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Merge branch 'master' into fix-eva

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James A. Fellows Yates 2022-03-29 12:50:54 +02:00 committed by GitHub
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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: Please follow these steps before submitting your PR:
* [ ] If your PR is a work in progress, include `[WIP]` in its title - [ ] If your PR is a work in progress, include `[WIP]` in its title
* [ ] Your PR targets the `master` branch - [ ] Your PR targets the `master` branch
* [ ] You've included links to relevant issues, if any - [ ] You've included links to relevant issues, if any
Steps for adding a new config profile: 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 config file to the `conf/` directory
* [ ] Add your custom profile to the `nfcore_custom.config` file in the top-level directory - [ ] Add your documentation file to the `docs/` directory
* [ ] Add your custom profile to the `README.md` file in the top-level directory - [ ] Add your custom profile to the `nfcore_custom.config` file in the top-level directory
* [ ] Add your profile name to the `profile:` scope in `.github/workflows/main.yml` - [ ] 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 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

32
.github/workflows/linting.yml vendored
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@ -1,18 +1,22 @@
name: Markdown linting name: Code Linting
# This workflow is triggered on pushes and PRs to the repository. on:
on: [push, pull_request] pull_request:
push:
branches:
- master
jobs: jobs:
Markdown: prettier:
runs-on: ubuntu-18.04 runs-on: ubuntu-latest
steps: steps:
- uses: actions/checkout@v1 - name: Check out repository
- uses: actions/setup-node@v2 uses: actions/checkout@v2
- name: Install markdownlint
run: |
npm install -g markdownlint-cli
- name: Run Markdownlint
run: |
markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
- 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}

131
.github/workflows/main.yml vendored
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@ -1,6 +1,7 @@
name: Configs tests name: Configs tests
on: [pull_request, push] on: [pull_request, push]
jobs: jobs:
test_all_profiles: test_all_profiles:
runs-on: ubuntu-latest runs-on: ubuntu-latest
@ -8,70 +9,82 @@ jobs:
steps: steps:
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Check whether profiles are all tested - name: Check whether profiles are all tested
run: python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
check_nextflow_config:
runs-on: ubuntu-latest
name: Check if nextflow config runs in repository root
steps:
- uses: actions/checkout@v1
- name: Install Nextflow
run: | run: |
python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- run: nextflow config -show-profiles ${GITHUB_WORKSPACE}
profile_test: profile_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
name: Run ${{ matrix.profile }} profile name: Run ${{ matrix.profile }} profile
needs: test_all_profiles needs: test_all_profiles
strategy: strategy:
matrix: matrix:
profile: profile:
- 'abims' - "abims"
- 'alice' - "alice"
- 'aws_tower' - "aws_tower"
- 'awsbatch' - "awsbatch"
- 'azurebatch' - "azurebatch"
- 'bi' - "bi"
- 'bigpurple' - "bigpurple"
- 'binac' - "binac"
- 'biohpc_gen' - "biohpc_gen"
- 'cambridge' - "cambridge"
- 'leicester' - "leicester"
- 'cbe' - "cbe"
- 'ccga_dx' - "ccga_dx"
- 'ccga_med' - "ccga_med"
- 'cfc' - "cfc"
- 'cfc_dev' - "cfc_dev"
- 'cheaha' - "cheaha"
- 'computerome' - "computerome"
- 'crick' - "crick"
- 'denbi_qbic' - "denbi_qbic"
- 'ebc' - "ebc"
- 'eddie' - "eddie"
- 'eva' - "eva"
- 'fgcz' - "fgcz"
- 'genotoul' - "genotoul"
- 'genouest' - "genouest"
- 'gis' - "gis"
- 'google' - "google"
- 'hasta' - "hasta"
- 'hebbe' - "hebbe"
- 'icr_davros' - "icr_davros"
- 'ifb_core' - "ifb_core"
- 'imperial' - "imperial"
- 'jax' - "jax"
- 'lugh' - "lugh"
- 'marvin' - "marvin"
- 'maestro' - "maestro"
- 'mpcdf' - "mpcdf"
- 'munin' - "munin"
- 'nu_genomics' - "nu_genomics"
- 'nihbiowulf' - "nihbiowulf"
- 'oist' - "oist"
- 'pasteur' - "pasteur"
- 'phoenix' - "phoenix"
- 'prince' - "prince"
- 'rosalind' - "rosalind"
- 'sanger' - "sahmri"
- 'seg_globe' - "sanger"
- 'uct_hpc' - "seg_globe"
- 'unibe_ibu' - "uct_hpc"
- 'uppmax' - "unibe_ibu"
- 'utd_ganymede' - "uppmax"
- 'utd_sysbio' - "utd_ganymede"
- 'uzh' - "utd_sysbio"
- 'vai' - "uzh"
- "vai"
steps: steps:
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Install Nextflow - name: Install Nextflow
@ -82,4 +95,4 @@ jobs:
env: env:
SCRATCH: "~" SCRATCH: "~"
NXF_GLOBAL_CONFIG: awsbatch.config NXF_GLOBAL_CONFIG: awsbatch.config
run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf -profile ${{ matrix.profile }}

