millironx/nf-configs
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12
.editorconfig Normal file
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@ -0,0 +1,12 @@
root = true
[*]
charset = utf-8
end_of_line = lf
insert_final_newline = true
trim_trailing_whitespace = true
indent_size = 4
indent_style = space
[*.{md,yml,yaml}]
indent_size = 2

17
.github/PULL_REQUEST_TEMPLATE.md vendored
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@ -5,16 +5,17 @@ about: A new cluster config
Please follow these steps before submitting your PR:
* [ ] If your PR is a work in progress, include `[WIP]` in its title
* [ ] Your PR targets the `master` branch
* [ ] You've included links to relevant issues, if any
- [ ] If your PR is a work in progress, include `[WIP]` in its title
- [ ] Your PR targets the `master` branch
- [ ] You've included links to relevant issues, if any
Steps for adding a new config profile:
* [ ] Add your custom config file to the `conf/` directory
* [ ] Add your documentation file to the `docs/` directory
* [ ] Add your custom profile to the `nfcore_custom.config` file in the top-level directory
* [ ] Add your custom profile to the `README.md` file in the top-level directory
* [ ] Add your profile name to the `profile:` scope in `.github/workflows/main.yml`
- [ ] Add your custom config file to the `conf/` directory
- [ ] Add your documentation file to the `docs/` directory
- [ ] Add your custom profile to the `nfcore_custom.config` file in the top-level directory
- [ ] Add your custom profile to the `README.md` file in the top-level directory
- [ ] Add your profile name to the `profile:` scope in `.github/workflows/main.yml`
<!--
If you require/still waiting for a review, please feel free to request from @nf-core/configs-team

5
.github/markdownlint.yml vendored
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@ -1,5 +0,0 @@
# Markdownlint configuration file
default: true,
line-length: false
no-duplicate-header:
siblings_only: true

30
.github/workflows/linting.yml vendored
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@ -1,18 +1,22 @@
name: Markdown linting
# This workflow is triggered on pushes and PRs to the repository.
on: [push, pull_request]
name: Code Linting
on:
pull_request:
push:
branches:
- master
jobs:
Markdown:
runs-on: ubuntu-18.04
prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: actions/setup-node@v2
- name: Install markdownlint
run: |
npm install -g markdownlint-cli
- name: Run Markdownlint
run: |
markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
- name: Check out repository
uses: actions/checkout@v2
- name: Install NodeJS
uses: actions/setup-node@v2
- name: Install Prettier
run: npm install -g prettier
- name: Run Prettier --check
run: prettier --check ${GITHUB_WORKSPACE}

114
.github/workflows/main.yml vendored
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@ -3,7 +3,6 @@ name: Configs tests
on: [pull_request, push]
jobs:
test_all_profiles:
runs-on: ubuntu-latest
name: Check if all profiles are tested
@ -30,61 +29,64 @@ jobs:
strategy:
matrix:
profile:
- 'abims'
- 'alice'
- 'aws_tower'
- 'awsbatch'
- 'azurebatch'
- 'bi'
- 'bigpurple'
- 'binac'
- 'biohpc_gen'
- 'cambridge'
- 'leicester'
- 'cbe'
- 'ccga_dx'
- 'ccga_med'
- 'cfc'
- 'cfc_dev'
- 'cheaha'
- 'computerome'
- 'crick'
- 'denbi_qbic'
- 'ebc'
- 'eddie'
- 'eva'
- 'fgcz'
- 'genotoul'
- 'genouest'
- 'gis'
- 'google'
- 'hasta'
- 'hebbe'
- 'icr_davros'
- 'ifb_core'
- 'imperial'
- 'jax'
- 'lugh'
- 'marvin'
- 'maestro'
- 'mpcdf'
- 'munin'
- 'nu_genomics'
- 'nihbiowulf'
- 'oist'
- 'pasteur'
- 'phoenix'
- 'prince'
- 'rosalind'
- 'sanger'
- 'seg_globe'
- 'uct_hpc'
- 'unibe_ibu'
- 'uppmax'
- 'utd_ganymede'
- 'utd_sysbio'
- 'uzh'
- 'vai'
- "abims"
- "alice"
- "aws_tower"
- "awsbatch"
- "azurebatch"
- "bi"
- "bigpurple"
- "binac"
- "biohpc_gen"
- "cambridge"
- "leicester"
- "cbe"
- "ccga_dx"
- "ccga_med"
- "cedars"
- "cfc"
- "cfc_dev"
- "cheaha"
- "computerome"
- "crick"
- "denbi_qbic"
- "ebc"
- "eddie"
- "eva"
- "fgcz"
- "genotoul"
- "genouest"
- "gis"
- "google"
- "hasta"
- "hebbe"
- "icr_davros"
- "ifb_core"
- "imperial"
- "jax"
- "lugh"
- "marvin"
- "maestro"
- "mpcdf"
- "munin"
- "nu_genomics"
- "nihbiowulf"
- "oist"
- "pasteur"
- "phoenix"
- "prince"
- "rosalind"
- "sahmri"
- "sanger"
- "seg_globe"
- "uct_hpc"
- "unibe_ibu"
- "uppmax"
- "utd_ganymede"
- "utd_sysbio"
- "uzh"
- "vai"
- "vsc_ugent"
steps:
- uses: actions/checkout@v1
- name: Install Nextflow

7
.prettierignore Normal file
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@ -0,0 +1,7 @@
# gitignore
.nextflow*
work/
data/
results/
.DS_Store
*.code-workspace

1
.prettierrc.yml Normal file
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@ -0,0 +1 @@
printWidth: 120

183
README.md
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@ -6,20 +6,20 @@ A repository for hosting Nextflow configuration files containing custom paramete
## Table of contents <!-- omit in toc -->
* [Using an existing config](#using-an-existing-config)
* [Configuration and parameters](#configuration-and-parameters)
* [Offline usage](#offline-usage)
* [Adding a new config](#adding-a-new-config)
* [Checking user hostnames](#checking-user-hostnames)
* [Testing](#testing)
* [Documentation](#documentation)
* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
* [Pipeline-specific institutional documentation](#pipeline-specific-institutional-documentation)
* [Pipeline-specific documentation](#pipeline-specific-documentation)
* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
* [Help](#help)
- [Using an existing config](#using-an-existing-config)
- [Configuration and parameters](#configuration-and-parameters)
- [Offline usage](#offline-usage)
- [Adding a new config](#adding-a-new-config)
- [Checking user hostnames](#checking-user-hostnames)
- [Testing](#testing)
- [Documentation](#documentation)
- [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
- [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
- [Pipeline-specific institutional documentation](#pipeline-specific-institutional-documentation)
- [Pipeline-specific documentation](#pipeline-specific-documentation)
- [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
- [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
- [Help](#help)
## Using an existing config
@ -86,68 +86,70 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
Currently documentation is available for the following systems:
* [ABIMS](docs/abims.md)
* [ALICE](docs/alice.md)
* [AWSBATCH](docs/awsbatch.md)
* [AWS_TOWER](docs/aws_tower.md)
* [AZUREBATCH](docs/azurebatch.md)
* [BIGPURPLE](docs/bigpurple.md)
* [BI](docs/bi.md)
* [BINAC](docs/binac.md)
* [BIOHPC_GEN](docs/biohpc_gen.md)
* [CAMBRIDGE](docs/cambridge.md)
* [CBE](docs/cbe.md)
* [CCGA_DX](docs/ccga_dx.md)
* [CCGA_MED](docs/ccga_med.md)
* [CFC](docs/cfc.md)
* [CHEAHA](docs/cheaha.md)
* [Computerome](docs/computerome.md)
* [CRICK](docs/crick.md)
* [CZBIOHUB_AWS](docs/czbiohub.md)
* [DENBI_QBIC](docs/denbi_qbic.md)
* [EBC](docs/ebc.md)
* [EVA](docs/eva.md)
* [FGCZ](docs/fgcz.md)
* [GENOTOUL](docs/genotoul.md)
* [GENOUEST](docs/genouest.md)
* [GIS](docs/gis.md)
* [GOOGLE](docs/google.md)
* [HASTA](docs/hasta.md)
* [HEBBE](docs/hebbe.md)
* [ICR_DAVROS](docs/icr_davros.md)
* [IMPERIAL](docs/imperial.md)
* [JAX](docs/jax.md)
* [LUGH](docs/lugh.md)
* [MAESTRO](docs/maestro.md)
* [MARVIN](docs/marvin.md)
* [MPCDF](docs/mpcdf.md)
* [MUNIN](docs/munin.md)
* [NU_GENOMICS](docs/nu_genomics.md)
* [NIHBIOWULF](docs/nihbiowulf.md)
* [OIST](docs/oist.md)
* [PASTEUR](docs/pasteur.md)
* [PHOENIX](docs/phoenix.md)
* [PRINCE](docs/prince.md)
* [ROSALIND](docs/rosalind.md)
* [SANGER](docs/sanger.md)
* [SEG_GLOBE](docs/seg_globe.md)
* [UCT_HPC](docs/uct_hpc.md)
* [UNIBE_IBU](docs/unibe_ibu.md)
* [UPPMAX](docs/uppmax.md)
* [UTD_GANYMEDE](docs/utd_ganymede.md)
* [UTD_SYSBIO](docs/utd_sysbio.md)
* [UZH](docs/uzh.md)
* [VAI](docs/vai.md)
- [ABIMS](docs/abims.md)
- [ALICE](docs/alice.md)
- [AWSBATCH](docs/awsbatch.md)
- [AWS_TOWER](docs/aws_tower.md)
- [AZUREBATCH](docs/azurebatch.md)
- [BIGPURPLE](docs/bigpurple.md)
- [BI](docs/bi.md)
- [BINAC](docs/binac.md)
- [BIOHPC_GEN](docs/biohpc_gen.md)
- [CAMBRIDGE](docs/cambridge.md)
- [CBE](docs/cbe.md)
- [CCGA_DX](docs/ccga_dx.md)
- [CCGA_MED](docs/ccga_med.md)
- [Cedars-Sinai](docs/cedars.md)
- [CFC](docs/cfc.md)
- [CHEAHA](docs/cheaha.md)
- [Computerome](docs/computerome.md)
- [CRICK](docs/crick.md)
- [CZBIOHUB_AWS](docs/czbiohub.md)
- [DENBI_QBIC](docs/denbi_qbic.md)
- [EBC](docs/ebc.md)
- [EVA](docs/eva.md)
- [FGCZ](docs/fgcz.md)
- [GENOTOUL](docs/genotoul.md)
- [GENOUEST](docs/genouest.md)
- [GIS](docs/gis.md)
- [GOOGLE](docs/google.md)
- [HASTA](docs/hasta.md)
- [HEBBE](docs/hebbe.md)
- [ICR_DAVROS](docs/icr_davros.md)
- [IMPERIAL](docs/imperial.md)
- [JAX](docs/jax.md)
- [LUGH](docs/lugh.md)
- [MAESTRO](docs/maestro.md)
- [MARVIN](docs/marvin.md)
- [MPCDF](docs/mpcdf.md)
- [MUNIN](docs/munin.md)
- [NU_GENOMICS](docs/nu_genomics.md)
- [NIHBIOWULF](docs/nihbiowulf.md)
- [OIST](docs/oist.md)
- [PASTEUR](docs/pasteur.md)
- [PHOENIX](docs/phoenix.md)
- [PRINCE](docs/prince.md)
- [ROSALIND](docs/rosalind.md)
- [SANGER](docs/sanger.md)
- [SEG_GLOBE](docs/seg_globe.md)
- [UCT_HPC](docs/uct_hpc.md)
- [UNIBE_IBU](docs/unibe_ibu.md)
- [UPPMAX](docs/uppmax.md)
- [UTD_GANYMEDE](docs/utd_ganymede.md)
- [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`
[Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account.
Within the local clone of your fork:
* **add** the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory
* **add** the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory
* **edit** and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone
* **edit** and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone
- **add** the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory
- **add** the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory
- **edit** and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone
- **edit** and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone
In order to ensure that the config file is tested automatically with GitHub Actions please add your profile name to the `profile:` scope (under strategy matrix) in [`.github/workflows/main.yml`](.github/workflows/main.yml). If you forget to do this the tests will fail with the error:
@ -186,25 +188,30 @@ Note that pipeline-specific configs are not required and should only be added if
Currently documentation is available for the following pipelines within specific profiles:
* ampliseq
* [BINAC](docs/pipeline/ampliseq/binac.md)
* [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
* eager
* [EVA](docs/pipeline/eager/eva.md)
* rnafusion
* [MUNIN](docs/pipeline/rnafusion/munin.md)
* sarek
* [MUNIN](docs/pipeline/sarek/munin.md)
* [UPPMAX](docs/pipeline/sarek/uppmax.md)
* rnavar
* [MUNIN](docs/pipeline/rnavar/munin.md)
- ampliseq
- [BINAC](docs/pipeline/ampliseq/binac.md)
- [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)
- taxprofiler
- [EVA](docs/pipeline/taxprofiler/eva.md)
- [hasta](docs/pipeline/taxprofiler/hasta.md)
### Pipeline-specific documentation
Currently documentation is available for the following pipeline:
* viralrecon
* [genomes](docs/pipeline/viralrecon/genomes.md)
- viralrecon
- [genomes](docs/pipeline/viralrecon/genomes.md)
### Enabling pipeline-specific configs within a pipeline
@ -233,7 +240,7 @@ We will be notified automatically when you have created your pull request, and p
[Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account.
And add or edit the following files in the local clone of your fork.
* `pipeline/<PIPELINE>.config`
- `pipeline/<PIPELINE>.config`
If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
@ -243,18 +250,18 @@ profiles {
}
```
* `conf/pipeline/<PIPELINE>/<PROFILE>.config`
- `conf/pipeline/<PIPELINE>/<PROFILE>.config`
Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory.
Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` to the top of `pipeline/<PIPELINE>.config` and set to reasonable values.
