normal file
16
conf/pipeline/taxprofiler/hasta.config
Normal file
|
@ -0,0 +1,16 @@
|
|||
params {
|
||||
// Specific nf-core/configs params
|
||||
config_profile_contact = 'Sofia Stamouli (@sofstam)'
|
||||
config_profile_description = 'nf-core/taxprofiler HASTA profile provided by nf-core/configs'
|
||||
}
|
||||
|
||||
process {
|
||||
|
||||
withName:'BBMAP_BBDUK' {
|
||||
memory = { check_max( 80.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
withName: 'MALT_RUN' {
|
||||
memory = { check_max( 80.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
}
|
117
conf/vsc_ugent.config
Normal file
117
conf/vsc_ugent.config
Normal file
|
@ -0,0 +1,117 @@
|
|||
// Define the Scratch directory
|
||||
def scratch_dir = System.getenv("VSC_SCRATCH_VO_USER") ?: "scratch/"
|
||||
|
||||
// Specify the work directory
|
||||
workDir = "$scratch_dir/work"
|
||||
|
||||
// Perform work directory cleanup when the run has succesfully completed
|
||||
// cleanup = true
|
||||
|
||||
// Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
|
||||
executor {
|
||||
submitRateLimit = '10 sec'
|
||||
}
|
||||
|
||||
// Specify that singularity should be used and where the cache dir will be for the images
|
||||
singularity {
|
||||
enabled = true
|
||||
autoMounts = true
|
||||
cacheDir = "$scratch_dir/singularity"
|
||||
}
|
||||
|
||||
env {
|
||||
SINGULARITY_CACHEDIR="$scratch_dir/.singularity"
|
||||
}
|
||||
|
||||
// Define profiles for each cluster
|
||||
profiles {
|
||||
skitty {
|
||||
params {
|
||||
config_profile_description = 'HPC_SKITTY profile for use on the Skitty cluster of the VSC HPC.'
|
||||
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
|
||||
config_profile_url = 'https://www.ugent.be/hpc/en'
|
||||
max_memory = 177.GB
|
||||
max_cpus = 36
|
||||
max_time = 72.h
|
||||
}
|
||||
|
||||
process {
|
||||
executor = 'slurm'
|
||||
queue = 'skitty'
|
||||
maxRetries = 2
|
||||
scratch = "$scratch_dir"
|
||||
}
|
||||
}
|
||||
|
||||
swalot {
|
||||
params {
|
||||
config_profile_description = 'HPC_SWALOT profile for use on the Swalot cluster of the VSC HPC.'
|
||||
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
|
||||
config_profile_url = 'https://www.ugent.be/hpc/en'
|
||||
max_memory = 116.GB
|
||||
max_cpus = 20
|
||||
max_time = 72.h
|
||||
}
|
||||
|
||||
process {
|
||||
executor = 'slurm'
|
||||
queue = 'swalot'
|
||||
maxRetries = 2
|
||||
scratch = "$scratch_dir"
|
||||
}
|
||||
}
|
||||
|
||||
victini {
|
||||
params {
|
||||
config_profile_description = 'HPC_VICTINI profile for use on the Victini cluster of the VSC HPC.'
|
||||
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
|
||||
config_profile_url = 'https://www.ugent.be/hpc/en'
|
||||
max_memory = 88.GB
|
||||
max_cpus = 36
|
||||
max_time = 72.h
|
||||
}
|
||||
|
||||
process {
|
||||
executor = 'slurm'
|
||||
queue = 'victini'
|
||||
maxRetries = 2
|
||||
scratch = "$scratch_dir"
|
||||
}
|
||||
}
|
||||
|
||||
kirlia {
|
||||
params {
|
||||
config_profile_description = 'HPC_KIRLIA profile for use on the Kirlia cluster of the VSC HPC.'
|
||||
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
|
||||
config_profile_url = 'https://www.ugent.be/hpc/en'
|
||||
max_memory = 738.GB
|
||||
max_cpus = 36
|
||||
max_time = 72.h
|
||||
}
|
||||
|
||||
process {
|
||||
executor = 'slurm'
|
||||
queue = 'kirlia'
|
||||
maxRetries = 2
|
||||
scratch = "$scratch_dir"
|
||||
}
|
||||
}
|
||||
|
||||
doduo {
|
||||
params {
|
||||
config_profile_description = 'HPC_DODUO profile for use on the Doduo cluster of the VSC HPC.'