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

176
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 --> ## Table of contents <!-- omit in toc -->
* [Using an existing config](#using-an-existing-config) - [Using an existing config](#using-an-existing-config)
* [Configuration and parameters](#configuration-and-parameters) - [Configuration and parameters](#configuration-and-parameters)
* [Offline usage](#offline-usage) - [Offline usage](#offline-usage)
* [Adding a new config](#adding-a-new-config) - [Adding a new config](#adding-a-new-config)
* [Checking user hostnames](#checking-user-hostnames) - [Checking user hostnames](#checking-user-hostnames)
* [Testing](#testing) - [Testing](#testing)
* [Documentation](#documentation) - [Documentation](#documentation)
* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) - [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config) - [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
* [Pipeline-specific institutional documentation](#pipeline-specific-institutional-documentation) - [Pipeline-specific institutional documentation](#pipeline-specific-institutional-documentation)
* [Pipeline-specific documentation](#pipeline-specific-documentation) - [Pipeline-specific documentation](#pipeline-specific-documentation)
* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline) - [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) - [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
* [Help](#help) - [Help](#help)
## Using an existing config ## Using an existing config
@ -86,68 +86,68 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
Currently documentation is available for the following systems: Currently documentation is available for the following systems:
* [ABIMS](docs/abims.md) - [ABIMS](docs/abims.md)
* [ALICE](docs/alice.md) - [ALICE](docs/alice.md)
* [AWSBATCH](docs/awsbatch.md) - [AWSBATCH](docs/awsbatch.md)
* [AWS_TOWER](docs/aws_tower.md) - [AWS_TOWER](docs/aws_tower.md)
* [AZUREBATCH](docs/azurebatch.md) - [AZUREBATCH](docs/azurebatch.md)
* [BIGPURPLE](docs/bigpurple.md) - [BIGPURPLE](docs/bigpurple.md)
* [BI](docs/bi.md) - [BI](docs/bi.md)
* [BINAC](docs/binac.md) - [BINAC](docs/binac.md)
* [BIOHPC_GEN](docs/biohpc_gen.md) - [BIOHPC_GEN](docs/biohpc_gen.md)
* [CAMBRIDGE](docs/cambridge.md) - [CAMBRIDGE](docs/cambridge.md)
* [CBE](docs/cbe.md) - [CBE](docs/cbe.md)
* [CCGA_DX](docs/ccga_dx.md) - [CCGA_DX](docs/ccga_dx.md)
* [CCGA_MED](docs/ccga_med.md) - [CCGA_MED](docs/ccga_med.md)
* [CFC](docs/cfc.md) - [CFC](docs/cfc.md)
* [CHEAHA](docs/cheaha.md) - [CHEAHA](docs/cheaha.md)
* [Computerome](docs/computerome.md) - [Computerome](docs/computerome.md)
* [CRICK](docs/crick.md) - [CRICK](docs/crick.md)
* [CZBIOHUB_AWS](docs/czbiohub.md) - [CZBIOHUB_AWS](docs/czbiohub.md)
* [DENBI_QBIC](docs/denbi_qbic.md) - [DENBI_QBIC](docs/denbi_qbic.md)
* [EBC](docs/ebc.md) - [EBC](docs/ebc.md)
* [EVA](docs/eva.md) - [EVA](docs/eva.md)
* [FGCZ](docs/fgcz.md) - [FGCZ](docs/fgcz.md)
* [GENOTOUL](docs/genotoul.md) - [GENOTOUL](docs/genotoul.md)
* [GENOUEST](docs/genouest.md) - [GENOUEST](docs/genouest.md)
* [GIS](docs/gis.md) - [GIS](docs/gis.md)
* [GOOGLE](docs/google.md) - [GOOGLE](docs/google.md)
* [HASTA](docs/hasta.md) - [HASTA](docs/hasta.md)
* [HEBBE](docs/hebbe.md) - [HEBBE](docs/hebbe.md)
* [ICR_DAVROS](docs/icr_davros.md) - [ICR_DAVROS](docs/icr_davros.md)
* [IMPERIAL](docs/imperial.md) - [IMPERIAL](docs/imperial.md)
* [JAX](docs/jax.md) - [JAX](docs/jax.md)
* [LUGH](docs/lugh.md) - [LUGH](docs/lugh.md)
* [MAESTRO](docs/maestro.md) - [MAESTRO](docs/maestro.md)
* [MARVIN](docs/marvin.md) - [MARVIN](docs/marvin.md)
* [MPCDF](docs/mpcdf.md) - [MPCDF](docs/mpcdf.md)
* [MUNIN](docs/munin.md) - [MUNIN](docs/munin.md)
* [NU_GENOMICS](docs/nu_genomics.md) - [NU_GENOMICS](docs/nu_genomics.md)
* [NIHBIOWULF](docs/nihbiowulf.md) - [NIHBIOWULF](docs/nihbiowulf.md)
* [OIST](docs/oist.md) - [OIST](docs/oist.md)
* [PASTEUR](docs/pasteur.md) - [PASTEUR](docs/pasteur.md)
* [PHOENIX](docs/phoenix.md) - [PHOENIX](docs/phoenix.md)
* [PRINCE](docs/prince.md) - [PRINCE](docs/prince.md)
* [ROSALIND](docs/rosalind.md) - [ROSALIND](docs/rosalind.md)
* [SANGER](docs/sanger.md) - [SANGER](docs/sanger.md)
* [SEG_GLOBE](docs/seg_globe.md) - [SEG_GLOBE](docs/seg_globe.md)
* [UCT_HPC](docs/uct_hpc.md) - [UCT_HPC](docs/uct_hpc.md)
* [UNIBE_IBU](docs/unibe_ibu.md) - [UNIBE_IBU](docs/unibe_ibu.md)
* [UPPMAX](docs/uppmax.md) - [UPPMAX](docs/uppmax.md)
* [UTD_GANYMEDE](docs/utd_ganymede.md) - [UTD_GANYMEDE](docs/utd_ganymede.md)
* [UTD_SYSBIO](docs/utd_sysbio.md) - [UTD_SYSBIO](docs/utd_sysbio.md)
* [UZH](docs/uzh.md) - [UZH](docs/uzh.md)
* [VAI](docs/vai.md) - [VAI](docs/vai.md)
### Uploading to `nf-core/configs` ### 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. [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: 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 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 - **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 [`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 - **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: 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 +186,25 @@ 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: Currently documentation is available for the following pipelines within specific profiles:
* ampliseq - ampliseq
* [BINAC](docs/pipeline/ampliseq/binac.md) - [BINAC](docs/pipeline/ampliseq/binac.md)
* [UPPMAX](docs/pipeline/ampliseq/uppmax.md) - [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
* eager - eager
* [EVA](docs/pipeline/eager/eva.md) - [EVA](docs/pipeline/eager/eva.md)