Users will get information on who wrote the pipeline-specific configuration profile then when executing the nf-core pipeline and can report back if there are things missing for example.
* `docs/pipeline/<PIPELINE>/<PROFILE>.md`
- `docs/pipeline/<PIPELINE>/<PROFILE>.md`
Add the documentation file to the `docs/pipeline/<PIPELINE>/` directory.
You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone.
* `README.md`
- `README.md`
Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation

26
conf/cedars.config Normal file
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@ -0,0 +1,26 @@
//Profile config names for nf-core/configs
params {
config_profile_description = 'Cedars-Sinai Medical Center HPC Profile'
config_profile_contact = 'Alex Rajewski (@rajewski)'
config_profile_url = 'https://www.cedars-sinai.edu/research/cores/informatics-computing/resources.html'
max_memory = 90.GB
max_cpus = 10
max_time = 240.h
}
// Specify the queing system
executor {
name = "sge"
}
process {
penv = 'smp'
beforeScript =
"""
module load 'singularity/3.6.0'
"""
}
singularity {
enabled = true
}

6
conf/eva.config
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@ -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 {
@ -36,8 +36,8 @@ profiles {
}
process {
queue = 'archgen.q'
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
queue = { task.memory > 700.GB ? 'bigmem.q' : 'archgen.q' }
clusterOptions = { "-S /bin/bash -V -j y -o output.sge -l h_vmem=${task.memory.toGiga()}G" }
}
singularity {

3
conf/google.config
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@ -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
}

1
conf/hasta.config
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@ -10,6 +10,7 @@ params {
singularity {
enabled = true
envWhitelist = ['_JAVA_OPTIONS']
}
params {

11
conf/ifb_core.config
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@ -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
}

4
conf/munin.config
View file

@ -20,9 +20,9 @@ process {
maxForks = 46
// Limit cpus for Mutect2
withName:'Mutect2|Mutect2Single' {
withName:'Mutect2|Mutect2Single|PileupSummariesForMutect2' {
time = {48.h * task.attempt}
maxForks = 23
maxForks = 12
}
}

36
conf/pipeline/eager/eva.config
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@ -70,6 +70,11 @@ process {
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: fastqc_after_clipping {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
@ -184,6 +189,25 @@ process {
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName:get_software_versions {
cache = false
clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName:eigenstrat_snp_coverage {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
}
withName:kraken_merge {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
}
withName:multiqc {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
}
}
profiles {
@ -256,6 +280,11 @@ profiles {
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: fastqc_after_clipping {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
@ -358,7 +387,6 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
}
}
}
@ -430,6 +458,11 @@ profiles {
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: fastqc_after_clipping {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
@ -533,7 +566,6 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
}
}
}

14
conf/pipeline/mag/eva.config Normal file
View 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' }
}
}

3
conf/pipeline/raredisease/hasta.config
View file

@ -7,4 +7,7 @@ process {
cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 80.GB * task.attempt, 'memory' ) }
}
withName:'QUALIMAP_BAMQC' {
ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" }
}
}

2
conf/pipeline/sarek/munin.config
View file

@ -23,7 +23,7 @@ params {
// Specific nf-core/sarek process configuration
process {
withLabel:sentieon {
module = {params.sentieon ? 'sentieon/202112.00' : null}
module = {params.sentieon ? 'sentieon/202112.02' : null}
container = {params.sentieon ? null : container}
}
}

5
conf/pipeline/sarek/uppmax.config
View file

@ -26,3 +26,8 @@ if (hostname ==~ "r.*") {
if (hostname ==~ "i.*") {
params.single_cpu_mem = 15.GB
}
// Miarka-specific config
if (hostname ==~ "m.*") {
params.single_cpu_mem = 7.GB
}

29
conf/pipeline/taxprofiler/eva.config Normal file
View 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
View 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' ) }
}
}

34
conf/sahmri.config Normal file
View file

@ -0,0 +1,34 @@
params {
config_profile_description = 'South Australian Health and Medical Research Institute (SAHMRI) HPC cluster profile.'