|
||||
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)'
|
||||
config_profile_url = 'https://www.ugent.be/hpc/en'
|
||||
max_memory = 250.GB
|
||||
max_cpus = 96
|
||||
max_time = 72.h
|
||||
}
|
||||
|
||||
process {
|
||||
executor = 'slurm'
|
||||
queue = 'doduo'
|
||||
maxRetries = 2
|
||||
scratch = "$scratch_dir"
|
||||
}
|
||||
}
|
||||
}
|
|
@ -6,7 +6,8 @@ To use, run the pipeline with `-profile ifb_core`. This will download and launch
|
|||
|
||||
## How to use on IFB core
|
||||
|
||||
Before running the pipeline you will need to load Nextflow using the environment module system on IFB core. You can do this by issuing the commands below:
|
||||
Here is [the link to the cluster's documentation](https://ifb-elixirfr.gitlab.io/cluster/doc/quick-start/).
|
||||
Before running the pipeline you will need to load Nextflow and other dependencies using the environment module system on IFB core. You can do this by issuing the commands below:
|
||||
|
||||
```bash
|
||||
# Login to a compute node
|
||||
|
@ -14,7 +15,10 @@ srun --pty bash
|
|||
|
||||
## Load Nextflow and Singularity environment modules
|
||||
module purge
|
||||
module load nextflow/20.04.1
|
||||
module load nextflow
|
||||
module load singularity
|
||||
module load openjdk
|
||||
|
||||
|
||||
# Run a downloaded/git-cloned nextflow workflow from
|
||||
nextflow run \\
|
||||
|
|
31
docs/mjolnir_globe.md
Normal file
31
docs/mjolnir_globe.md
Normal file
|
@ -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.
|
15
docs/pipeline/mag/eva.md
Normal file
15
docs/pipeline/mag/eva.md
Normal file
|
@ -0,0 +1,15 @@
|
|||
# nf-core/configs: eva mag specific configuration
|
||||
|
||||
Extra specific configuration for mag pipeline
|
||||
|
||||
## Usage
|
||||
|
||||
To use, run the pipeline with `-profile eva`.
|
||||
|
||||
This will download and launch the mag specific [`eva.config`](../../../conf/pipeline/mag/eva.config) which has been pre-configured with a setup suitable for the MPI-EVA cluster.
|
||||
|
||||
Example: `nextflow run nf-core/mag -profile eva`
|
||||
|
||||
## mag specific configurations for eva
|
||||
|
||||
Specific configurations for eva has been made for mag, primarily adjusting SGE memory requirements of Java tools (e.g. FastQC).
|
19
docs/pipeline/taxprofiler/eva.md
Normal file
19
docs/pipeline/taxprofiler/eva.md
Normal file
|
@ -0,0 +1,19 @@
|
|||
# nf-core/configs: eva taxprofiler specific configuration
|
||||
|
||||
Extra specific configuration for taxprofiler pipeline
|
||||
|
||||
## Usage
|
||||
|
||||
To use, run the pipeline with `-profile eva`.
|
||||
|
||||
This will download and launch the taxprofiler specific [`eva.config`](../../../conf/pipeline/taxprofiler/eva.config) which has been pre-configured with a setup suitable for the MPI-EVA cluster.
|
||||
|
||||
Example: `nextflow run nf-core/taxprofiler -profile eva`
|
||||
|
||||
## taxprofiler specific configurations for eva
|
||||
|
||||
Specific configurations for eva has been made for taxprofiler.
|
||||
|
||||
### General profiles
|
||||
|
||||
- The general MPI-EVA profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues SGE have with Java and python tools, nameling: BBDUK, MALT, MetaPhlAn3, and MEGAN
|
19
docs/pipeline/taxprofiler/hasta.md
Normal file
19
docs/pipeline/taxprofiler/hasta.md
Normal file
|
@ -0,0 +1,19 @@
|
|||
# nf-core/configs: eva taxprofiler specific configuration
|
||||
|
||||
Extra specific configuration for taxprofiler pipeline
|
||||
|
||||
## Usage
|
||||
|
||||
To use, run the pipeline with `-profile hasta`.
|
||||
|
||||
This will download and launch the taxprofiler specific [`hasta.config`](../../../conf/pipeline/taxprofiler/hasta.config) which has been pre-configured with a setup suitable for the hasta cluster.