* rnafusion - rnafusion
* [MUNIN](docs/pipeline/rnafusion/munin.md) - [MUNIN](docs/pipeline/rnafusion/munin.md)
* sarek - sarek
* [MUNIN](docs/pipeline/sarek/munin.md) - [MUNIN](docs/pipeline/sarek/munin.md)
* [UPPMAX](docs/pipeline/sarek/uppmax.md) - [UPPMAX](docs/pipeline/sarek/uppmax.md)
* rnavar - rnavar
* [MUNIN](docs/pipeline/rnavar/munin.md) - [MUNIN](docs/pipeline/rnavar/munin.md)
### Pipeline-specific documentation ### Pipeline-specific documentation
Currently documentation is available for the following pipeline: Currently documentation is available for the following pipeline:
* viralrecon - viralrecon
* [genomes](docs/pipeline/viralrecon/genomes.md) - [genomes](docs/pipeline/viralrecon/genomes.md)
### Enabling pipeline-specific configs within a pipeline ### Enabling pipeline-specific configs within a pipeline
@ -233,7 +233,7 @@ 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. [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. 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 If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
@ -243,18 +243,18 @@ profiles {
} }
``` ```
* `conf/pipeline/<PIPELINE>/<PROFILE>.config` - `conf/pipeline/<PIPELINE>/<PROFILE>.config`
Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory. 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. 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. 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. 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. 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 Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation

2
conf/eva.config
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@ -36,7 +36,7 @@ profiles {
} }
process { process {
queue = 'archgen.q' queue = { task.memory > 700.GB ? 'bigmem.q' : 'archgen.q' }
clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
} }

6
conf/munin.config
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@ -18,6 +18,12 @@ params {
process { process {
executor = 'local' executor = 'local'
maxForks = 46 maxForks = 46
// Limit cpus for Mutect2
withName:'Mutect2|Mutect2Single|PileupSummariesForMutect2' {
time = {48.h * task.attempt}
maxForks = 12
}
} }
singularity { singularity {

16
conf/pipeline/eager/eva.config
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@ -74,6 +74,22 @@ process {
clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: bwa {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
}
withName: bwamem {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
}
withName: bowtie2 {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
}
withName: samtools_flagstat { withName: samtools_flagstat {
clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }

5
conf/pipeline/sarek/uppmax.config
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@ -26,3 +26,8 @@ if (hostname ==~ "r.*") {
if (hostname ==~ "i.*") { if (hostname ==~ "i.*") {
params.single_cpu_mem = 15.GB params.single_cpu_mem = 15.GB
} }
// Miarka-specific config
if (hostname ==~ "m.*") {
params.single_cpu_mem = 7.GB
}

20
conf/prince.config
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@ -1,6 +1,6 @@
singularityDir = "$SCRATCH/singularity_images_nextflow" def singularityDir = set_singularity_path()
singularityModule = "singularity/3.2.1" def singularityModule = "singularity/3.2.1"
squashfsModule = "squashfs/4.3" def squashfsModule = "squashfs/4.3"
params { params {
config_profile_description = """ config_profile_description = """
@ -13,11 +13,21 @@ params {
} }
singularity { singularity {
enabled = true enabled = true
cacheDir = singularityDir cacheDir = singularityDir
} }
process { process {
beforeScript = "module load $singularityModule $squashfsModule" beforeScript = "module load $singularityModule $squashfsModule"
executor = 'slurm' executor = 'slurm'
} }
def set_singularity_path() {
def scratch = System.getenv('SCRATCH')
if(scratch == null){
System.err.println("WARNING: prince.config requires the SCRATCH env var to be set.")
return null
} else {
return "$SCRATCH/singularity_images_nextflow"
}
}

34
conf/sahmri.config Normal file
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@ -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
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@ -23,7 +23,7 @@ singularity {
def hostname = "r1" def hostname = "r1"
try { 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) { } catch (java.io.IOException e) {
System.err.println("WARNING: Could not run sinfo to determine current cluster, defaulting to rackham") System.err.println("WARNING: Could not run sinfo to determine current cluster, defaulting to rackham")
} }
@ -36,6 +36,20 @@ def clusterOptionsCreator = { m ->
return base 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) { if (m <= 250.GB) {
return base + " -p node -C mem256GB " 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.' 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 // Cluster: Rackham
if (hostname.startsWith("r")) { if (hostname.startsWith("r")) {
params.max_cpus = 20 params.max_cpus = 20

2
docs/alice.md
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@ -13,7 +13,7 @@ module load Nextflow/21.03.0
module load Java/11.0.2 module load Java/11.0.2
``` ```
We also 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 `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`. We also highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`.
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. 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 completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. The 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.