config_profile_contact = 'Nathan Watson-Haigh (nathan.watson-haigh@sahmri.com)'
config_profile_url = "https://sahmri.org.au"
max_memory = 375.GB
max_cpus = 32
max_time = 14.d
igenomes_base = '/cancer/storage/shared/igenomes/references/'
}
process {
executor = 'slurm'
queue = 'sahmri_prod_hpc,sahmri_cancer_hpc'
maxRetries = 2
cpus = { check_max( 2 * task.attempt, 'cpus') }
memory = { check_max( 1.GB * task.attempt, 'memory') }
time = { check_max( 10.m * task.attempt, 'time') }
}
executor {
queueSize = 50
submitRateLimit = '10 sec'
}
singularity {
enabled = true
autoMounts = true
beforeScript = 'export PATH=/apps/opt/singularity/latest/bin:${PATH}'
cacheDir = '/cancer/storage/shared/simg'
}
cleanup = true
profiles {
debug {
cleanup = false
}
}

24
conf/uppmax.config
View file

@ -23,7 +23,7 @@ singularity {
def hostname = "r1"
try {
hostname = "sinfo --local -N -h | grep -m 1 -F -v CLUSTER: | cut -f1 -d' ' ".execute().text.trim()
hostname = ['/bin/bash', '-c', 'sinfo --local -N -h | grep -m 1 -F -v CLUSTER: | cut -f1 -d" "'].execute().text.trim()
} catch (java.io.IOException e) {
System.err.println("WARNING: Could not run sinfo to determine current cluster, defaulting to rackham")
}
@ -36,6 +36,20 @@ def clusterOptionsCreator = { m ->
return base
}
// cluster is miarka
if (hostname.startsWith("m")) {
// job will fit on a regular node
if (m <= 357.GB) {
return base
}
// job requires at least a 2TB node
if (m <= 2000.GB) {
return base + " --mem 2TB "
}
// job requires the largest node
return base + " -C mem4TB "
}
if (m <= 250.GB) {
return base + " -p node -C mem256GB "
}
@ -77,6 +91,14 @@ if (hostname.startsWith("i")) {
params.config_profile_description = 'UPPMAX (Irma) cluster profile provided by nf-core/configs.'
}
// Cluster: Miarka
if (hostname.startsWith("m")) {
params.max_memory = 357.GB
params.max_cpus = 48
params.max_time = 480.h
params.config_profile_description = 'UPPMAX (Miarka) cluster profile provided by nf-core/configs.'
}
// Cluster: Rackham
if (hostname.startsWith("r")) {
params.max_cpus = 20

115
conf/vsc_ugent.config Normal file
View file

@ -0,0 +1,115 @@
// Specify the work directory
workDir = "$VSC_SCRATCH_VO_USER/work"
// Perform work directory cleanup when the run has succesfully completed
cleanup = true
// Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
executor {
submitRateLimit = '10 sec'
}
// Specify that singularity should be used and where the cache dir will be for the images
singularity {
enabled = true
autoMounts = true
cacheDir = "$VSC_SCRATCH_VO_USER/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
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
}
}
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
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
}
}
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
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
}
}
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
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
}
}
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
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
}
}
}

2
docs/cambridge.md
View file

@ -15,4 +15,4 @@ has finished successfully because it can get quite large, and all of the main ou
> NB: You will need an account to use the Cambridge HPC cluster in order to run the pipeline. If in doubt contact IT.
> NB: Nextflow will need to submit the jobs via SLURM to the Cambridge HPC cluster and as such the commands above will have to be executed on one of the login
nodes. If in doubt contact IT.
> nodes. If in doubt contact IT.

1
docs/ccga_dx.md
View file

@ -5,4 +5,5 @@ Deployment and testing of nf-core pipelines at the CCGA DX cluster is on-going.
To use, run the pipeline with `-profile ccga_dx`. This will download and launch the [`ccga_dx.config`](../conf/ccga_dx.config) which has been pre-configured with a setup suitable for the CCGA cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Before running the pipeline you will need to have Nextflow installed.
> NB: Access to the CCGA DX cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).

7
docs/cedars.md Normal file
View file

@ -0,0 +1,7 @@
# Cedars-Sinai Medical Center HPC
- You will need HPC access from EIS, which can be requested in the Service Center.
- You will need to load the nextflow module on the HPC before running any pipelines (`module load nextflow`). This should automatically load Java as well.
- Run this with `-profile cedars`
- By default this config file does not specify a queue for submission, and things will thus go to `all.q`. Because of that, the memory and cpu limits have been set accordingly.
- We highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`

2
docs/cheaha.md
View file

@ -17,7 +17,7 @@ All of the intermediate files required to run the pipeline will be stored in the
> NB: You will need an account to use the HPC cluster on Cheaha in order to run the pipeline. If in doubt contact UAB IT Research Computing.</br></br>
> NB: Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be executed on one of the login nodes (or alternatively in an interactive partition, but be aware of time limit). If in doubt contact UAB IT Research Computing.</br></br>
>NB: Instead of using `module load Nextflow`, you may instead create a conda environment (e.g: `conda create -p $USER_DATA/nf-core_nextflow_env nf-core nextflow`) if you would like to have a more personalized environment of Nextflow (versions which may not be modules yet) and nf-core tools. This __requires__ you to instead do the following:
> NB: Instead of using `module load Nextflow`, you may instead create a conda environment (e.g: `conda create -p $USER_DATA/nf-core_nextflow_env nf-core nextflow`) if you would like to have a more personalized environment of Nextflow (versions which may not be modules yet) and nf-core tools. This **requires** you to instead do the following:
```bash
module purge

4
docs/czbiohub.md
View file

@ -22,7 +22,7 @@ Now you can run pipelines with abandon!
