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maxulysse authored Jan 29, 2024
2 parents 4b9b5e7 + 517e677 commit fac63bd
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136 changes: 136 additions & 0 deletions .github/CODEOWNERS
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@@ -0,0 +1,136 @@
**abims** @lecorguille
**adcra** @kalayaneech
**alice** @osteobjorn
**apollo** @coh.org
**aws_tower** @ggabernet
**awsbatch** @apeltzer
**azurebatch** @adamrtalbot
**azurebatchdev** @abhi18av
**bi** @apeltzer
**bigpurple** @tobsecret
**binac** @apeltzer
**biohpc_gen** @phue
**biowulf** @hpc.nih.gov'
**cambridge** @cam.ac.uk
**cbe** @phue
**ccga_dx** @marchoeppner
**ccga_med** @marchoeppner
**cedars** @rajewski
**ceres** @MillironX
**cfc** @FriederikeHanssen
**cfc_dev** @FriederikeHanssen
**cheaha** @uab.edu
**computerome** @marcmtk
**crg** @joseespinosa
**crick** @chris-cheshire
**crukmi** @sppearce
**czbiohub_aws** @olgabot
**denbi_qbic** @apeltzer
**dkfz** @dkfz-heidelberg.de'
**ebc** @marcel-keller
**ebi_codon** @saulpierotti-ebi
**ebi_codon_slurm** @saulpierotti-ebi
**eddie** @ameynert
**engaging** @PhilPalmer
**ethz_euler** @hest.ethz.ch
**eva** @jfy133
**fgcz** @fgcz.ethz.ch"
**fub_curta** @zedat.fu-berlin.de'
**genotoul** @inra.fr'
**genouest** @abretaud
**gis** @andreas-wilm
**google** @evanfloden
**googlebatch** @hnawar'
**googlels** @hnawar'
**hasta** config_profile_contact = 'Clinical Genomics, Stockholm'
**hki** @jfy133 @jfy133 @jfy133 @jfy133
**hypatia** @lusacristan
**icr_davros** @adrlar
**ifb_core** config_profile_contact = 'https://community.france-bioinformatique.fr'
**imperial** @imperial.ac.uk
**incliva** @incliva.es'
**ipop_up** @parisepigenetics.com'
**janelia** @janelia.hhmi.org
**jax** @flynnb
**ku_sund_dangpu** @sund.ku.dk>'
**leicester** @cam.ac.uk'
**lugh** @BarryDigby
**maestro** @pierrespc
**mana** config_profile_contact = 'Cedric Arisdakessian'
**marvin** @gmail.com (Pablo Carrion
**medair** @gu.se
**mjolnir_globe** @ashildv
**mpcdf** @jfy133
**munin** @maxulysse
**nci_gadi** @mattdton
**nu_genomics** @NUjon
**oist** @oist.jp>'
**pasteur** @rplanel
**pawsey_nimbus** @SarahBeecroft'
**pawsey_setonix** @georgiesamaha
**pdc_kth** @pontus
**phoenix** @apeltzer
**binac** @apeltzer
**uppmax** @lnu.se
**aws_tower** @emiller88
**crick** @ChristopherBarrington
**eva** @jfy133 @jfy133 @jfy133
**maestro**
**mpcdf** @jfy133 @jfy133
**hki** @jfy133
**engaging** @PhilPalmer
**eva** @jfy133
**crg** @joseespinosa
**hasta**
**hasta**
**munin**
**azurebatch_pools_Edv4** @vsmalladi
**eddie**
**mpcdf** @jfy133
**utd_sysbio** @emiller88
**munin** @praveenraj2018
**cfc** @FriederikeHanssen
**eddie**
**eva** @jfy133
**icr_davros**
**munin** @maxulysse
**uppmax** @MaxUlysse
**imperial** config_profile_contact = 'NA'
**eva** @jfy133
**hasta** @sofstam
**eddie**
**genomes**
**prince** @tobsecret
**psmn** @l-modolo
**rosalind** config_profile_contact = 'Theo Portlock'
**rosalind_uge** @gregorysprenger
**sage** @BrunoGrandePhD
**sahmri** @sahmri.com
**sanbi_ilifu** @pvanheus
**sanger** @priyanka-surana
**scw** @bangor.ac.uk'
**seawulf** @davidecarlson
**seg_globe** @ashildv
**software_license** @maxulysse
**tigem** @giusmar
**tubingen_apg** @sc13-bioinf
**tuos_stanage** @sheffield.ac.uk
**ucd_sonic** @brucemoran
**ucl_myriad** @ucl.ac.uk
**uct_hpc** @kviljoen
**uge** @gregorysprenger
**unc_lccc** @alanhoyle
**unibe_ibu** @bioinformatics.unibe.ch"
**uod_hpc** @dundee.ac.uk
**uppmax** @ewels
**utd_ganymede** @emiller88
**utd_sysbio** @emiller88
**uw_hyak_pedslabs** @CarsonJM
**uzh** @apeltzer
**vai** @njspix
**vsc_kul_uhasselt** @kuleuven.be' @kuleuven.be' @kuleuven.be'
**vsc_ugent** @nvnieuwk @matthdsm [email protected]
**wcm** @DoaneAS
**wehi** @wehi.edu.au
**wustl_htcf** @wustl.edu>"
**xanadu** @uconn.edu'
3 changes: 1 addition & 2 deletions .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@ Please follow these steps before submitting your PR:
- [ ] If your PR is a work in progress, include `[WIP]` in its title
- [ ] Your PR targets the `master` branch
- [ ] You've included links to relevant issues, if any
- [ ] Requested review from @nf-core/maintainers and/or #request-review on slack

