Merge branch 'master' into rnafusion_update_resources

.github/CODEOWNERS

@@ -0,0 +1,135 @@
+**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
+**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'

.github/PULL_REQUEST_TEMPLATE.md

@@ -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:
 
@@ -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

.github/generate_codeowners.sh

@@ -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

.github/workflows/main.yml

@@ -76,11 +76,13 @@ jobs:
           - "hypatia"
           - "icr_davros"
           - "ifb_core"
+          - "imb"
           - "imperial"
           - "incliva"
           - "ipop_up"
           - "janelia"
           - "jax"
+          - "jex"
           - "ku_sund_dangpu"
           - "leicester"
           - "lugh"
@@ -96,6 +98,8 @@ jobs:
           - "oist"
           - "pasteur"
           - "pawsey_nimbus"
+          - "pawsey_setonix"
+          - "pdc_kth"
           - "phoenix"
           - "prince"
           - "psmn"
@@ -117,6 +121,7 @@ jobs:
           - "uge"
           - "unibe_ibu"
           - "unc_lccc"
+          - "uod_hpc"
           - "uppmax"
           - "utd_ganymede"
           - "utd_sysbio"

README.md

@@ -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.
@@ -134,10 +134,12 @@ Currently documentation is available for the following systems:
 - [ICR_DAVROS](docs/icr_davros.md)
 - [IFB](docs/ifb_core.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)
@@ -152,6 +154,8 @@ Currently documentation is available for the following systems:
 - [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)
@@ -171,6 +175,7 @@ Currently documentation is available for the following systems:
 - [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)

conf/cambridge.config

@@ -1,18 +1,22 @@
+// Description is overwritten with user specific flags
 params {
   config_profile_description = 'Cambridge HPC cluster profile.'
   config_profile_contact = 'Andries van Tonder ([email protected])'
   config_profile_url = "https://docs.hpc.cam.ac.uk/hpc"
+  partition = null 
+  project = null
+  max_memory = 192.GB 
+  max_cpus = 56
+  max_time = 12.h 
 }
+
+// Description is overwritten with user specific flags 
 singularity {
   enabled = true
   autoMounts = true
-}
+} 
+
 process {
   executor = 'slurm'
-  clusterOptions = '-p cclake'
-}
-params {
-  max_memory = 192.GB
-  max_cpus = 56
-  max_time = 12.h
+  clusterOptions = "-A $params.project -p $params.partition"
 }

conf/cheaha.config

@@ -23,7 +23,7 @@ process {
     executor = 'slurm'
     queue = { task.memory <= 50.GB ? (task.time <= 2.h ? 'express' : task.time <= 12.h ? 'short' : task.time <= 50.h ? 'medium' : 'long') : (task.time <= 50.h ? 'largemem' : 'largemem-long')}
     maxRetries = 3
-    beforeScript = 'module load Singularity'
+    beforeScript = 'module load Singularity/3.5.2-GCC-5.4.0-2.26'
 }
 
 params {

conf/crg.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_description = 'Centre for Genomic Regulation (CRG) cluster profile provided by nf-core/configs'
-  config_profile_contact = 'Athanasios Baltzis (@athbaltzis)'
+  config_profile_contact = 'Jose Espinosa-Carrasco (@joseespinosa)'
   config_profile_url = 'http://www.linux.crg.es/index.php/Main_Page'
 }
 

conf/crick.config

@@ -8,6 +8,7 @@ params {
 singularity {
   enabled = true
   autoMounts = true
+  runOptions = '--bind /nemo --bind /flask'
 }
 
 process {

conf/crukmi.config

@@ -12,7 +12,7 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load apps/apptainer/1.2.0'
+  beforeScript = 'module load apps/apptainer'
   executor     = 'slurm'
   queue        = { task.memory <= 240.GB ? 'compute' : 'hmem' }
 

conf/fub_curta.config

@@ -1,20 +1,23 @@
 // Config profile metadata
 params {
+    config_profile_contact = 'Wassim Salam (@wassimsalam01)'
     config_profile_name = 'FUB Curta'
-    config_profile_description = 'Freie Universität Berlin HPC cluster (Curta) profile'
-    config_profile_contact = '[email protected]'
+    config_profile_description = 'Freie Universität Berlin HPC (Curta) profile'
     config_profile_url = 'https://www.fu-berlin.de/en/sites/high-performance-computing/index.html'
-    max_memory = 93.GB
-    max_time = 14.d
+
     max_cpus = 32
+    max_memory = 385.GB
+    max_time = 14.d
+    // These parameters exclude the 4 x 772.GB compute nodes on 'main'
 }
 
+def membership = ['/bin/bash', '-c', 'groups'].execute().text.trim()
+
 // Slurm configuration parameters
 process {
-    scratch = true
     executor = 'slurm'
-    clusterOptions = '--qos=standard'
-    maxRetries = 2
+    maxRetries = 3
+    clusterOptions = { (membership.startsWith("b") ? '--partition=begendiv,main ' : '--partition=main ') << ( task.time <= 3.h ? '--qos=hiprio' : ( task.time <= 3.d ? '--qos=prio' : '--qos=standard' ) ) }
 }
 
 // Singularity parameters

conf/imb.config

@@ -0,0 +1,30 @@
+
+params {
+    config_profile_description    = 'Institute of Molecular Biology (IMB) HPC cluster profile provided by nf-core/configs'
+    config_profile_contact        = 'Patrick Hüther (@phue)'
+    config_profile_url            = 'https://imb-mainz.de/'
+    config_profile_name           = 'IMB HPC cluster'
+
+    max_cpus   = 32
+    max_memory = 1.TB
+    max_time   = 7.d
+}
+
+singularity {
+  enabled    = true
+  autoMounts = true
+}
+
+executor {
+    name      = 'slurm'
+    jobName   = { "${task.process.split(':').last()}" }
+    queueSize = 20
+}
+
+process {
+    scratch = '/jobdir/$SLURM_JOB_ID'
+    cache   = 'lenient'
+    queue   = "groups".execute().text.contains('imb-bioinfocf')
+            ? { task.time <= 5.h ? 'bcfshort' : 'bcflong' }
+            : { task.time <= 5.h ? 'short' : 'long' }
+}