### 2. Make a GitHub repo for your workflows (optional :)
To make sharing your pipelines and commands easy between your teammates, it's best to share code in a GitHub repository. One way is to store the commands in a Makefile ([example](https://github.com/czbiohub/kh-workflows/blob/master/nf-kmer-similarity/Makefile)) which can contain multiple `nextflow run` commands so that you don't need to remember the S3 bucket or output directory for every single one. [Makefiles](https://kbroman.org/minimal_make/) are broadly used in the software community for running many complex commands. Makefiles can have a lot of dependencies and be confusing, so we're only going to write *simple* Makefiles.
To make sharing your pipelines and commands easy between your teammates, it's best to share code in a GitHub repository. One way is to store the commands in a Makefile ([example](https://github.com/czbiohub/kh-workflows/blob/master/nf-kmer-similarity/Makefile)) which can contain multiple `nextflow run` commands so that you don't need to remember the S3 bucket or output directory for every single one. [Makefiles](https://kbroman.org/minimal_make/) are broadly used in the software community for running many complex commands. Makefiles can have a lot of dependencies and be confusing, so we're only going to write _simple_ Makefiles.
```bash
rnaseq:
@ -125,7 +125,7 @@ For Human and Mouse, we use [GENCODE](https://www.gencodegenes.org/) gene annota
## High Priority Queue
If you would like to run with the *High Priority* queue, specify the `highpriority` config profile after `czbiohub_aws`. When applied after the main `czbiohub_aws` config, it overwrites the process `queue` identifier.
If you would like to run with the _High Priority_ queue, specify the `highpriority` config profile after `czbiohub_aws`. When applied after the main `czbiohub_aws` config, it overwrites the process `queue` identifier.
To use it, submit your run with with `-profile czbiohub_aws,highpriority`.

9
docs/eva.md
View file

@ -4,7 +4,11 @@ All nf-core pipelines have been successfully configured for use on the Departmen
To use, run the pipeline with `-profile eva`. You can further with optimise submissions by specifying which cluster queue you are using e,g, `-profile eva,archgen`. This will download and launch the [`eva.config`](../conf/eva.config) which has been pre-configured with a setup suitable for the `all.q` queue. The number of parallel jobs that run is currently limited to 8.
Using this profile, a docker image containing all of the required software will be downloaded, and converted to a `singularity` image before execution of the pipeline. The image will currently be centrally stored here:
Using this profile, a docker image containing all of the required software will be downloaded, and converted to a `singularity` image before execution of the pipeline.
Institute-specific pipeline profiles exists for:
- eager
## Additional Profiles
@ -16,9 +20,10 @@ If you specify `-profile eva,archgen` you will be able to use the nodes availabl
Note the following characteristics of this profile:
- By default, job resources are assigned a maximum number of CPUs of 32, 256 GB maximum memory and 720.h maximum wall time.
- By default, job resources are assigned a maximum number of CPUs of 32, 256 GB maximum memory and 365 day maximum wall time.
- Using this profile will currently store singularity images in a cache under `/mnt/archgen/users/singularity_scratch/cache/`. All archgen users currently have read/write access to this directory, however this will likely change to a read-only directory in the future that will be managed by the IT team.
- Intermediate files will be _automatically_ cleaned up (see `debug` below if you don't want this to happen) on successful run completion.
- Jobs submitted with >700.GB will automatically be submitted to the dynamic `bigmem.q`.
> NB: You will need an account and VPN access to use the cluster at MPI-EVA in order to run the pipeline. If in doubt contact the IT team.
> NB: Nextflow will need to submit the jobs via SGE to the clusters and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT.

12
docs/genotoul.md
View file

@ -65,11 +65,11 @@ sbatch nfcore-rnaseq.sh
By default, available mount points are:
* /bank
* /home
* /save
* /work
* /work2
- /bank
- /home
- /save
- /work
- /work2
To have access to specific other mount point (such as nosave or project)
you can add a config profile file with option `-profile` and which contain:
@ -85,4 +85,4 @@ our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/)
to search for your favorite genome.
> NB: You will need an account to use the HPC cluster on Genotoul in order
to run the pipeline. If in doubt see [http://bioinfo.genotoul.fr/](http://bioinfo.genotoul.fr/).
> to run the pipeline. If in doubt see [http://bioinfo.genotoul.fr/](http://bioinfo.genotoul.fr/).

8
docs/ifb_core.md
View file

@ -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 \\

4
docs/lugh.md
View file

@ -23,12 +23,12 @@ The configuration file will load prerequisite modules for users (`Java` & `Singu
## Queue Resources
| Queue | Hostnames | Max Memory | Max CPUS | Max Time |
|---------|----------------|------------|----------|----------|
| ------- | -------------- | ---------- | -------- | -------- |
| MSC | compute[01-03] | 32GB | 16 | 336.h |
| Normal | compute[10-29] | 64GB | 16 | 240.h |
| Highmem | compute[04-09] | 128GB | 32 | 2880.h |
***
---
The configuration profile design is very simple. If your process exceeds 64GB memory or 16 cpus, it is sent to the `highmem` queue. If not, it is sent to the `normal` queue. Please do not use the `MSC` queue, this is reserved for Masters students.

2
docs/pipeline/ampliseq/binac.md
View file

@ -14,4 +14,4 @@ Example: `nextflow run nf-core/ampliseq -profile binac`
Specific configurations for BINAC has been made for ampliseq.
* Specifies the `TZ` `ENV` variable to be `Europe/Berlin` to fix a QIIME2 issue
- Specifies the `TZ` `ENV` variable to be `Europe/Berlin` to fix a QIIME2 issue

2
docs/pipeline/ampliseq/uppmax.md
View file

@ -14,4 +14,4 @@ Example: `nextflow run nf-core/ampliseq -profile uppmax`
Specific configurations for UPPMAX has been made for ampliseq.
* Makes sure that a fat node is allocated for training and applying a Bayesian classifier.
- Makes sure that a fat node is allocated for training and applying a Bayesian classifier.

0
docs/pipeline/eager/mpcdf.config → docs/pipeline/eager/mpcdf.md
View file

15
docs/pipeline/mag/eva.md Normal file
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@ -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).

4
docs/pipeline/rnafusion/munin.md
View file

@ -14,5 +14,5 @@ Example: `nextflow run nf-core/rnafusion -profile munin`
Specific configurations for `MUNIN` has been made for rnafusion.
* `cpus`, `memory` and `time` max requirements.
* Paths to specific references and indexes
- `cpus`, `memory` and `time` max requirements.
- Paths to specific references and indexes

44
docs/pipeline/rnavar/munin.md
View file

@ -16,34 +16,34 @@ Specific configurations for `MUNIN` has been made for rnavar.
Genome references
* Path to `fasta`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa`
* Path to `fasta_fai`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai`
* Path to `gtf`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf`
* Path to `gene_bed`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.bed`
- Path to `fasta`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa`
- Path to `fasta_fai`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai`
- Path to `gtf`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf`
- Path to `gene_bed`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.bed`
Known genome resources
* Path to `dbsnp`: `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz`
* Path to `dbsnp_tbi`: `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi`
* Path to `known_indels`: `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz`
* Path to `known_indels_tbi`: `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi`
- Path to `dbsnp`: `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz`
- Path to `dbsnp_tbi`: `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi`
- Path to `known_indels`: `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz`
- Path to `known_indels_tbi`: `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi`
STAR index
* Path to `star_index`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/STAR.2.7.9a_2x151bp/`
* Params `read_length` set to `151`
- Path to `star_index`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/STAR.2.7.9a_2x151bp/`
- Params `read_length` set to `151`
Variant annotation configurations
* Params `annotation_cache` and `cadd_cache` set to `true`
* Params `snpeff_db` set to `GRCh38.99`
* Params `vep_cache_version` set to `99`
* Params `vep_genome` set to `GRCh38`
* Path to `snpeff_cache`: `/data1/cache/snpEff/`
* Path to `vep_cache`: `/data1/cache/VEP/`
* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
* Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz`
* Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi`
* Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz`
* Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`
- Params `annotation_cache` and `cadd_cache` set to `true`
- Params `snpeff_db` set to `GRCh38.99`
- Params `vep_cache_version` set to `99`
- Params `vep_genome` set to `GRCh38`
- Path to `snpeff_cache`: `/data1/cache/snpEff/`
- Path to `vep_cache`: `/data1/cache/VEP/`
- Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
- Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
- Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz`
- Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi`
- Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz`
- Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`

22
docs/pipeline/sarek/munin.md
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@ -14,14 +14,14 @@ Example: `nextflow run nf-core/sarek -profile munin`
Specific configurations for `MUNIN` has been made for sarek.