Steps for adding a new config profile:

Expand All @@ -19,7 +18,7 @@ Steps for adding a new config profile:
- [ ] 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/maintainers
If you require/still waiting for a review, please feel free to request a review from @nf-core/maintainers
Please see uploading to`nf-core/configs` for more details:
https://github.com/nf-core/configs#uploading-to-nf-coreconfigs
Expand Down
22 changes: 22 additions & 0 deletions .github/generate_codeowners.sh
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@@ -0,0 +1,22 @@
#!/usr/bin/env bash

CONFIGS=$(fd . -e .config 'conf/')

output_file=".github/CODEOWNERS"
rm $output_file

for file in $CONFIGS; do
# Get the line of the file that starts with config_profile_contact
line=$(rg "config_profile_contact" "$file")
# and then get the username after the @ and remove anything after it
username=$(echo "$line" | sed 's/^.*@/@/g')
# Remove the )'
username=$(echo "$username" | sed 's/).*$//g')

# Get the insitute name
# conf/<institute>.config
institute=$(echo "$file" | sed 's/^.*\///g' | sed 's/\.config$//g')

# # Remove quotes from authors
echo "**$institute**" $username >> $output_file
done
23 changes: 18 additions & 5 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,15 @@ jobs:
runs-on: ubuntu-latest
name: Check if all profiles are tested
steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- 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
- uses: actions/checkout@v4
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
Expand Down Expand Up @@ -52,9 +52,12 @@ jobs:
- "cfc_dev"
- "cheaha"
- "computerome"
- "create"
- "crg"
- "crick"
- "crukmi"
- "csiro_petrichor"
- "daisybio"
- "denbi_qbic"
- "dkfz"
- "ebc"
Expand All @@ -77,11 +80,14 @@ jobs:
- "hypatia"
- "icr_davros"
- "ifb_core"
- "imb"
- "ilifu"
- "imperial"
- "incliva"
- "ipop_up"
- "janelia"
- "jax"
- "jex"
- "ku_sund_dangpu"
- "leicester"
- "lugh"
Expand All @@ -94,34 +100,41 @@ jobs:
- "munin"
- "nci_gadi"
- "nu_genomics"
- "nygc"
- "nyu_hpc"
- "oist"
- "pasteur"
- "pawsey_nimbus"
- "pawsey_setonix"
- "pdc_kth"
- "phoenix"
- "prince"
- "psmn"
- "rosalind"
- "rosalind_uge"
- "sage"
- "sahmri"
- "sanger"
- "sbc_sharc"
- "scw"
- "seawulf"
- "self_hosted_runner"
- "seg_globe"
- "software_license"
- "tigem"
- "tubingen_apg"
- "tuos_stanage"
- "ucl_myriad"
- "uct_hpc"
- "ucd_sonic"
- "uge"
- "unibe_ibu"
- "unc_lccc"
- "uod_hpc"
- "uppmax"
- "utd_ganymede"
- "utd_sysbio"
- "uw_hyak_pedslabs"
- "uzh"
- "uzl_omics"
- "vai"
- "vsc_kul_uhasselt"
- "vsc_ugent"
Expand All @@ -130,7 +143,7 @@ jobs:
- "xanadu"

steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v4
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
Expand Down
26 changes: 17 additions & 9 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ If you decide to upload your custom config file to `nf-core/configs` then this w
You will simply have to specify `-profile <config_name>` in the command used to run the pipeline.
See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.

Before adding your config file to nf-core/configs, we highly recommend writing and testing your own custom config file (as described [above](Using an existing config)), and then continuing with the next steps.
Before adding your config file to nf-core/configs, we highly recommend writing and testing your own custom config file (as described [above](https://github.com/nf-core/configs#using-an-existing-config)), and then continuing with the next steps.

N.B. In your config file, please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values.
Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example.
Expand Down Expand Up @@ -108,10 +108,13 @@ Currently documentation is available for the following systems:
- [CFC](docs/cfc.md)
- [CHEAHA](docs/cheaha.md)
- [Computerome](docs/computerome.md)
- [CREATE](docs/create.md)
- [CRG](docs/crg.md)
- [CRICK](docs/crick.md)
- [Cancer Research UK Manchester Institute](docs/crukmi.md)
- [CSIRO PETRICHOR](docs/csiro_petrichor.md)
- [CZBIOHUB_AWS](docs/czbiohub.md)
- [DaiSyBio](docs/daisybio.md)
- [DENBI_QBIC](docs/denbi_qbic.md)
- [DKFZ](docs/dkfz.md)
- [EBC](docs/ebc.md)
Expand All @@ -133,11 +136,14 @@ Currently documentation is available for the following systems:
- [HYPATIA](docs/hypatia.md)
- [ICR_DAVROS](docs/icr_davros.md)
- [IFB](docs/ifb_core.md)
- [ILIFU](docs/ilifu.md)
- [IMPERIAL](docs/imperial.md)
- [IMB](docs/imb.md)
- [INCLIVA](docs/incliva.md)
- [iPOP-UP](docs/ipop_up.md)
- [Janelia Research Campus](docs/janelia.md)
- [JAX](docs/jax.md)
- [Jex](docs/jex.md)
- [KU SUND DANGPU](docs/ku_sund_dangpu.md)
- [LUGH](docs/lugh.md)
- [MAESTRO](docs/maestro.md)
Expand All @@ -149,33 +155,39 @@ Currently documentation is available for the following systems:
- [MUNIN](docs/munin.md)
- [NCI GADI](docs/nci_gadi.md)
- [NU_GENOMICS](docs/nu_genomics.md)
- [NYGC](docs/nygc.md)
- [NYU_HPC](docs/nyu_hpc.md)
- [OIST](docs/oist.md)
- [PASTEUR](docs/pasteur.md)
- [PAWSEY NIMBUS](docs/pawsey_nimbus.md)
- [PAWSEY SETONIX](docs/pawsey_setonix.md)
- [PDC](docs/pdc_kth.md)
- [PHOENIX](docs/phoenix.md)
- [PRINCE](docs/prince.md)
- [PSMN](docs/psmn.md)
- [ROSALIND](docs/rosalind.md)
- [ROSALIND_UGE](docs/rosalind_uge.md)
- [SAGE BIONETWORKS](docs/sage.md)
- [SANGER](docs/sanger.md)
- [SBC_SHARC](docs/sbc_sharc.md)
- [SEAWULF](docs/seawulf.md)
- [SEG_GLOBE](docs/seg_globe.md)
- [self-hosted-runner](docs/self-hosted-runner.md)
- [Super Computing Wales](docs/scw.md)
- [TIGEM](docs/tigem.md)
- [TUBINGEN_APG](docs/tubingen_apg.md)
- [TUOS_STANAGE](docs/tuos_stanage.md)
- [UCD_SONIC](docs/ucd_sonic.md)
- [UCL_MYRIAD](docs/ucl_myriad.md)
- [UCT_HPC](docs/uct_hpc.md)
- [UNC_LCCC](docs/unc_lccc.md)
- [UGE](docs/uge.md)
- [UNIBE_IBU](docs/unibe_ibu.md)
- [UOD_HPC](docs/uod_hpc.md)
- [UPPMAX](docs/uppmax.md)
- [UTD_GANYMEDE](docs/utd_ganymede.md)
- [UTD_SYSBIO](docs/utd_sysbio.md)
- [UW_HYAK_PEDSLABS](docs/uw_hyak_pedslabs.md)
- [UZH](docs/uzh.md)
- [UZL_OMICS](docs/uzl_omics.md)
- [VAI](docs/vai.md)
- [VSC_KUL_UHASSELT](docs/vsc_kul_uhasselt.md)
- [VSC_UGENT](docs/vsc_ugent.md)
Expand Down Expand Up @@ -233,10 +245,6 @@ Currently documentation is available for the following pipelines within specific
- ampliseq
- [BINAC](docs/pipeline/ampliseq/binac.md)
- [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
- atacseq
- [SBC_SHARC](docs/pipeline/atacseq/sbc_sharc.md)
- chipseq
- [SBC_SHARC](docs/pipeline/chipseq/sbc_sharc.md)
- demultiplex
- [AWS_TOWER](docs/pipeline/demultiplex/aws_tower.md)
- eager
Expand All @@ -246,18 +254,18 @@ Currently documentation is available for the following pipelines within specific
- mag
- [Engaging](docs/pipeline/mag/engaging.md)
- [EVA](docs/pipeline/mag/eva.md)
- methylseq
- [FUB Curta](docs/pipeline/methylseq/fub_curta.md)
- rnafusion
- [HASTA](docs/pipeline/rnafusion/hasta.md)
- [MUNIN](docs/pipeline/rnafusion/munin.md)
- rnaseq
- [AZUREBATCH](docs/pipeline/rnaseq/azurebatch.md)
- [SBC_SHARC](docs/pipeline/rnaseq/sbc_sharc.md)
- rnavar
- [MUNIN](docs/pipeline/rnavar/munin.md)
- sarek
- [EVA](docs/pipeline/sarek/eva.md)
- [MUNIN](docs/pipeline/sarek/munin.md)
- [SBC_SHARC](docs/pipeline/sarek/sbc_sharc.md)
- [UPPMAX](docs/pipeline/sarek/uppmax.md)
- taxprofiler
- [EVA](docs/pipeline/taxprofiler/eva.md)
Expand Down
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