Merge all

.travis.yml

@@ -17,8 +17,8 @@ install:
   - mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
 
 env:
-  - NXF_VER='18.10.1' # Specify a minimum NF version that should be tested and work
-  - NXF_VER='' # Plus: get the latest NF version and check, that it works
+  - NXF_VER='18.10.1' SCRATCH='~' # Specify a minimum NF version that should be tested and work. Set SCRATCH for prince.config.
+  - NXF_VER='' SCRATCH='~'        # Plus: get the latest NF version and check, that it works. Set SCRATCH for prince.config.
 
 script:
   # Run the pipeline with the test profile and test remote config
@@ -26,4 +26,5 @@ script:
       grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
       tr -s ' ' | \
       cut -d " " -f 2 | \
-      xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}
+      grep -v "czbiohub_aws" | \
+      xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf --custom_config_base=${TRAVIS_BUILD_DIR} -profile {}

README.md

@@ -84,12 +84,17 @@ Currently documentation is available for the following clusters:
 
 * [BIGPURPLE](docs/bigpurple.md)
 * [BINAC](docs/binac.md)
+* [CBE](docs/cbe.md)
 * [CCGA](docs/ccga.md)
 * [CCGA_DX](/docs/ccga_dx.md)
 * [CFC](docs/binac.md)
 * [CRICK](docs/crick.md)
+* [CZBIOHUB_AWS](docs/czbiohub.md)
+* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
+* [GENOUEST](docs/genouest.md)
 * [GIS](docs/gis.md)
 * [HEBBE](docs/hebbe.md)
+* [KRAKEN](docs/kraken.md)
 * [MENDEL](docs/mendel.md)
 * [MUNIN](docs/munin.md)
 * [PASTEUR](docs/pasteur.md)
@@ -98,7 +103,7 @@ Currently documentation is available for the following clusters:
 * [SHH](docs/shh.md)
 * [UCT_HEX](docs/uct_hex.md)
 * [UPPMAX](docs/uppmax.md)
-* [UPPMAX-DEVEL](docs/uppmax-devel.md)
+* [UPPMAX_DEVEL](docs/uppmax.md)
 * [UZH](docs/uzh.md)
 
 ### Uploading to `nf-core/configs`
@@ -111,4 +116,4 @@ We will be notified automatically when you have created your pull request, and p
 
 ## Help
 
-If you have any questions or issues please send us a message on [Slack](https://nf-core-invite.herokuapp.com/).
+If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).

conf/binac.config

@@ -21,3 +21,8 @@ params {
   max_cpus = 28
   max_time = 48.h
 }
+
+weblog{
+  enabled = true
+  url = 'https://services.qbic.uni-tuebingen.de/flowstore/workflows'
+}

conf/cbe.config

@@ -0,0 +1,32 @@
+//Profile config names for nf-core/configs
+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/'
+}
+
+process {
+  executor = 'slurm'
+  module = 'singularity/3.2.1'
+  queue = 'c'
+}
+
+singularity.enabled = true
+
+params {
+  target_qos = 'medium'
+  params.max_cpus = 36
+  params.max_memory = 170.GB
+  igenomesIgnore = true
+}
+
+if (params.target_qos == 'short') {
+  params.max_time = 8.h
+  process.clusterOptions = '--qos short'
+} else if (params.target_qos == 'medium') {
+  params.max_time = 2.d
+  process.clusterOptions = '--qos medium'
+} else {
+  params.max_time = 14.d
+  process.clusterOptions = '--qos long'
+}

conf/ccga.config

@@ -14,6 +14,7 @@ params {
 singularity {
   enabled = true
   runOptions = "-B /ifs -B /scratch -B /work_beegfs"
+  cacheDir = "/ifs/data/nfs_share/ikmb_repository/singularity_cache/"
 }
 
 executor {

conf/ccga_dx.config

@@ -13,6 +13,7 @@ params {
 
 singularity {
   enabled = true
+  runOptions = "-B /mnt"
 }
 
 executor {

conf/cfc.config

@@ -7,6 +7,7 @@ params {
 
 singularity {
   enabled = true
+  cacheDir = '/nfsmounts/container'
 }
 
 process {
@@ -16,7 +17,7 @@ process {
 
 weblog{
   enabled = true
-  url = 'http://services.qbic.uni-tuebingen.de:8080/workflowservice/workflows'
+  url = 'https://services.qbic.uni-tuebingen.de/flowstore/workflows'
 }
 
 params {

conf/genouest.config

@@ -0,0 +1,23 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'The GenOuest cluster profile'
+  config_profile_contact = 'Anthony Bretaudeau (@abretaud)'
+  config_profile_url = 'https://www.genouest.org'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  runOptions = '-B /scratch:/scratch -B /local:/local -B /db:/db'
+}
+
+process {
+  executor = 'slurm'
+}
+
+params {
+  igenomesIgnore = true
+  max_memory = 750.GB
+  max_cpus = 80
+  max_time = 336.h
+}

conf/kraken.config

@@ -0,0 +1,24 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_name = 'KRAKEN'
+  config_profile_description = 'Jenkins cluster provided by nf-core/configs.'
+  config_profile_contact = 'Maxime Garcia or Johannes Alneberg'
+  config_profile_url = 'kraken.dyn.scilifelab.se'
+}
+
+process {
+  executor = 'local'
+}
+
+docker {
+  enabled = true
+  mountFlags = 'z'
+  fixOwnership = true
+}
+
+params {
+  max_memory = 60.GB
+  max_cpus = 16
+  max_time = 72.h
+  igenomes_base = '/share/igenomes/'
+}

conf/munin.config

@@ -1,20 +1,21 @@
 //Profile config names for nf-core/configs
 params {
-  config_profile_description = 'Big iron cluster profile provided by nf-core/configs.'
+  config_profile_description = 'MUNIN profile provided by nf-core/configs.'
   config_profile_contact = 'Szilveszter Juhos (@szilva)'
   config_profile_url = ''
 }
 
 process {
   executor = 'local'
+  maxForks = 46
 }
 
+// To use singularity, use nextflow run -profile munin,singularity
 singularity {
   enabled = true
-  autoMounts = true
 }
 
-// To use docker instead of singularity, use nextflow run -profile munin,docker
+// To use docker, use nextflow run -profile munin,docker
 docker {
   enabled = false
   mountFlags = 'z'
@@ -22,11 +23,11 @@ docker {
 }
 
 params {
-  saveReference = true
-
-  max_memory = 128.GB
-  max_cpus = 16
+  // general params
+  max_memory = 752.GB
+  max_cpus = 46
   max_time = 72.h
-  // illumina iGenomes reference file paths on UPPMAX
+
+  // Local AWS iGenomes reference file paths on munin
   igenomes_base = '/data1/references/igenomes/'
 }

conf/shh.config

@@ -14,7 +14,7 @@ singularity {
 
 process {
     executor = 'slurm'
-    queue = 'short'
+    queue = { task.memory > 756.GB ? 'supercruncher': task.time <= 2.h ? 'short' : task.time <= 48.h ? 'medium': 'long' }
 }
 
 executor {
@@ -22,9 +22,9 @@ executor {
 }
 
 params {
-  max_memory = 256.GB
+  max_memory = 2.TB
   max_cpus = 32
-  max_time = 2.h
+  max_time = 720.h
   //Illumina iGenomes reference file path
   igenomes_base = "/projects1/public_data/igenomes/"
 }

docs/cbe.md

@@ -0,0 +1,18 @@
+# nf-core/configs: CBE Configuration
+
+All nf-core pipelines have been successfully configured for use on the CLIP BATCH ENVIRONMENT (CBE) cluster at the Vienna BioCenter (VBC).
+
+To use, run the pipeline with `-profile cbe`. This will download and launch the [`cbe.config`](../conf/cbe.config) which has been pre-configured with a setup suitable for the CBE 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.
+
+Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CBE. You can do this by issuing the commands below:
+
+```bash
+## Load Nextflow and Singularity environment modules
+module purge
+module load nextflow/19.04.0
+module load singularity/3.2.1
+```
+
+>NB: You will need an account to use the HPC cluster on CBE in order to run the pipeline. If in doubt contact IT.
+
+>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