2
docs/bi.md
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@ -6,4 +6,4 @@ To use, run the pipeline with `-profile bi`. This will download and launch the [
Before running the pipeline you will need to follow the internal documentation to run Nextflow on our systems. Similar to that, you need to set an environment variable `NXF_GLOBAL_CONFIG` to the path of the internal global config which is not publicly available here. Before running the pipeline you will need to follow the internal documentation to run Nextflow on our systems. Similar to that, you need to set an environment variable `NXF_GLOBAL_CONFIG` to the path of the internal global config which is not publicly available here.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

4
docs/bigpurple.md
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@ -21,5 +21,5 @@ git clone this repo, copy the `bigpurple.config` from the conf folder and then y
`nextflow run nf-core/<pipeline name> -c bigpurple.config <additional flags>` `nextflow run nf-core/<pipeline name> -c bigpurple.config <additional flags>`
>NB: You will need an account to use the HPC cluster BigPurple in order to run the pipeline. If in doubt contact MCIT. > NB: You will need an account to use the HPC cluster BigPurple in order to run the pipeline. If in doubt contact MCIT.
>NB: You will need to install nextflow in your home directory - instructions are on nextflow.io (or ask the writer of this profile). The reason there is no module for nextflow on the cluster, is that the development cycle of nextflow is rapid and it's easy to update yourself: `nextflow self-update` > NB: You will need to install nextflow in your home directory - instructions are on nextflow.io (or ask the writer of this profile). The reason there is no module for nextflow on the cluster, is that the development cycle of nextflow is rapid and it's easy to update yourself: `nextflow self-update`

4
docs/binac.md
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@ -13,5 +13,5 @@ module load devel/java_jdk/1.8.0u112
module load devel/singularity/3.0.1 module load devel/singularity/3.0.1
``` ```
>NB: You will need an account to use the HPC cluster BINAC in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC cluster BINAC in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

6
docs/biohpc_gen.md
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@ -12,6 +12,6 @@ module purge
module load nextflow charliecloud/0.22 module load nextflow charliecloud/0.22
``` ```
>NB: Charliecloud support requires Nextflow version `21.03.0-edge` or later. > NB: Charliecloud support requires Nextflow version `21.03.0-edge` or later.
>NB: You will need an account to use the LRZ Linux cluster as well as group access to the biohpc_gen cluster in order to run nf-core pipelines. > NB: You will need an account to use the LRZ Linux cluster as well as group access to the biohpc_gen cluster in order to run nf-core pipelines.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes.

4
docs/cambridge.md
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@ -3,7 +3,7 @@
All nf-core pipelines have been successfully configured for use on the Cambridge HPC cluster at the [The University of Cambridge](https://www.cam.ac.uk/). All nf-core pipelines have been successfully configured for use on the Cambridge HPC cluster at the [The University of Cambridge](https://www.cam.ac.uk/).
To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) which has been pre-configured To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) which has been pre-configured
with a setup suitable for the Cambridge HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded, with a setup suitable for the Cambridge 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. 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 Cambridge HPC cluster. You will need to install it into a directory you have write access to. The latest version of Nextflow is not installed by default on the Cambridge HPC cluster. You will need to install it into a directory you have write access to.
Follow these instructions from the Nextflow documentation. Follow these instructions from the Nextflow documentation.
@ -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: 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 > 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.

4
docs/cbe.md
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@ -14,5 +14,5 @@ module load nextflow/21.10.6
A local copy of the [AWS-iGenomes](https://registry.opendata.aws/aws-igenomes/) resource has been made available on CBE so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter. A local copy of the [AWS-iGenomes](https://registry.opendata.aws/aws-igenomes/) resource has been made available on CBE so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter.
>NB: You will need an account to use the HPC cluster on CBE in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC cluster on CBE in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

3
docs/ccga_dx.md
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@ -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. 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. 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).
> NB: Access to the CCGA DX cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).

2
docs/ccga_med.md
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@ -13,4 +13,4 @@ module load nextflow
module load singularity module load singularity
``` ```
>NB: Access to the CCGA Med cluster is restricted to IKMB/CCGA employees. Please talk to Marc Hoeppner to get access (@marchoeppner). > NB: Access to the CCGA Med cluster is restricted to IKMB/CCGA employees. Please talk to Marc Hoeppner to get access (@marchoeppner).

4
docs/cfc.md
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@ -13,7 +13,7 @@ module load devel/java_jdk/1.8.0u121
module load devel/singularity/3.4.2 module load devel/singularity/3.4.2
``` ```
>NB: You will need an account to use the HPC cluster CFC in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC cluster CFC in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
The queues are set to be `qbic` or `compute` and will be chosen automatically for you depending on your job submission. The queues are set to be `qbic` or `compute` and will be chosen automatically for you depending on your job submission.

