Merge branch 'eva' of github.com:jfy133/configs into eva

README.md

@@ -6,20 +6,20 @@ A repository for hosting Nextflow configuration files containing custom paramete
 
 ## 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
 
@@ -114,6 +114,7 @@ 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/awsbatch.config

@@ -7,10 +7,22 @@ params {
   awsqueue = false
   awsregion = 'eu-west-1'
   awscli = '/home/ec2-user/miniconda/bin/aws'
-  tracedir = './'
+}
+
+timeline {
+  overwrite = true
+}
+report {
+  overwrite = true
+}
+trace {
+  overwrite = true
+}
+dag {
+  overwrite = true
 }
 
 process.executor = 'awsbatch'
 process.queue = params.awsqueue
 aws.region = params.awsregion
-executor.awscli = params.awscli
+aws.batch.cliPath = params.awscli

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/ccga_dx.config

@@ -13,7 +13,7 @@ params {
 
 singularity {
   enabled = true
-  runOptions = "-B /mnt"
+  runOptions = "-B /mnt -B /work_ifs"
 }
 
 executor {
@@ -30,7 +30,7 @@ process {
 
 params {
   // illumina iGenomes reference file paths on DX Cluster
-  igenomes_base = '/mnt/ld_ng_out/sukmb352/references/iGenomes/references/'
+  igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/'
   saveReference = true
   max_memory = 250.GB
   max_cpus = 20

conf/eddie.config

@@ -0,0 +1,50 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'University of Edinburgh (eddie) cluster profile provided by nf-core/configs.'
+  config_profile_contact = 'Alison Meynert (@ameynert)'
+  config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'
+}
+
+executor {
+  name = "sge"
+  queueSize = "100"
+}
+
+process {
+  clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus}" : null }
+  scratch = true
+  penv = { task.cpus > 1 ? "sharedmem" : null }
+
+  // common SGE error statuses
+  errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
+  maxErrors = '-1'
+  maxRetries = 3
+
+  beforeScript =
+  """
+  . /etc/profile.d/modules.sh
+  module load 'roslin/singularity/3.5.3'
+  export SINGULARITY_TMPDIR="\$TMPDIR"
+  """
+}
+
+params {
+  saveReference = true
+  // iGenomes reference base
+  igenomes_base = '/exports/igmm/eddie/NextGenResources/igenomes'
+  max_memory = 384.GB
+  max_cpus = 32
+  max_time = 240.h
+}
+
+env {
+  MALLOC_ARENA_MAX=1
+}
+
+singularity {
+  envWhitelist = "SINGULARITY_TMPDIR"
+  runOptions = '-p'
+  enabled = true
+  autoMounts = true
+}
+

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 +1,25 @@
+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'
+      singularity_cache_dir = '/fastscratch/singularity_cache_nfcore'
+    }
+
+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
+    autoMounts = true
+    cacheDir = params.singularity_cache_dir
+}
+params {
+      max_memory = 768.GB
+      max_cpus = 70
+      max_time = 336.h
+    }

conf/pipeline/rnaseq/eddie.config

@@ -0,0 +1,15 @@
+process {
+
+withName : "PICARD_MARKDUPLICATES" {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+}
+
+withName : "QUALIMAP_RNASEQ" {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+}
+
+withName : "FASTQC" {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+}
+
+}

conf/pipeline/sarek/eddie.config

@@ -0,0 +1,27 @@
+process {
+
+  withName:MapReads {
+    cpus = 16
+  }
+  withName:BuildDict {
+    cpus = 1
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:BamQC {
+    cpus = 8
+    memory = 128.GB
+    clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
+  }
+  withName:MarkDuplicates {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:BaseRecalibrator {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:ApplyBQSR {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GatherBQSRReports {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+}