docs/genouest.md

@@ -0,0 +1,38 @@
+# nf-core/configs: GenOuest Configuration
+
+All nf-core pipelines have been successfully configured for use on the GenOuest cluster.
+
+To use, run the pipeline with `-profile genouest`. This will download and launch the [`genouest.config`](../conf/genouest.config) which has been pre-configured with a setup suitable for the GenOuest 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 GenOuest cluster
+
+Nextflow is installed on the GenOuest cluster. Some documentation is available on the [GenOuest website](https://www.genouest.org/howto/#nextflow).
+
+You need to activate it like this:
+
+```bash
+source /local/env/envnextflow-19.07.0.sh
+```
+
+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 the submission node but on a compute node. Run nextflow from a compute node:
+
+```bash
+# Login to a compute node
+srun --pty bash
+
+# Load the dependencies if not done before
+source /local/env/envnextflow-19.07.0.sh
+
+# Run a downloaded/git-cloned nextflow workflow from
+nextflow run \\
+/path/to/nf-core/workflow \\
+-resume
+-profile genouest \\
+--email my-email@example.org  \\
+-c my-specific.config
+...
+
+# Or use the nf-core client
+nextflow run nf-core/rnaseq ...
+```

docs/kraken.md

@@ -0,0 +1,10 @@
+# nf-core/configs: KRAKEN Configuration
+
+This profile can be **only** combined with `jenkins.config`. It is used for
+testing pipeline with real data on **in-house** cluster located at SciLifeLab.
+
+To use, run the pipeline with `-profile kraken`. This will download and launch
+the [`kraken.config`](../conf/kraken.config) which has been pre-configured to
+test the pipeline using `docker` by default.
+
+Example: `nextflow run -profile kraken,jenkins`

docs/munin.md

@@ -1,15 +1,31 @@
 # nf-core/configs: MUNIN Configuration
 
-All nf-core pipelines have been successfully configured for use on the MUNIN cluster aka big iron.
+All nf-core pipelines have been successfully configured for use on the MUNIN cluster.
 
-To use, run the pipeline with `-profile munin`. This will download and launch the [`munin.config`](../conf/munin.config) which has been pre-configured with a setup suitable for the MUNIN 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.
+## Usage
+
+To use, run the pipeline with `-profile munin`.
+
+This will download and launch the [`munin.config`](../conf/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster.
 
 Example: `nextflow run -profile munin`
 
-## Docker
+### Singularity
+
+This is the default behavior of this configuration profile.
+
+Using this profile, if no singularity image are available, one will be downloaded from dockerhub, and converted to a Singularity image before execution of the pipeline.
+
+It is also possible to specify the singularity profile:
+
+Example: `nextflow run -profile munin,singularity`
+
+### Docker
 
 It is also possible to execute the pipeline using Docker.
 
+Using this profile, if no docker image are available, one will be downloaded from dockerhub before execution of the pipeline.
+
 Example: `nextflow run -profile munin,docker`
 
 ## Below are non-mandatory information on iGenomes specific configuration

nfcore_custom.config

@@ -14,17 +14,17 @@ params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/$
 profiles {
   bigpurple    { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
   binac        { includeConfig "${params.custom_config_base}/conf/binac.config" }
+  cbe          { includeConfig "${params.custom_config_base}/conf/cbe.config" }
   ccga         { includeConfig "${params.custom_config_base}/conf/ccga.config" }
   ccga_dx      { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
-  czbiohub_aws_highpriority {
-    includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"
-    includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"
-   }
+  czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
+  genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
+  kraken       { includeConfig "${params.custom_config_base}/conf/kraken.config" }
   mendel       { includeConfig "${params.custom_config_base}/conf/mendel.config" }
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }
   pasteur      { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
@@ -33,7 +33,7 @@ profiles {
   shh          { includeConfig "${params.custom_config_base}/conf/shh.config" }
   uct_hex      { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
-  uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" }
+  uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax_devel.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }
 }
 
@@ -44,6 +44,7 @@ params {
   // This is a groovy map, not a nextflow parameter set
   hostnames = [
     crick: ['.thecrick.org'],
+    genouest: ['.genouest.org'],
     uppmax: ['.uppmax.uu.se']
   ]
 }