10
docs/cheaha.md
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@ -15,16 +15,16 @@ module load Nextflow
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. 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 HPC cluster on Cheaha in order to run the pipeline. If in doubt contact UAB IT Research Computing.</br></br> > 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: 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 ```bash
module purge module purge
module load Singularity module load Singularity
module load Anaconda3 module load Anaconda3
# change path/enviroment name if according to what you created # change path/enviroment name if according to what you created
conda activate $USER_DATA/nf-core_nextflow_env conda activate $USER_DATA/nf-core_nextflow_env
``` ```
>NB: while the jobs for each process of the pipeline are sent to the appropriate nodes, the current session must remain active while the pipeline is running. We recommend to use `screen` prior to loading any modules/environments. Once the pipeline starts you can detach the screen session by typing `Ctrl-a d` so you can safely logout of HPC, while keeping the pipeline active (and you may resume the screen session with `screen -r`). Other similar tools (e.g. `tmux`) may also be used. > NB: while the jobs for each process of the pipeline are sent to the appropriate nodes, the current session must remain active while the pipeline is running. We recommend to use `screen` prior to loading any modules/environments. Once the pipeline starts you can detach the screen session by typing `Ctrl-a d` so you can safely logout of HPC, while keeping the pipeline active (and you may resume the screen session with `screen -r`). Other similar tools (e.g. `tmux`) may also be used.

46
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@ -1,23 +1,23 @@
# nf-core/configs: Crick (CAMP HPC) Configuration # nf-core/configs: Crick (CAMP HPC) Configuration
All nf-core pipelines have been successfully configured for use on the CAMP HPC cluster at the [The Francis Crick Institute](https://www.crick.ac.uk/). All nf-core pipelines have been successfully configured for use on the CAMP HPC cluster at the [The Francis Crick Institute](https://www.crick.ac.uk/).
To use, run the pipeline with `-profile crick`. This will download and launch the [`crick.config`](../conf/crick.config) which has been pre-configured with a setup suitable for the CAMP HPC 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. To use, run the pipeline with `-profile crick`. This will download and launch the [`crick.config`](../conf/crick.config) which has been pre-configured with a setup suitable for the CAMP HPC 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 load Nextflow and Singularity using the environment module system on CAMP. Please check the main README of the pipeline to make sure that the version of Nextflow is compatible with that required to run the pipeline. You can do this by issuing the commands below: Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CAMP. Please check the main README of the pipeline to make sure that the version of Nextflow is compatible with that required to run the pipeline. You can do this by issuing the commands below:
```bash ```bash
## Load Nextflow and Singularity environment modules ## Load Nextflow and Singularity environment modules
module purge module purge
module load Nextflow/21.04.0 module load Nextflow/21.04.0
module load Singularity/3.4.2 module load Singularity/3.4.2
``` ```
A local copy of the [AWS-iGenomes](https://github.com/ewels/AWS-iGenomes) resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.config), and if your genome of interest is not present please contact [BABS](mailto:bioinformatics@crick.ac.uk). A local copy of the [AWS-iGenomes](https://github.com/ewels/AWS-iGenomes) resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.config), and if your genome of interest is not present please contact [BABS](mailto:bioinformatics@crick.ac.uk).
Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://nf-co.re/usage/reference_genomes) for instructions). Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://nf-co.re/usage/reference_genomes) for instructions).
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. 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 HPC cluster on CAMP in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC cluster on CAMP in order to run the pipeline. If in doubt contact IT.
>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. If in doubt contact IT. > 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. If in doubt contact IT.

8
docs/czbiohub.md
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@ -22,7 +22,7 @@ Now you can run pipelines with abandon!
### 2. Make a GitHub repo for your workflows (optional :) ### 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 ```bash
rnaseq: rnaseq:
@ -120,12 +120,12 @@ You can do this by simply using the `--genome <GENOME_ID>` parameter.
For Human and Mouse, we use [GENCODE](https://www.gencodegenes.org/) gene annotations. This doesn't change how you would specify the genome name, only that the pipelines run with the `czbiohub_aws` profile would be with GENCODE rather than iGenomes. For Human and Mouse, we use [GENCODE](https://www.gencodegenes.org/) gene annotations. This doesn't change how you would specify the genome name, only that the pipelines run with the `czbiohub_aws` profile would be with GENCODE rather than iGenomes.
>NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
## High Priority Queue ## 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`. To use it, submit your run with with `-profile czbiohub_aws,highpriority`.

4
docs/denbi_qbic.md
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@ -4,5 +4,5 @@ All nf-core pipelines have been successfully configured for use on the de.NBI Cl
To use, run the pipeline with `-profile denbi_qbic`. This will download and launch the [`denbi_qbic.config`](../conf/denbi_qbic.config) which has been pre-configured with a setup suitable for the automatically created 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. To use, run the pipeline with `-profile denbi_qbic`. This will download and launch the [`denbi_qbic.config`](../conf/denbi_qbic.config) which has been pre-configured with a setup suitable for the automatically created 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.
>NB: You will need an account to use de.NBI Cluster in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use de.NBI Cluster in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

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@ -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. 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 ## Additional Profiles
@ -16,12 +20,13 @@ If you specify `-profile eva,archgen` you will be able to use the nodes availabl
Note the following characteristics of this profile: 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. - 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. - 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: 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. > 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.
### debug ### debug

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@ -65,11 +65,11 @@ sbatch nfcore-rnaseq.sh
By default, available mount points are: By default, available mount points are:
* /bank - /bank
* /home - /home
* /save - /save
* /work - /work
* /work2 - /work2
To have access to specific other mount point (such as nosave or project) 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: you can add a config profile file with option `-profile` and which contain:
@ -84,5 +84,5 @@ A local copy of several genomes are available in `/bank` directory. See
our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/) our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/)
to search for your favorite genome. to search for your favorite genome.
>NB: You will need an account to use the HPC cluster on Genotoul in order > 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/).

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@ -1,22 +1,22 @@
# nf-core/configs: Institute of Cancer Research (Davros HPC) Configuration # nf-core/configs: Institute of Cancer Research (Davros HPC) Configuration
Deployment and testing of nf-core pipelines at the Davros cluster is on-going. Deployment and testing of nf-core pipelines at the Davros cluster is on-going.
To run an nf-core pipeline on Davros, run the pipeline with `-profile icr_davros`. This will download and launch the [`icr_davros.config`](../conf/icr_davros.config) which has been pre-configured with a setup suitable for the Davros HPC 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. To run an nf-core pipeline on Davros, run the pipeline with `-profile icr_davros`. This will download and launch the [`icr_davros.config`](../conf/icr_davros.config) which has been pre-configured with a setup suitable for the Davros HPC 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 load Nextflow using the environment module system. You can do this by issuing the commands below: Before running the pipeline you will need to load Nextflow using the environment module system. You can do this by issuing the commands below:
```bash ```bash
## Load Nextflow environment modules ## Load Nextflow environment modules
module load Nextflow/19.10.0 module load Nextflow/19.10.0
``` ```
Singularity is installed on the compute nodes of Davros, but not the login nodes. There is no module for Singularity. Singularity is installed on the compute nodes of Davros, but not the login nodes. There is no module for Singularity.
A subset of the [AWS-iGenomes](https://github.com/ewels/AWS-iGenomes) resource has been made available locally on Davros so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline you want to execute. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto Davros so have a look in the `igenomes_base` path specified in [`icr_davros.config`](../conf/icr_davros.config), and if your genome of interest isn't present please contact [Scientific Computing](mailto:schelpdesk@icr.ac.uk). A subset of the [AWS-iGenomes](https://github.com/ewels/AWS-iGenomes) resource has been made available locally on Davros so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline you want to execute. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto Davros so have a look in the `igenomes_base` path specified in [`icr_davros.config`](../conf/icr_davros.config), and if your genome of interest isn't present please contact [Scientific Computing](mailto:schelpdesk@icr.ac.uk).
Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://nf-co.re/usage/reference_genomes) for instructions). Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://nf-co.re/usage/reference_genomes) for instructions).
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. All of the main output files will be saved in the `results/` directory. 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. All of the main output files will be saved in the `results/` directory.
>NB: Nextflow will need to submit the jobs via LSF to the HPC cluster. This can be done from an interactive or normal job. If in doubt contact Scientific Computing. > NB: Nextflow will need to submit the jobs via LSF to the HPC cluster. This can be done from an interactive or normal job. If in doubt contact Scientific Computing.

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@ -37,4 +37,4 @@ A local copy of several genomes are available in `/shared/bank` directory. See
our [databank page](https://ifb-elixirfr.gitlab.io/cluster/doc/banks/) our [databank page](https://ifb-elixirfr.gitlab.io/cluster/doc/banks/)
to search for your favorite genome. to search for your favorite genome.
>NB: You will need an account to use the HPC cluster on IFB core in order to run the pipeline. If in doubt contact IT or go to [account page](https://my.cluster.france-bioinformatique.fr/manager2/login). > NB: You will need an account to use the HPC cluster on IFB core in order to run the pipeline. If in doubt contact IT or go to [account page](https://my.cluster.france-bioinformatique.fr/manager2/login).

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@ -12,7 +12,7 @@ module load anaconda3/personal
conda install -c bioconda nextflow conda install -c bioconda nextflow
``` ```
>NB: You will need an account to use the HPC cluster CX1 in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC cluster CX1 in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
>NB: To submit jobs to the Imperial College MEDBIO cluster, use `-profile imperial,medbio` instead. > NB: To submit jobs to the Imperial College MEDBIO cluster, use `-profile imperial,medbio` instead.
>NB: You will need a restricted access account to use the HPC cluster MEDBIO. > NB: You will need a restricted access account to use the HPC cluster MEDBIO.