|
||||
|
||||
Example: `nextflow run nf-core/taxprofiler -profile hasta`
|
||||
|
||||
## taxprofiler specific configurations for hasta
|
||||
|
||||
Specific configurations for hasta has been made for taxprofiler.
|
||||
|
||||
### General profiles
|
||||
|
||||
- The general hasta profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues with: BBDUK and MALT.
|
35
docs/vsc_ugent.md
Normal file
35
docs/vsc_ugent.md
Normal file
|
@ -0,0 +1,35 @@
|
|||
# nf-core/configs: University of Ghent High Performance Computing Infrastructure (VSC)
|
||||
|
||||
> **NB:** You will need an [account](https://www.ugent.be/hpc/en/access/faq/access) to use the HPC cluster to run the pipeline.
|
||||
|
||||
First you should go to the cluster you want to run the pipeline on. You can check what clusters have the most free space on this [link](https://shieldon.ugent.be:8083/pbsmon-web-users/). Use the following commands to easily switch between clusters:
|
||||
|
||||
```shell
|
||||
module purge
|
||||
module swap cluster/<CLUSTER>
|
||||
```
|
||||
|
||||
Before running the pipeline you will need to create a PBS script to submit as a job.
|
||||
|
||||
```bash
|
||||
#!/bin/bash
|
||||
|
||||
module load Nextflow
|
||||
|
||||
nextflow run <pipeline> -profile vsc_ugent,<CLUSTER> <Add your other parameters>
|
||||
```
|
||||
|
||||
All of the intermediate 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 config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. The default work directory is set to `$VSC_SCRATCH_VO_USER/work` per this configuration
|
||||
|
||||
You can also add several TORQUE options to the PBS script. More about this on this [link](http://hpcugent.github.io/vsc_user_docs/pdf/intro-HPC-linux-gent.pdf#appendix.B).
|
||||
|
||||
To submit your job to the cluster by using the following command:
|
||||
|
||||
```shell
|
||||
qsub <script name>.pbs
|
||||
```
|
||||
|
||||
> **NB:** The profile only works for the clusters `skitty`, `swalot`, `victini`, `kirlia` and `doduo`.
|
||||
|
||||
> **NB:** The default directory where the `work/` and `singularity/` (cache directory for images) is located in `$VSC_SCRATCH_VO_USER`.
|
|
@ -49,6 +49,7 @@ profiles {
|
|||
lugh { includeConfig "${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" }
|
||||
|
@ -68,4 +69,5 @@ profiles {
|
|||
utd_sysbio { includeConfig "${params.custom_config_base}/conf/utd_sysbio.config" }
|
||||
uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
|
||||
vai { includeConfig "${params.custom_config_base}/conf/vai.config" }
|
||||
vsc_ugent { includeConfig "${params.custom_config_base}/conf/vsc_ugent.config" }
|
||||
}
|
||||
|
|
13
pipeline/mag.config
Normal file
13
pipeline/mag.config
Normal file
|
@ -0,0 +1,13 @@
|
|||
/*
|
||||
* -------------------------------------------------
|
||||
* nfcore/mag custom profile Nextflow config file
|
||||
* -------------------------------------------------
|
||||
* Config options for custom environments.
|
||||
* Cluster-specific config options should be saved
|
||||
* in the conf/pipeline/mag folder and imported
|
||||
* under a profile name here.
|
||||
*/
|
||||
|
||||
profiles {
|
||||
eva { includeConfig "${params.custom_config_base}/conf/pipeline/mag/eva.config" }
|
||||
}
|
14
pipeline/taxprofiler.config
Normal file
14
pipeline/taxprofiler.config
Normal file
|
@ -0,0 +1,14 @@
|
|||
/*
|
||||
* -------------------------------------------------
|
||||
* nfcore/taxprofiler custom profile Nextflow config file
|
||||
* -------------------------------------------------
|
||||
* Config options for custom environments.
|
||||
* Cluster-specific config options should be saved
|
||||
* in the conf/pipeline/taxprofiler folder and imported
|
||||
* under a profile name here.
|
||||
*/
|
||||
|
||||
profiles {
|
||||
hasta { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/hasta.config" }
|
||||
eva { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/eva.config" }
|
||||
}
|
Loading…
Reference in a new issue