Merge pull request #13 from nf-core/master

Sync latest changes

.github/workflows/main.yml

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

README.md

@@ -94,6 +94,7 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
 
 Currently documentation is available for the following systems:
 
+* [ABIMS](docs/abims.md)
 * [AWSBATCH](docs/awsbatch.md)
 * [BIGPURPLE](docs/bigpurple.md)
 * [BI](docs/bi.md)

conf/abims.config

@@ -0,0 +1,24 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'The ABiMS cluster profile'
+  config_profile_contact = 'Gildas Le Corguillé (@lecorguille)'
+  config_profile_url = 'https://abims.sb-roscoff.fr'
+}
+
+singularity {
+  enabled = true
+  autoMounts = false
+  runOptions = '-B /scratch:/scratch -B /scratch2:/scratch2 -B /shared:/shared'
+}
+
+process {
+  executor = 'slurm'
+}
+
+params {
+  igenomes_ignore = true
+  igenomesIgnore = true //deprecated
+  max_memory = 750.GB
+  max_cpus = 200
+  max_time = 24.h
+}

conf/pipeline/sarek/uppmax.config

@@ -4,18 +4,25 @@ params {
   config_profile_contact = 'Maxime Garcia (@MaxUlysse)'
   config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs'
 
-  singleCPUmem = 7000.MB
+  single_cpu_mem = 7000.MB
 // Just useful until iGenomes is updated on UPPMAX
-  igenomeIgnore = true
+  igenomes_ignore = true
   genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle'
 }
 
 def hostname = "hostname".execute().text.trim()
 
 if (hostname ==~ "r.*") {
-  params.singleCPUmem = 6400.MB
+  params.single_cpu_mem = 6400.MB
+
+  process {
+    withName:BamQC {
+      cpus = {params.max_cpus}
+      memory = {params.max_memory}
+    }
+  }
 }
 
 if (hostname ==~ "i.*") {
-  params.singleCPUmem = 15.GB
+  params.single_cpu_mem = 15.GB
 }

conf/shh.config

@@ -15,7 +15,6 @@ cleanup = true
 singularity {
     enabled = true
     autoMounts = true
-    runOptions = '-B /run/shm:/run/shm'
     cacheDir = "/projects1/singularity_scratch/cache/"
 }
 
@@ -25,7 +24,7 @@ process {
 }
 
 executor {
-    queueSize = 16
+    queueSize = 8
 }
 
 profiles {

conf/uppmax.config

@@ -15,7 +15,7 @@ process {
 }
 
 params {
-  saveReference = true
+  save_reference = true
 
   max_memory = 125.GB
   max_cpus = 16

conf/utd_ganymede.config

@@ -12,13 +12,13 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load singularity/2.4.5'
+  beforeScript = 'module load singularity/3.2.1'
   executor = 'slurm'
-  queue = 'genomics'
+  queue = { task.memory >= 32.GB && task.cpu <= 12 ? 'Kim': task.memory <= 24.GB && task.cpu <= 8 ? 'smallmem' : 'genomics' }
 }
 
 params {
-  max_memory = 32.GB
+  max_memory = 128.GB
   max_cpus = 16
-  max_time = 48.h
+  max_time = 96.h
 }

docs/abims.md

@@ -0,0 +1,80 @@
+# nf-core/configs: ABiMS Configuration
+
+All nf-core pipelines have been successfully configured for use on the ABiMS cluster.
+
+To use, run the pipeline with `-profile abims`. This will download and launch the [`abims.config`](../conf/abims.config) which has been pre-configured with a setup suitable for the ABiMS 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.
+
+## Request an account
+
+You will need an account to use the HPC cluster on ABiMS in order
+to run the pipeline. If in doubt see [http://abims.sb-roscoff.fr/account](http://abims.sb-roscoff.fr/account).
+
+## Running the workflow on the ABiMS cluster
+
+Nextflow is installed on the ABiMS cluster.
+
+You need to activate it like this:
+
+```bash
+module load nextflow slurm-drmaa graphviz
+```
+
+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
+# Load the dependencies if not done before
+module load nextflow slurm-drmaa graphviz
+
+# Run a downloaded/git-cloned nextflow workflow from
+srun nextflow run \
+/path/to/nf-core/workflow \
+-profile abims \
+--email my-email@example.org  \
+-c my-specific.config
+...
+
+# Or use let nf-core client download the workflow
+srun nextflow run nf-core/rnaseq -profile abims ...
+
+# To launch in background
+sbatch --wrap "nextflow run nf-core/rnaseq -profile abims ..."
+```
+
+Or write a sbatch script
+
+> nfcore-rnaseq.sh
+
+```bash
+#!/bin/bash
+#SBATCH -p fast
+#SBATCH --mem=4G
+
+module load nextflow slurm-drmaa graphviz
+nextflow run nf-core/rnaseq -profile abims ...
+```
+
+Launch on the cluster with sbatch:
+
+```bash
+sbatch nfcore-rnaseq.sh
+```
+
+### Hello, world
+
+nf-core provides some test for each workflow:
+
+```bash
+module load nextflow slurm-drmaa graphviz
+nextflow run nf-core/rnaseq -profile abims,test
+```
+
+## Singularity images mutualized directory
+
+To reduce the disk usage, nf-core images can be stored in a mutualized directory: `/shared/software/singularity/images/nf-core/`
+
+The environment variable `NXF_SINGULARITY_CACHEDIR: /shared/data/cache/nextflow` will indicate this directory to nextflow.
+
+## Databanks
+
+A local copy of several genomes are available in `/shared/bank/` directory.

nfcore_custom.config

@@ -10,6 +10,7 @@
 
 //Please use a new line per include Config section to allow easier linting/parsing. Thank you.
 profiles {
+  abims        { includeConfig "${params.custom_config_base}/conf/abims.config" }
   awsbatch     { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
   bi           { includeConfig "${params.custom_config_base}/conf/bi.config" }
   bigpurple    { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }