Merge branch 'master' into master

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
+          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -113,6 +113,7 @@ Currently documentation is available for the following systems:
 * [GOOGLE](docs/google.md)
 * [HEBBE](docs/hebbe.md)
 * [ICR_DAVROS](docs/icr_davros.md)
+* [JAX](docs/jax.md)
 * [KRAKEN](docs/kraken.md)
 * [MPCDF](docs/mpcdf.md)
 * [MUNIN](docs/munin.md)

conf/cbe.config

@@ -2,13 +2,13 @@
 params {
   config_profile_description = 'CLIP BATCH ENVIRONMENT (CBE) cluster profile provided by nf-core/configs'
   config_profile_contact = 'Patrick Hüther (@phue)'
-  config_profile_url = 'http://www.gmi.oeaw.ac.at/'
+  config_profile_url = 'https://clip.science'
 }
 
 process {
   executor = 'slurm'
   queue = { task.memory <= 170.GB ? 'c' : 'm' }
-  clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
+  clusterOptions = { task.time <= 1.h ? '--qos rapid' : task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
   module = 'anaconda3/2019.10'
 }
 

conf/ifb_core.config

@@ -0,0 +1,24 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'The IFB core cluster profile'
+  config_profile_contact = 'https://community.france-bioinformatique.fr'
+  config_profile_url = 'https://www.france-bioinformatique.fr/'
+}
+
+singularity {
+  // need one image per execution
+  enabled = true
+  runOptions = '-B /shared'
+}
+
+process {
+  executor = 'slurm'
+}
+
+params {
+  igenomes_ignore = true
+  // Max resources requested by a normal node on genotoul.
+  max_memory = 240.GB
+  max_cpus = 28
+  max_time = 96.h
+}

conf/jax.config

@@ -0,0 +1,21 @@
+params {
+      config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.'
+      config_profile_contact = 'Asaf Peer (@peera)'
+      config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx'
+    }
+
+executor.$slurm.queueSize = 250
+process {
+    executor = "slurm"
+    queue = "compute"
+    clusterOptions = {task.time < 72.h ? '-q batch' : '-q long'}
+    module = "slurm"
+    beforeScript = 'module load singularity'
+}
+singularity.enabled = true
+singularity.autoMounts = true
+params {
+      max_memory = 768.GB
+      max_cpus = 70
+      max_time = 336.h
+    }

conf/utd_ganymede.config

@@ -5,6 +5,11 @@ params {
   config_profile_url = 'http://docs.oithpc.utdallas.edu/'
 }
 
+env {
+    TMPDIR = '/home/$USER/scratch/tmp'
+    SINGULARITY_CACHEDIR = '/home/$USER/scratch/tmp'
+}
+
 singularity {
   enabled = true
   envWhitelist='SINGULARITY_BINDPATH'
@@ -15,6 +20,28 @@ process {
   beforeScript = 'module load singularity/3.2.1'
   executor = 'slurm'
   queue = { task.memory >= 32.GB && task.cpu <= 12 ? 'Kim': task.memory <= 24.GB && task.cpu <= 8 ? 'smallmem' : 'genomics' }
+
+  withName:TRIMGALORE {
+    memory = 31.GB
+  }
+
+  withLabel:process_low {
+    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
+    memory = { check_max( 12.GB * task.attempt, 'memory' ) }
+    time = { check_max( 6.h * task.attempt, 'time' ) }
+  }
+
+  withLabel:process_medium {
+    cpus = { check_max( 16 * task.attempt, 'cpus' ) }
+    memory = { check_max( 31.GB * task.attempt, 'memory' ) }
+    time = { check_max( 8.h * task.attempt, 'time' ) }
+  }
+
+  withLabel:process_high {
+    cpus = { check_max( 12 * task.attempt, 'cpus' ) }
+    memory = { check_max( 120.GB * task.attempt, 'memory' ) }
+    time = { check_max( 16.h * task.attempt, 'time' ) }
+  }
 }
 
 params {

conf/wcm.config

@@ -0,0 +1,28 @@
+singularityDir = "/athena/elementolab/scratch/reference/.singularity/singularity_images_nextflow"
+
+params {
+  config_profile_description = 'Weill Cornell Medicine, Scientific Computing Unit Slurm cluster profile provided by nf-core/configs'
+  config_profile_contact = 'Ashley Stephen Doane, PhD (@DoaneAS)'
+  igenomes_base = '/athena/elementolab/scratch/reference/igenomes'
+}
+
+singularity {
+  enabled = true
+  envWhitelist='SINGULARITY_BINDPATH'
+  cacheDir =  "/athena/elementolab/scratch/reference/.singularity/singularity_images_nextflow"
+  autoMounts = true
+}
+
+process {
+  executor = 'slurm'
+  queue = 'panda_physbio'
+  scratch = true
+  scratch = '/scratchLocal/`whoami`_${SLURM_JOBID}'
+}
+
+params {
+  max_memory = 32.GB
+  max_cpus = 8
+  max_time = 24.h
+}
+

docs/ifb_core.md

@@ -0,0 +1,40 @@
+# nf-core/configs: IFB core Configuration
+
+All nf-core pipelines have been successfully configured for use on the cluster of the IFB (Institut Francais de Bioinformatique).
+
+To use, run the pipeline with `-profile ifb_core`. This will download and launch the [`ifb_core.config`](../conf/ifb_core.config) which has been pre-configured with a setup suitable for the IFB core 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.
+
+## How to use on IFB core
+
+Before running the pipeline you will need to load Nextflow using the environment module system on IFB core. You can do this by issuing the commands below:
+
+```bash
+# Login to a compute node
+srun --pty bash
+
+## Load Nextflow and Singularity environment modules
+module purge
+module load nextflow/20.04.1
+
+# Run a downloaded/git-cloned nextflow workflow from
+nextflow run \\
+nf-core/workflow \\
+-resume
+-profile ifb_core \\
+--email my-email@example.org  \\
+-c my-specific.config
+...
+
+
+# Or use the nf-core client
+nextflow run nf-core/rnaseq ...
+
+```
+
+## Databanks
+
+A local copy of several genomes are available in `/shared/bank` directory. See
+our [databank page](https://ifb-elixirfr.gitlab.io/cluster/doc/banks/)
+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).

docs/jax.md

@@ -0,0 +1,8 @@
+# nf-core/configs: JAX Configuration
+
+All nf-core pipelines have been successfully configured for use on the JAX Sumner cluster at The Jackson Laboratory.
+
+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: Nextflow should not be executed on the login nodes. If in doubt contact IT.

docs/wcm.md

@@ -0,0 +1,24 @@
+# nf-core/configs: Weill Cornell Medicine Configuration
+
+All nf-core pipelines have been successfully configured for use on the panda cluster at the WCM.
+
+To use, run the pipeline with `-profile wcm`. This will download and launch the [`wcm.config`](../conf/wcm.config) which has been pre-configured with a setup suitable for the WCM slurm 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.
+
+## Running the workflow on the Pasteur cluster
+
+Nextflow is not installed by default on the WCM cluster.
+
+- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
+
+Nextflow manages each process as a separate job that is submitted to the cluster by using the `sbatch` command.
+Nextflow shouldn't run directly on a login node but on a compute node or lab-specific interactive server when configured as a submit host.
+
+1. Run nextflow on a compute node or interactive server with submit host capability:
+
+```bash
+# Run nextflow workflow
+nextflow run \\
+nf-core/chipseq \\
+-resume \\
+-profile test,wcm
+```

nfcore_custom.config

@@ -25,6 +25,7 @@ profiles {
   ebc          { includeConfig "${params.custom_config_base}/conf/ebc.config" }
   eddie	  { includeConfig "${params.custom_config_base}/conf/eddie.config" }
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
+  ifb_core     { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
   imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }  
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
@@ -46,6 +47,7 @@ profiles {
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
   utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }
+  jax          { includeConfig "${params.custom_config_base}/conf/jax.config" }
 }
 
 // If user hostnames contain one of these substring and they are