4
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@ -4,5 +4,5 @@ All nf-core pipelines have been successfully configured for use on the JAX Sumne
To use, run the pipeline with `-profile jax`. This will download and launch the [`jax.config`](../conf/jax.config) which has been pre-configured with a setup suitable for JAX Sumner 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 and slurm will be used as well. To use, run the pipeline with `-profile jax`. This will download and launch the [`jax.config`](../conf/jax.config) which has been pre-configured with a setup suitable for JAX Sumner 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 and slurm will be used as well.
>NB: You will need an account to use the HPC cluster JAX in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC cluster JAX in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow should not be executed on the login nodes. If in doubt contact IT. > NB: Nextflow should not be executed on the login nodes. If in doubt contact IT.

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@ -2,7 +2,7 @@
All nf-core pipelines have been successfully configured for use on the ALICE and SPECTRE cluster at the University of Leicester. All nf-core pipelines have been successfully configured for use on the ALICE and SPECTRE cluster at the University of Leicester.
To use, run the pipeline with `-profile leicester`. This will download and launch the [`leicester.config`](../conf/leicester.config ) which has been pre-configured with a setup suitable for the Leicester 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. To use, run the pipeline with `-profile leicester`. This will download and launch the [`leicester.config`](../conf/leicester.config) which has been pre-configured with a setup suitable for the Leicester 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.
>NB: You will need an account to use the ALICE and SPECTRE cluster in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the ALICE and SPECTRE cluster in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

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@ -23,12 +23,12 @@ The configuration file will load prerequisite modules for users (`Java` & `Singu
## Queue Resources ## Queue Resources
| Queue | Hostnames | Max Memory | Max CPUS | Max Time | | Queue | Hostnames | Max Memory | Max CPUS | Max Time |
|---------|----------------|------------|----------|----------| | ------- | -------------- | ---------- | -------- | -------- |
| MSC | compute[01-03] | 32GB | 16 | 336.h | | MSC | compute[01-03] | 32GB | 16 | 336.h |
| Normal | compute[10-29] | 64GB | 16 | 240.h | | Normal | compute[10-29] | 64GB | 16 | 240.h |
| Highmem | compute[04-09] | 128GB | 32 | 2880.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. 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.

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@ -10,7 +10,7 @@ Currently profiles for the following clusters are supported: `cobra`, `raven`
All profiles use `singularity` as the corresponding containerEngine. To prevent repeatedly downloading the same singularity image for every pipeline run, for all profiles we recommend specifying a cache location in your `~/.bash_profile` with the `$NXF_SINGULARITY_CACHEDIR` bash variable. All profiles use `singularity` as the corresponding containerEngine. To prevent repeatedly downloading the same singularity image for every pipeline run, for all profiles we recommend specifying a cache location in your `~/.bash_profile` with the `$NXF_SINGULARITY_CACHEDIR` bash variable.
>NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. Check the [MPCDF documentation](https://www.mpcdf.mpg.de/services/computing). > NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. Check the [MPCDF documentation](https://www.mpcdf.mpg.de/services/computing).
## Global Profiles ## Global Profiles

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@ -33,4 +33,4 @@ Example: `nextflow run -profile munin,docker`
A local copy of the iGenomes resource has been made available on the MUNIN cluster so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. A local copy of the iGenomes resource has been made available on the MUNIN cluster so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
You can do this by simply using the `--genome <GENOME_ID>` parameter. You can do this by simply using the `--genome <GENOME_ID>` parameter.
>NB: You will need an account to use the MUNIN cluster in order to run the pipeline. If in doubt contact @szilva. > NB: You will need an account to use the MUNIN cluster in order to run the pipeline. If in doubt contact @szilva.

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@ -21,5 +21,5 @@ A partial local copy of the iGenomes resource is available on Biowulf. This is a
You can do this by simply using the `--genome <GENOME_ID>` parameter. You can do this by simply using the `--genome <GENOME_ID>` parameter.
>NB: You will need an account to use the HPC cluster on Biowulf in order to run the pipeline. If in doubt contact CIT. > NB: You will need an account to use the HPC cluster on Biowulf in order to run the pipeline. If in doubt contact CIT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster. The master process submitting jobs should be run either as a batch job or on an interactive node - not on the biowulf login node. If in doubt contact Biowulf staff. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster. The master process submitting jobs should be run either as a batch job or on an interactive node - not on the biowulf login node. If in doubt contact Biowulf staff.

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@ -3,19 +3,19 @@
The nf-core pipelines [rnaseq](https://nf-co.re/rnaseq) and The nf-core pipelines [rnaseq](https://nf-co.re/rnaseq) and
[eager](https://nf-co.re/eager) have been successfully tested on the _Deigo_ [eager](https://nf-co.re/eager) have been successfully tested on the _Deigo_
cluster at the Okinawa Institute of Science and Technology Graduate University cluster at the Okinawa Institute of Science and Technology Graduate University
([OIST](https://www.oist.jp)). We have no reason to expect that other ([OIST](https://www.oist.jp)). We have no reason to expect that other
pipelines would not work. pipelines would not work.
To use, run the pipeline with `-profile oist`. This will download and launch To use, run the pipeline with `-profile oist`. This will download and launch
the [`oist.config`](../conf/oist.config) which has been pre-configured with a the [`oist.config`](../conf/oist.config) which has been pre-configured with a
setup suitable for _Deigo_. Using this profile, a docker image containing all setup suitable for _Deigo_. Using this profile, a docker image containing all
of the required software will be downloaded, and converted to a Singularity of the required software will be downloaded, and converted to a Singularity
image before execution of the pipeline. image before execution of the pipeline.
## Below are non-mandatory information e.g. on modules to load etc ## Below are non-mandatory information e.g. on modules to load etc
Before running the pipeline you will need to load Nextflow and Singularity Before running the pipeline you will need to load Nextflow and Singularity
using the environment module system on _Deigo_. You can do this by issuing the using the environment module system on _Deigo_. You can do this by issuing the
commands below: commands below:
```bash ```bash
@ -25,9 +25,9 @@ ml bioinfo-ugrp-modules
ml Other/Nextflow ml Other/Nextflow
``` ```
>NB: You will need an account to use the _Deigo_ cluster in order to run the > NB: You will need an account to use the _Deigo_ cluster in order to run the
>pipeline. If in doubt contact IT. > pipeline. If in doubt contact IT.
> >
>NB: Nextflow will submit the jobs via the SLURM scheduler to the HPC cluster > NB: Nextflow will submit the jobs via the SLURM scheduler to the HPC cluster
>and as such the commands above will have to be executed on one of the login > 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.

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@ -18,15 +18,15 @@ To do that:
1. Create a virtualenv to install nf-core 1. Create a virtualenv to install nf-core
```bash ```bash
module purge module purge
module load Python/3.6.0 module load Python/3.6.0
module load java module load java
module load singularity module load singularity
cd /path/to/nf-core/workflows cd /path/to/nf-core/workflows
virtualenv .venv -p python3 virtualenv .venv -p python3
. .venv/bin/activate . .venv/bin/activate
``` ```
2. Install nf-core: [here](https://nf-co.re/tools#installation) 2. Install nf-core: [here](https://nf-co.re/tools#installation)
3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use) 3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use)

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@ -14,4 +14,4 @@ Example: `nextflow run nf-core/ampliseq -profile binac`
Specific configurations for BINAC has been made for ampliseq. 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

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@ -14,4 +14,4 @@ Example: `nextflow run nf-core/ampliseq -profile uppmax`
Specific configurations for UPPMAX has been made for ampliseq. 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.

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

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@ -16,34 +16,34 @@ Specific configurations for `MUNIN` has been made for rnavar.
Genome references 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`: `/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 `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 `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 `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 Known genome resources
* Path to `dbsnp`: `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz` - 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 `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`: `/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 `known_indels_tbi`: `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi`
STAR index 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/` - 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` - Params `read_length` set to `151`
Variant annotation configurations Variant annotation configurations
* Params `annotation_cache` and `cadd_cache` set to `true` - Params `annotation_cache` and `cadd_cache` set to `true`
* Params `snpeff_db` set to `GRCh38.99` - Params `snpeff_db` set to `GRCh38.99`
* Params `vep_cache_version` set to `99` - Params `vep_cache_version` set to `99`
* Params `vep_genome` set to `GRCh38` - Params `vep_genome` set to `GRCh38`
* Path to `snpeff_cache`: `/data1/cache/snpEff/` - Path to `snpeff_cache`: `/data1/cache/snpEff/`
* Path to `vep_cache`: `/data1/cache/VEP/` - Path to `vep_cache`: `/data1/cache/VEP/`
* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz` - Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi` - 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`: `/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_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`: `/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` - Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`

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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. Specific configurations for `MUNIN` has been made for sarek.
* Params `annotation_cache` and `cadd_cache` set to `true` - Params `annotation_cache` and `cadd_cache` set to `true`
* Params `vep_cache_version` set to `95` - Params `vep_cache_version` set to `95`
* Path to `snpeff_cache`: `/data1/cache/snpEff/` - Path to `snpeff_cache`: `/data1/cache/snpEff/`
* Path to `vep_cache`: `/data1/cache/VEP/` - Path to `vep_cache`: `/data1/cache/VEP/`
* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz` - Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi` - 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`: `/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_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`: `/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` - 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 - 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. Specific configurations for uppmax clusters has been made for sarek.
* Set paths to reference genomes - Set paths to reference genomes
* Set path to singularity containers for `irma`

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. Specific configurations for Imperial have been made for scflow.
* Singularity `enabled` and `autoMounts` set to `true` - Singularity `enabled` and `autoMounts` set to `true`
* Singularity `cacheDir` path set to an RDS location - Singularity `cacheDir` path set to an RDS location
* Singularity `runOptions` path set to bind (`-B`) RDS paths with container paths. - Singularity `runOptions` path set to bind (`-B`) RDS paths with container paths.
* Params `ctd_folder` set to an RDS location. - Params `ctd_folder` set to an RDS location.
* Parms `ensembl_mappings` set to an RDS location. - Parms `ensembl_mappings` set to an RDS location.

4
docs/prince.md
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@ -16,5 +16,5 @@ git clone this repo, copy the `prince.config` from the conf folder and then you
`nextflow run nf-core/<pipeline name> -c prince.config <additional flags>` `nextflow run nf-core/<pipeline name> -c prince.config <additional flags>`
>NB: You will need an account to use the HPC cluster Prince in order to run the pipeline. If in doubt contact the HPC admins. > NB: You will need an account to use the HPC cluster Prince in order to run the pipeline. If in doubt contact the HPC admins.
>NB: Rather than using the nextflow module, I recommend you install nextflow in your home directory - instructions are on nextflow.io (or ask the writer of this profile). The reason this is better than using the module for nextflow on the cluster, is that the development cycle of nextflow is rapid and it's easy to update your installation yourself: `nextflow self-update`. > NB: Rather than using the nextflow module, I recommend you install nextflow in your home directory - instructions are on nextflow.io (or ask the writer of this profile). The reason this is better than using the module for nextflow on the cluster, is that the development cycle of nextflow is rapid and it's easy to update your installation yourself: `nextflow self-update`.

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docs/sahmri.md Normal file
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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.

4
docs/template.md
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@ -20,5 +20,5 @@ module load Singularity/2.6.0
A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
You can do this by simply using the `--genome <GENOME_ID>` parameter. You can do this by simply using the `--genome <GENOME_ID>` parameter.
>NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

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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: The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits:
* `rackham` - `rackham`
* cpus available: 20 cpus - cpus available: 20 cpus
* memory available: 125 GB - memory available: 125 GB
* `bianca` - `bianca`
* cpus available: 16 cpus - cpus available: 16 cpus
* memory available: 109 GB - memory available: 109 GB
* `irma` - `miarka`
* cpus available: 16 cpus - cpus available: 48 cpus
* memory available: 250 GB - memory available: 357 GB
## Development config ## Development config
@ -83,10 +83,10 @@ To use it, submit with `-profile uppmax,devel`.
> :warning: For more information, please follow the following guides: > :warning: For more information, please follow the following guides:
> >
> * [UPPMAX `bianca` user guide](http://uppmax.uu.se/support/user-guides/bianca-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 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). > - [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 `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. 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. 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.

4
docs/utd_ganymede.md
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@ -14,5 +14,5 @@ module load singularity
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. 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 HPC cluster on Ganymede in order to run the pipeline. If in doubt contact Ganymedeadmins. > NB: You will need an account to use the HPC cluster on Ganymede in order to run the pipeline. If in doubt contact Ganymedeadmins.
>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. If in doubt contact GanymedeAdmins. > 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. If in doubt contact GanymedeAdmins.

4
docs/utd_sysbio.md
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@ -12,5 +12,5 @@ module purge
module load singularity module load singularity
``` ```
>NB: You will need an account to use the HPC cluster on Sysbio in order to run the pipeline. If in doubt contact OIT. > NB: You will need an account to use the HPC cluster on Sysbio in order to run the pipeline. If in doubt contact OIT.
>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. If in doubt contact OIT. > 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. If in doubt contact OIT.

4
docs/uzh.md
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@ -4,5 +4,5 @@ All nf-core pipelines have been successfully configured for use on the UZH clust
To use, run the pipeline with `-profile uzh`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH 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. To use, run the pipeline with `-profile uzh`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH 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.
>NB: You will need an account to use the HPC cluster UZH in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC cluster UZH in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

6
docs/vai.md
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@ -9,6 +9,6 @@ module load singularity
NXF_OPTS="-Xmx500m" MALLOC_ARENA_MAX=4 nextflow run <pipeline> NXF_OPTS="-Xmx500m" MALLOC_ARENA_MAX=4 nextflow run <pipeline>
``` ```
>NB: You will need an account to use the HPC in order to run the pipeline. If in doubt contact IT. > NB: You will need an account to use the HPC in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on the login node. If in doubt contact IT. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on the login node. If in doubt contact IT.
>NB: The submit node limits the amount of memory available to each user. The `NXF_OPTS` and `MALLOC_ARENA_MAX` parameters above prevent Nextflow from allocating more memory than the scheduler will allow. > NB: The submit node limits the amount of memory available to each user. The `NXF_OPTS` and `MALLOC_ARENA_MAX` parameters above prevent Nextflow from allocating more memory than the scheduler will allow.

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nextflow.config
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@ -1 +1,2 @@
params.custom_config_base = "."
includeConfig("nfcore_custom.config") includeConfig("nfcore_custom.config")

1
nfcore_custom.config
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@ -57,6 +57,7 @@ profiles {
phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
prince { includeConfig "${params.custom_config_base}/conf/prince.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
rosalind { includeConfig "${params.custom_config_base}/conf/rosalind.config" } rosalind { includeConfig "${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"} sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"}
seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }