Make all configs strict syntax compatible

[nvnieuwk]

Hi everyone!

In April a new Nextflow version will release where the new strict syntax will be enabled by default. This means that a lot of configs in this repository will start failing because of incompatible code. @jfy133 and I wrote a blog post about this to help you in the migration process.

It would be awesome if everyone pinged in this issue could try and update their config files in the repository and properly test them with and without the strict syntax enabled.

All configs that are not updated by the end of March will get a warning added to them to alert the users that this config will start failing soon and will be deprecated.

Summary of failing configs with their respective authors

Note that this is the status in the master branch, some have already been updated in PRs

Please check off your config if the fixes have been merged into the master branch, that way we have a quick overview of the progress 🚀

• conf/alliance_canada.config | Jerry Li (@jerryakii)
• conf/bi.config | Alexander Peltzer (@apeltzer)
• conf/bigpurple.config | Tobias Schraink (@tobsecret)
• conf/bih.config | BIH-HPC IT Team hpc-helpdesk@bih-charite.de (@sellth)|
• conf/binac.config | Felix Bartusch (@fbartusch)
• conf/binac2.config | Felix Bartusch (@fbartusch)
• conf/biowulf.config | staff@hpc.nih.gov (@qiyubio)
• conf/bluebear.config | Alex Lyttle (@alexlyttle)
• conf/cannon.config | Lei Ma (@microlei)
• conf/ceci_dragon2.config | Martin Grignard (@MartinGrignard)
• conf/ceci_nic5.config | Martin Grignard (@MartinGrignard)
• conf/ceres.config | Thomas A. Christensen II (@MillironX)
• conf/cfc.config | Sabrina Krakau (@skrakau)
• conf/cfc_dev.config | Sabrina Krakau (@skrakau)
• conf/cheaha.config | Lara Ianov (@lianov) or Austyn Trull (@atrull314)
• conf/daisybio.config | Johannes Kersting (@JohannesKersting)
• conf/dirac.config | Vincent Aaskov (@VincentAaskov )
• conf/einstein.config | Ashot Margaryan (@ashotmarg)
• conf/embl_hd.config | @fullama
• conf/fub_curta.config | Wassim Salam (@wassimsalam01)
• conf/imb.config | Patrick Hüther (@phue)
• conf/imperial.config | Nurun Fancy (@nfancy)
• conf/incliva.config | Sheila Zúñiga Trejos (@nevinwu)
• conf/iris.config | Nikhil Kumar (@nikhil)
• conf/kaust.config | Husen Umer (@husensofteng )
• conf/lovelace.config | Ashot Margaryan (@ashotmarg), Vincent Aaskov (@VincentAaskov)
• conf/m3c.config | Sabrina Krakau (@skrakau)
• conf/mana.config | Cedric Arisdakessian (@Puumanamana)
• conf/marjorie.config | Ashot Margaryan (@ashotmarg), Vincent Aaskov (@VincentAaskov)
• conf/nci_gadi.config | Georgie Samaha (@georgiesamaha), Matthew Downton (@mattdton)
• conf/nygc.config | John Zinno (@jzinno)
• conf/pdc_kth.config | Pontus Freyhult (@pontus)
• conf/pe2.config | John Zinno (@jzinno)
• conf/pipeline/deepmodeloptim/crg.config | Luisa Santus (@luisas)
• conf/pipeline/eager/eva.config | James Fellows Yates (@jfy133)
• conf/pipeline/eager/maestro.config | @pierrespc
• conf/pipeline/multiplesequencealign/crg.config | Luisa Santus (@luisas)
• conf/pipeline/proteinfold/nci_gadi.config | Mitchell O\Brien (@Mitchob)
• conf/pipeline/sarek/cfc.config | Friederike Hanssen (@FriederikeHanssen) @famosab
• conf/pipeline/sarek/icr_davros.config | @adrlar
• conf/pipeline/scflow/imperial.config | @combiz
• conf/qmul_apocrita.config | Simon Murray (@just-simon-5) & @chriswyatt1
• conf/sage.config | Bruno Grande (@BrunoGrandePhD)
• conf/sanger.config | Priyanka Surana (@priyanka-surana)
• conf/seadragon.config | Jiawei Gu @jiawku
• conf/software_license.config | Maxime U Garcia (@maxulysse)
• conf/ucl_cscluster.config | Simon Murray (@just-simon-5)
• conf/ucl_myriad.config | Chris Wyatt (@chriswyatt1), Fernando Duarte (@FernandoDuarteF)
• conf/unsw_katana.config | @jscgh
• conf/utd_ganymede.config | Edmund Miller @edmundmiller
• conf/utd_juno.config | Anne Fu @eternal-flame-AD
• conf/vsc_calcua.config | @pmoris
• conf/vsc_kul_uhasselt.config | @Joon-Klaps
• conf/vsc_ugent.config | @nvnieuwk & @matthdsm
• conf/wustl_htcf.config | @Pandapip1

[nvnieuwk]

Some configs already have changes coming in, please check the PRs first 👀

[FriederikeHanssen]

@famosab pinging you for the cfc sarek config to escalate to the right person :)

[tobsecret]

Thanks for the helpful article and example config. I've updated mine in a PR and am waiting on a colleague to test it on the cluster I no longer have access to before I merge.

[tobsecret]

Have tested both locally and on the cluster and the changes seem to work.

[jfy133]

cfc, cfc_dev, m3c: https://github.com/nf-core/configs/pull/1024/changes

[jfy133]

ucl: #1023

[jfy133]

Btw @TCLamnidis will address the eva specific pipeline config for eager

[wassimsalam01]

Hello @jfy133,

Hope you're well! I've been out of my institution (FUB) for some time now since graduation (2023/2024). I am currently contacting the responsible IT department to find someone to take over maintenance of the FUB Curta config in the long-term. Is there any standard way to denote the "original creator" and "current person in charge" in the config? Please let me know :)

Thank you and best wishes,

Wassim

[nvnieuwk]

Hi @wassimsalam01

You can remove yourself as the contact person in the config and ask the potential future maintainer to add their name instead :). You can find the contact person information in the config itself

[famosab]

For me the CI does not run through:

But I think the PR can be merged.

[wassimsalam01]

Hi @wassimsalam01

You can remove yourself as the contact person in the config and ask the potential future maintainer to add their name instead :). You can find the contact person information in the config itself

Hi @nvnieuwk, I've managed to contact the FUB HPC Team, and a representative will soon make a PR to reflect changes to the config, while taking the upcoming update into consideration.

[nvnieuwk]

@famosab the CI currently isn't working because it tests all configs (of which some are broken) Please run a test locally to confirm if it works instead.