Merge branch 'master' into master

conf/binac.config

@@ -18,9 +18,9 @@ process {
 
 params {
   igenomes_base = '/nfsmounts/igenomes'
-  max_memory = 1024.GB
+  max_memory = 128.GB
   max_cpus = 28
-  max_time = 168.h
+  max_time = 48.h
 }
 
 weblog{

conf/cbe.config

@@ -8,25 +8,16 @@ params {
 process {
   executor = 'slurm'
   module = 'singularity/3.2.1'
-  queue = 'c'
+  queue = { task.memory <= 170.GB ? 'c' : 'm' }
+  clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
 }
 
 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'
+  params.max_cpus = 36
-}
+  params.max_memory = 4.TB
+  igenomes_ignore = true
+  igenomesIgnore = true //deprecated
+}

conf/czbiohub_aws.config

@@ -55,7 +55,8 @@ params {
   awsregion = "us-west-2"
   awsqueue = "nextflow"
 
-  igenomesIgnore = true
+  igenomes_ignore = true
+  igenomesIgnore = true //deprecated
 
   fc_extra_attributes = 'gene_name'
   fc_group_features = 'gene_id'

conf/genouest.config

@@ -16,7 +16,8 @@ process {
 }
 
 params {
-  igenomesIgnore = true
+  igenomes_ignore = true
+  igenomesIgnore = true //deprecated
   max_memory = 750.GB
   max_cpus = 80
   max_time = 336.h

conf/hebbe.config

@@ -18,7 +18,8 @@ process {
 }
 
 params {
-  igenomesIgnore = true
+  igenomes_ignore = true
+  igenomesIgnore = true //deprecated
   saveReference = true
   max_memory = 64.GB
   max_cpus = 20

conf/mendel.config

@@ -19,5 +19,6 @@ params {
   max_cpus = 32
   max_memory = 128.GB
   max_time = 192.h
-  igenomesIgnore = true
+  igenomes_ignore = true
+  igenomesIgnore = true //deprecated
 }

conf/pasteur.config

@@ -16,7 +16,8 @@ process {
 }
 
 params {
-  igenomesIgnore = true
+  igenomes_ignore = true
+  igenomesIgnore = true //deprecated
   max_memory = 256.GB
   max_cpus = 28
   max_time = 24.h

docs/pasteur.md

@@ -4,38 +4,36 @@ All nf-core pipelines have been successfully configured for use on the tars clus
 
 To use, run the pipeline with `-profile pasteur`. This will download and launch the [`pasteur.config`](../conf/pasteur.config) which has been pre-configured with a setup suitable for the Pasteur 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 Pasteur 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 the submission node but on a compute node.
 The compute nodes don't have access to internet so you need to run it offline. 
 
 To do that:
-
 1. Create a virtualenv to install nf-core
-
+```bash
-    ```bash
+module purge
-    module purge
+module load Python/3.6.0
-    module load Python/3.6.0
+module load java
-    module load java
+module load singularity
-    module load singularity
+cd /path/to/nf-core/workflows
-    cd /path/to/nf-core/workflows
+virtualenv .venv -p python3
-    virtualenv .venv -p python3
+. .venv/bin/activate
-    . .venv/bin/activate
+```
-    ```
-
 2. Install nf-core: [here](https://nf-co.re/tools#installation)
 3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use)
-4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/configs#offline-usage)
+4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base)
-5. Run nextflow on a compute node:
+5. Run nextflow on a compute node:       
-
 ```bash
 # create a terminal
-tmux
+tmux 
 
 # Get a compute node
 salloc
@@ -48,7 +46,7 @@ module load singularity
 # Run nextflow workflow
 nextflow run \\
 /path/to/pipeline-dir/from/step/3/workflow \\
--resume
+-resume 
 -profile pasteur \\
 -with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\
 --email my-email@pasteur.fr  \\