Merge pull request #2 from nf-core/master

Syncing with latest versions

README.md

@@ -60,6 +60,7 @@ Currently documentation is available for the following clusters:
 * [GIS](docs/gis.md)
 * [HEBBE](docs/hebbe.md)
 * [MENDEL](docs/mendel.md)
+* [MUNIN](docs/munin.md)
 * [PHOENIX](docs/phoenix.md)
 * [SHH](docs/shh.md)
 * [UCT_HEX](docs/uct_hex.md)

conf/munin.config

@@ -0,0 +1,33 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_name = 'MUNIN'
+  config_profile_description = 'Big iron cluster profile provided by nf-core/configs.'
+  config_profile_contact = 'Szilveszter Juhos (@szilva)'
+  config_profile_url = ''
+}
+
+process {
+  executor = 'local'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+}
+
+// To use docker instead of singularity, use nextflow run -profile munin,docker
+docker {
+  enabled = false
+  mountFlags = 'z'
+  fixOwnership = true
+}
+
+params {
+  saveReference = true
+
+  max_memory = 128.GB
+  max_cpus = 16
+  max_time = 72.h
+  // illumina iGenomes reference file paths on UPPMAX
+  igenomes_base = '/data0/btb/references/igenomes/'
+}

docs/binac.md

@@ -2,7 +2,7 @@
 
 All nf-core pipelines have been successfully configured for use on the BinAC cluster at Baden-Württemberg HPC.
 
-To use, run the pipeline with `-profile binac`. This will download and launch the [`binac.config`](../conf/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline.
+To use, run the pipeline with `-profile binac`. This will download and launch the [`binac.config`](../conf/binac.config) which has been pre-configured with a setup suitable for the BINAC 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 BINAC cluster. You can do this by issuing the commands below:
 

docs/cfc.md

@@ -2,7 +2,7 @@
 
 All nf-core pipelines have been successfully configured for use on the CFC cluster at the insert institution here.
 
-To use, run the pipeline with `-profile cfc`. This will download and launch the [`cfc.config`](../conf/cfc.config) which has been pre-configured with a setup suitable for the CFC cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline.
+To use, run the pipeline with `-profile cfc`. This will download and launch the [`cfc.config`](../conf/cfc.config) which has been pre-configured with a setup suitable for the CFC 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 CFC cluster. You can do this by issuing the commands below:
 

docs/crick.md

@@ -2,7 +2,7 @@
 
 All nf-core pipelines have been successfully configured for use on the CAMP HPC cluster at the [The Francis Crick Institute](https://www.crick.ac.uk/).
 
-To use, run the pipeline with `-profile crick`. This will download and launch the [`crick.config`](../conf/crick.config) which has been pre-configured with a setup suitable for the CAMP HPC cluster. Using this profile, Nextflow will download a temporary singularity image with all of the required software before execution of the pipeline.
+To use, run the pipeline with `-profile crick`. This will download and launch the [`crick.config`](../conf/crick.config) which has been pre-configured with a setup suitable for the CAMP HPC 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 CAMP. You can do this by issuing the commands below:
 

docs/munin.md

@@ -0,0 +1,20 @@
+# nf-core/configs: MUNIN Configuration
+
+All nf-core pipelines have been successfully configured for use on the MUNIN cluster aka big iron.
+
+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.
+
+Example: `nextflow run -profile munin`
+
+## Docker
+
+It is also possible to execute the pipeline using Docker.
+
+Example: `nextflow run -profile munin,docker`
+
+## Below are non-mandatory information on iGenomes specific configuration
+
+A local copy of the iGenomes resource has been made available on the MUNIN cluster so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
+You can do this by simply using the `--genome <GENOME_ID>` parameter.
+
+>NB: You will need an account to use the MUNIN cluster in order to run the pipeline. If in doubt contact @szilva.

docs/shh.md

@@ -0,0 +1,21 @@
+# nf-core/configs: SHH Configuration
+
+All nf-core pipelines have been successfully configured for use on the Department of Archaeogenetic's SDAG cluster at the [Max Planck Institute for the Science of Human History (MPI-SHH)](http://shh.mpg.de).
+
+To use, run the pipeline with `-profile shh`. This will download and launch the [`shh.config`](../conf/shh.config) which has been pre-configured with a setup suitable for the SDAG 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.
+
+Note that the configuration file is currently optimised for `nf-core/eager`. It
+will submit to the medium queue but with a walltime of 48 hours.
+
+## Preparation
+Before running the pipeline you will need to create a the following folder in your `/projects1/users/` directory. This will be used to store the singularity software images, which will take up too much space for your home directory.
+
+This should be named as follows, replacing `<your_user>` with your username:
+
+```bash
+"/projects1/users/<your_user>/nextflow/nf_cache/singularity/"
+```
+
+>NB: You will need an account and VPN access to use the cluster at MPI-SHH 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 lhead nodes. If in doubt contact IT.

docs/template.md

@@ -2,9 +2,9 @@
 
 All nf-core pipelines have been successfully configured for use on the PROFILE CLUSTER at the insert institution here.
 
-To use, run the pipeline with `-profile PROFILENAME`. This will download and launch the [`profile.config`](../conf/profile.config) which has been pre-configured with a setup suitable for the PROFILE cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline.
+To use, run the pipeline with `-profile PROFILENAME`. This will download and launch the [`profile.config`](../conf/profile.config) which has been pre-configured with a setup suitable for the PROFILE 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.
 
-## Below are non-mandatory information e.g. on modules to load etc. 
+## Below are non-mandatory information e.g. on modules to load etc.
 
 Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on PROFILE CLUSTER. You can do this by issuing the commands below:
 

docs/uppmax.md

@@ -3,7 +3,7 @@
 All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters.
 
 ## Using the UPPMAX config profile
-To use, run the pipeline with `-profile uppmax` (one hyphen). This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline.
+To use, run the pipeline with `-profile uppmax` (one hyphen). This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. 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.
 
 In addition to this config profile, you will also need to specify an UPPMAX project id.
 You can do this with the `--project` flag (two hyphens) when launching nextflow. For example:

docs/uzh.md

@@ -1,8 +1,8 @@
 # nf-core/configs: UZH Configuration
 
-All nf-core pipelines have been successfully configured for use on the UZH cluster at the insert institution here.
+All nf-core pipelines have been successfully configured for use on the UZH cluster at the University of Zürich.
 
-To use, run the pipeline with `-profile uzh`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline.
+To use, run the pipeline with `-profile uzh`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH 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.
 
 
 >NB: You will need an account to use the HPC cluster UZH in order to run the pipeline. If in doubt contact IT.

nfcore_custom.config

@@ -18,6 +18,7 @@ profiles {
   gis          { includeConfig "${config_base}/gis.config" }
   hebbe        { includeConfig "${config_base}/hebbe.config" }
   mendel       { includeConfig "${config_base}/mendel.config" }
+  munin        { includeConfig "${config_base}/munin.config" }
   phoenix      { includeConfig "${config_base}/pheonix.config" }
   shh          { includeConfig "${config_base}/shh.config" }
   uct_hex      { includeConfig "${config_base}/uct_hex.config" }