* Params `annotation_cache` and `cadd_cache` set to `true`
* Params `vep_cache_version` set to `95`
* Path to `snpeff_cache`: `/data1/cache/snpEff/`
* Path to `vep_cache`: `/data1/cache/VEP/`
* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
* Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz`
* Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi`
* Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz`
* Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`
* Load module `Sentieon` for Processes with `sentieon` labels
- Params `annotation_cache` and `cadd_cache` set to `true`
- Params `vep_cache_version` set to `95`
- Path to `snpeff_cache`: `/data1/cache/snpEff/`
- Path to `vep_cache`: `/data1/cache/VEP/`
- Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
- Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
- Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz`
- Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi`
- Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz`
- Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`
- Load module `Sentieon` for Processes with `sentieon` labels

3
docs/pipeline/sarek/uppmax.md
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@ -14,5 +14,4 @@ Example: `nextflow run nf-core/sarek -profile uppmax`
Specific configurations for uppmax clusters has been made for sarek.
* Set paths to reference genomes
* Set path to singularity containers for `irma`
- Set paths to reference genomes

10
docs/pipeline/scflow/imperial.md
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@ -14,8 +14,8 @@ Example: `nextflow run nf-core/scflow -profile imperial`
Specific configurations for Imperial have been made for scflow.
* Singularity `enabled` and `autoMounts` set to `true`
* Singularity `cacheDir` path set to an RDS location
* Singularity `runOptions` path set to bind (`-B`) RDS paths with container paths.
* Params `ctd_folder` set to an RDS location.
* Parms `ensembl_mappings` set to an RDS location.
- Singularity `enabled` and `autoMounts` set to `true`
- Singularity `cacheDir` path set to an RDS location
- Singularity `runOptions` path set to bind (`-B`) RDS paths with container paths.
- Params `ctd_folder` set to an RDS location.
- Parms `ensembl_mappings` set to an RDS location.

19
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@ -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
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@ -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.

18
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@ -0,0 +1,18 @@
# nf-core/configs: SAHMRI HPC Configuration
All nf-core pipelines have been successfully configured for use on the HPC cluster at [SAHMRI](https://sahmri.org.au/).
To use, run the pipeline with `-profile sahmri`. This will download and launch the [`sahmri.config`](../conf/sahmri.config) which has been pre-configured
with a setup suitable for the SAHMRI HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded,
and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline.
The latest version of Nextflow is not installed by default on the SAHMRI HPC cluster. You will need to install it into a directory you have write access to.
Follow these instructions from the Nextflow documentation.
- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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.
> NB: You will need an account to use the SAHMRI HPC cluster in order to run the pipeline. If in doubt contact the ICT Service Desk.
> NB: Nextflow will need to submit the jobs via SLURM to the SAHMRI HPC cluster and as such the commands above will have to be executed on the login
> node. If in doubt contact ICT.

26
docs/uppmax.md
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@ -58,15 +58,15 @@ All jobs will be submitted to fat nodes using this method, so it's only for use
The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits:
* `rackham`
* cpus available: 20 cpus
* memory available: 125 GB
* `bianca`
* cpus available: 16 cpus
* memory available: 109 GB
* `irma`
* cpus available: 16 cpus
* memory available: 250 GB
- `rackham`
- cpus available: 20 cpus
- memory available: 125 GB
- `bianca`
- cpus available: 16 cpus
- memory available: 109 GB
- `miarka`
- cpus available: 48 cpus
- memory available: 357 GB
## Development config
@ -83,10 +83,10 @@ To use it, submit with `-profile uppmax,devel`.
> :warning: For more information, please follow the following guides:
>
> * [UPPMAX `bianca` user guide](http://uppmax.uu.se/support/user-guides/bianca-user-guide/).
> * [nf-core guide for running offline](https://nf-co.re/usage/offline)
> * [nf-core `tools` guide for downloading pipelines for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use).
> * [UPPMAX `Singularity` guide](https://www.uppmax.uu.se/support-sv/user-guides/singularity-user-guide/).
> - [UPPMAX `bianca` user guide](http://uppmax.uu.se/support/user-guides/bianca-user-guide/).
> - [nf-core guide for running offline](https://nf-co.re/usage/offline)
> - [nf-core `tools` guide for downloading pipelines for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use).
> - [UPPMAX `Singularity` guide](https://www.uppmax.uu.se/support-sv/user-guides/singularity-user-guide/).
For security reasons, there is no internet access on `bianca` so you can't download from or upload files to the cluster directly.
Before running a nf-core pipeline on `bianca` you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the `wharf` area to your own `bianca` project.

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@ -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`.

3
nfcore_custom.config
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@ -24,6 +24,7 @@ profiles {
cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" }
ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
cedars { includeConfig "${params.custom_config_base}/conf/cedars.config" }
cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
cfc_dev { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" }
cheaha { includeConfig "${params.custom_config_base}/conf/cheaha.config" }
@ -57,6 +58,7 @@ profiles {
phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
rosalind { includeConfig "${params.custom_config_base}/conf/rosalind.config" }
sahmri { includeConfig "${params.custom_config_base}/conf/sahmri.config" }
sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"}
seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
@ -66,4 +68,5 @@ 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" }
}

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@ -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
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@ -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" }
}