conf/pipeline/viralrecon/genomes.config

@@ -4,17 +4,41 @@
  * -------------------------------------------------
  * Defines viral reference genomes for all environments.
  */
- 
+
 params {
   // Genome reference file paths
   genomes {
     'NC_045512.2' {
-      fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz"
+      // This version of the reference has been kept here for backwards compatibility.
-      gff   = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz"
+      // Please use 'MN908947.3' if possible because all primer sets are available / have been pre-prepared relative to that assembly
+      fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
+      gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz'
     }
     'MN908947.3' {
-      fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz"
+      fasta            = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz'
-      gff   = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz"
+      gff              = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+      primer_sets {
+        artic {
+          '1' {
+            fasta      = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.reference.fasta'
+            gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+            primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.primer.bed'
+            scheme     = 'nCoV-2019'
+          }
+          '2' {
+            fasta      = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.reference.fasta'
+            gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+            primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.primer.bed'
+            scheme     = 'nCoV-2019'
+          }
+          '3' {
+            fasta      = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta'
+            gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+            primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed'
+            scheme     = 'nCoV-2019'
+          }
+        }
+      }
     }
   }
 }

conf/shh.config

@@ -1,10 +1,10 @@
 //Profile config names for nf-core/configs
 params {
-  config_profile_description = 'Generic MPI-SHH cluster(s) profile provided by nf-core/configs.'
+  config_profile_description = 'Generic MPI-SHH SDAG cluster profile provided by nf-core/configs.'
   config_profile_contact = 'James Fellows Yates (@jfy133), Maxime Borry (@Maxibor)'
   config_profile_url = 'https://shh.mpg.de'
-  max_memory = 256.GB
+  max_memory = 2.TB
-  max_cpus = 32
+  max_cpus = 128
   max_time = 720.h
   //Illumina iGenomes reference file path
   igenomes_base = "/projects1/public_data/igenomes/"
@@ -13,14 +13,9 @@ params {
 // Preform work directory cleanup after a successful run
 cleanup = true
 
-singularity {
-    enabled = true
-    autoMounts = true
-    cacheDir = "/projects1/singularity_scratch/cache/"
-}
-
 process {
     executor = 'slurm'
+    queue = { task.memory > 756.GB || task.cpus > 64 ? 'supercruncher': task.time <= 2.h ? 'short' : task.time <= 48.h ? 'medium': 'long' }
 }
 
 executor {
@@ -28,24 +23,10 @@ executor {
 }
 
 profiles {
-  cdag {
+  singularity {
-    params {
+    singularity.enabled = true
-      config_profile_description = 'CDAG MPI-SHH profile, provided by nf-core/configs.'
+    singularity.autoMounts = true
-    }
+    singularity.cacheDir = "/projects1/singularity_scratch/cache/"
-    // delete when CDAG will be fixed
-    process {
-      queue = 'long'
-    }
-  }
-  sdag {
-    params {
-          config_profile_description = 'SDAG MPI-SHH profile, provided by nf-core/configs.'
-          max_memory = 2.TB
-          max_cpus = 128
-      }
-      process {
-          queue = { task.memory > 756.GB || task.cpus > 64 ? 'supercruncher': task.time <= 2.h ? 'short' : task.time <= 48.h ? 'medium': 'long' }
-     }
   }
   // Profile to deactivate automatic cleanup of work directory after a successful run. Overwrites cleanup option.
   debug {

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/awsbatch.md

@@ -1,4 +1,6 @@
 # nf-core/configs: awsbatch Configuration
 
 To be used with `awsbatch`.
-Custom queue, region and CLI path can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively.
+Custom queue and region can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively.
+
+Allow `overwrite` of `trace`, `timeline`, `report` and `dag` to allow resuming pipelines.

docs/eddie.md

@@ -0,0 +1,104 @@
+# nf-core/configs: Eddie Configuration
+
+nf-core pipelines sarek, rnaseq, and atacseq have all been tested on the University of Edinburgh Eddie HPC.
+
+## Getting help
+
+There is a Slack channel dedicated to eddie users on the MRC IGMM Slack: [https://igmm.slack.com/channels/eddie3](https://igmm.slack.com/channels/eddie3)
+
+## Using the Eddie config profile
+
+To use, run the pipeline with `-profile eddie` (one hyphen).
+This will download and launch the [`eddie.config`](../conf/eddie.config) which has been pre-configured with a setup suitable for the [University of Edinburgh Eddie HPC](https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing).
+
+The configuration file supports running nf-core pipelines with Docker containers running under Singularity by default. Conda is not currently supported.
+
+```bash
+nextflow run nf-core/PIPELINE -profile eddie  # ...rest of pipeline flags
+```
+
+Before running the pipeline you will need to install Nextflow or load it from the module system. Generally the most recent version will be the one you want. If you want to run a Nextflow pipeline that is based on [DSL2](https://www.nextflow.io/docs/latest/dsl2.html), you will need a version that ends with '-edge'.
+
+To list versions:
+
+```bash
+module avail igmm/apps/nextflow
+```
+
+To load the most recent version:
+
+```bash
+module load igmm/apps/nextflow
+```
+
+This config enables Nextflow to manage the pipeline jobs via the SGE job scheduler and using Singularity for software management.
+
+## Singularity set-up
+
+Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to the NextGenResources path for the pipeline and version you want to run. If this does not exist, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have it added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.
+
+If you do not have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again.
+
+```bash
+module load singularity
+export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity/nf-core-rnaseq_v3.0"
+```
+
+Singularity will create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations.
+
+```bash
+cd $HOME
+mkdir /exports/eddie/path/to/my/area/.singularity
+ln -s /exports/eddie/path/to/my/area/.singularity .singularity
+```
+
+## Running Nextflow
+
+### On a login node
+
+You can use a qlogin to run Nextflow, if you request more than the default 2GB of memory. Unfortunately you can't submit the initial Nextflow run process as a job as you can't qsub within a qsub.
+
+```bash
+qlogin -l h_vmem=8G
+```
+
+If your eddie terminal disconnects your Nextflow job will stop. You can run Nextflow as a bash script on the command line using `nohup` to prevent this.
+
+```bash
+nohup ./nextflow_run.sh &
+```
+
+### On a wild west node - IGMM only
+
+Wild west nodes on eddie can be accessed via ssh (node2c15, node2c16, node3g22). To run Nextflow on one of these nodes, do it within a [screen session](https://linuxize.com/post/how-to-use-linux-screen/).
+
+Start a new screen session.
+
+```bash
+screen -S <session_name>
+```
+
+List existing screen sessions
+
+```bash
+screen -ls
+```
+
+Reconnect to an existing screen session
+
+```bash
+screen -r <session_name>
+```
+
+## Using iGenomes references
+
+A local copy of the iGenomes resource has been made available on the Eddie HPC for those with access to `/exports/igmm/eddie/NextGenResources` so you should be able to run the pipeline against any reference available in the `igenomes.config`.
+You can do this by simply using the `--genome <GENOME_ID>` parameter.
+
+## Adjusting maximum resources
+
+This config is set for IGMM standard nodes which have 32 cores and 384GB memory. If you are a non-IGMM user, please see the [ECDF specification](https://www.wiki.ed.ac.uk/display/ResearchServices/Memory+Specification) and adjust the `--clusterOptions` flag appropriately, e.g.
+
+```bash
+--clusterOptions "-C mem256GB" --max_memory "256GB"
+```

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

@@ -23,8 +23,10 @@ profiles {
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
   ebc          { includeConfig "${params.custom_config_base}/conf/ebc.config" }
+  eddie        { includeConfig "${params.custom_config_base}/conf/eddie.config" }
   eva          { includeConfig "${params.custom_config_base}/conf/eva.config" }
   icr_davros   { includeConfig "${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 +48,7 @@ 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

pipeline/rnaseq.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/rnaseq custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/rnaseq folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" }
+}

pipeline/sarek.config

@@ -12,4 +12,5 @@ profiles {
   munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
   uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" }
   icr_davros { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/icr_davros.config" }
+  eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" }
 }