Merge branch 'master' into UPPMAX

.github/workflows/main.yml

@@ -8,7 +8,7 @@ jobs:
     steps:
       - uses: actions/checkout@v1
       - name: Check whether profiles are all tested
-        run: | 
+        run: |
           python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
   profile_test:
     runs-on: ubuntu-latest
@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh_sdag', 'shh_cdag', 'uct_hex', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

conf/shh.config

@@ -1,6 +1,6 @@
 //Profile config names for nf-core/configs
 params {
-  config_profile_description = 'MPI-SHH SDAG cluster profile provided by nf-core/configs.'
+  config_profile_description = 'Generic MPI-SHH cluster(s) profile provided by nf-core/configs.'
   config_profile_contact = 'James Fellows Yates (@jfy133), Maxime Borry (@Maxibor)'
   config_profile_url = 'https://shh.mpg.de'
 }
@@ -22,9 +22,21 @@ executor {
 }
 
 params {
-  max_memory = 2.TB
+  max_memory = 256.GB
-  max_cpus = 128
+  max_cpus = 32
   max_time = 720.h
   //Illumina iGenomes reference file path
   igenomes_base = "/projects1/public_data/igenomes/"
 }
+
+
+profiles {
+  cdag {
+      config_profile_description = 'MPI-SHH CDAG profile, provided by nf-core/configs.'
+  }
+  sdag {
+      config_profile_description = 'MPI-SHH SDAG profile, provided by nf-core/configs.'
+      max_memory = 2.TB
+      max_cpus = 128
+  }
+}

conf/shh_cdag.config

@@ -1,30 +0,0 @@
-//Profile config names for nf-core/configs
-params {
-  config_profile_description = 'MPI-SHH CDAG cluster profile provided by nf-core/configs.'
-  config_profile_contact = 'James Fellows Yates (@jfy133), Maxime Borry (@Maxibor)'
-  config_profile_url = 'https://shh.mpg.de'
-}
-
-singularity {
-    enabled = true
-    autoMounts = true
-    runOptions = '-B /run/shm:/run/shm'
-    cacheDir = "/projects1/singularity_scratch/cache/"
-}
-
-process {
-    executor = 'slurm'
-    queue = { task.time <= 2.h ? 'short' : task.time <= 48.h ? 'medium': 'long' }
-}
-
-executor {
-    queueSize = 16
-}
-
-params {
-  max_memory = 256.GB
-  max_cpus = 32
-  max_time = 720.h
-  //Illumina iGenomes reference file path
-  igenomes_base = "/projects1/public_data/igenomes/"
-}

docs/shh.md

@@ -2,7 +2,7 @@
 
 All nf-core pipelines have been successfully configured for use on the Department of Archaeogenetic's SDAG/CDAG clusters at the [Max Planck Institute for the Science of Human History (MPI-SHH)](http://shh.mpg.de).
 
-To use, run the pipeline either with `-profile shh_sdag` or `-profile ssh_cdag`. This will download and launch the [`shh.config`](../conf/shh.config) which has been pre-configured with a setup suitable for the SDAG and CDAG clusters respectively. 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. The image will currently be centrally stored here:
+To use, run the pipeline with `-profile ssh`. You can further with optimise submissions by specifying which cluster you are using with `-profile shh,sdag` or `-profile ssh,cdag`. This will download and launch the [`shh.config`](../conf/shh.config) which has been pre-configured with a setup suitable for the SDAG and CDAG clusters respectively. 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. The image will currently be centrally stored here:
 
 ```bash
 /projects1/singularity_scratch/cache/
@@ -10,7 +10,7 @@ To use, run the pipeline either with `-profile shh_sdag` or `-profile ssh_cdag`.
 
 however this will likely change to a read-only directory in the future that will be managed by the IT team.
 
-This configuration will automatically choose the correct SLURM queue (`short`,`medium`,`long`) depending on the time and memory required by each process. `ssh_sdag` additionally allows for submission of jobs to the `supercruncher` when a job's requested memory exceeds 756GB.
+This configuration will automatically choose the correct SLURM queue (`short`,`medium`,`long`) depending on the time and memory required by each process. `-profile ssh,sdag` additionally allows for submission of jobs to the `supercruncher` queue when a job's requested memory exceeds 756GB.
 
 >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 the IT team.
 >NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT.

nfcore_custom.config

@@ -35,8 +35,7 @@ profiles {
   pasteur      { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
   phoenix      { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
   prince       { includeConfig "${params.custom_config_base}/conf/prince.config" }
-  shh_sdag     { includeConfig "${params.custom_config_base}/conf/shh_sdag.config" }
+  shh          { includeConfig "${params.custom_config_base}/conf/shh.config" }
-  shh_cdag     { includeConfig "${params.custom_config_base}/conf/shh_cdag.config" }
   uct_hex      { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }