Merge branch 'master' into bgrande/sage-aws

README.md

@@ -198,6 +198,7 @@ Currently documentation is available for the following pipelines within specific
 - mag
   - [EVA](docs/pipeline/mag/eva.md)
 - rnafusion
+  - [HASTA](docs/pipeline/rnafusion/hasta.md)
   - [MUNIN](docs/pipeline/rnafusion/munin.md)
 - rnavar
   - [MUNIN](docs/pipeline/rnavar/munin.md)

conf/cheaha.config

@@ -5,9 +5,15 @@ params {
     config_profile_url = 'https://www.uab.edu/cores/ircp/bds'
 }
 
+env {
+    TMPDIR="$USER_SCRATCH"
+    SINGULARITY_TMPDIR="$USER_SCRATCH"
+}
+
 singularity {
     enabled = true
     autoMounts = true
+    runOptions = "--contain --workdir $USER_SCRATCH"
 }
 
 process {

conf/google.config

@@ -19,4 +19,6 @@ google.lifeSciences.preemptible = params.google_preemptible
 if (google.lifeSciences.preemptible) {
   process.errorStrategy = { task.exitStatus in [8,10,14] ? 'retry' : 'terminate' }
   process.maxRetries = 5
-}
+}
+
+process.machineType = { task.memory > task.cpus * 6.GB ? ['custom', task.cpus, task.cpus * 6656].join('-') : null }

conf/pipeline/rnafusion/hasta.config

@@ -0,0 +1,7 @@
+// rnafusion/hasta specific profile config for Clinical Genomics Stockholm usage
+
+params {
+    all = true
+    trim = true
+    fusioninspector_filter = true
+}

docs/cheaha.md

@@ -13,6 +13,8 @@ module load Singularity
 module load Nextflow
 ```
 
+Various tasks will be run inside of Singularity containers and all temp files typically written to `/tmp` and `/var/tmp` are instead written to the path pointed to by the `USER_SCRATCH` environment variable. This means that these temp files are stored in a user specific location, making them inaccessible to other users for pipeline reruns. Some of these temp files can be large and cleanup is also the responsibility of the user.
+
 All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
 
 > NB: You will need an account to use the HPC cluster on Cheaha in order to run the pipeline. If in doubt contact UAB IT Research Computing.</br></br>

docs/pipeline/rnafusion/hasta.md

@@ -0,0 +1,19 @@
+# nf-core/configs: HASTA rnafusion specific configuration
+
+Extra specific configuration for rnafusion pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile hasta`.
+
+This will download and launch the rnafusion specific [`hasta.config`](../../../conf/pipeline/rnafusion/munin.config) which has been pre-configured with a setup suitable for the `HASTA` cluster.
+
+Example: `nextflow run nf-core/rnafusion -profile hasta`
+
+## rnafusion specific configurations for HASTA
+
+Specific configurations for `HASTA` has been made for rnafusion.
+
+- Always run all the analysis steps (all = true)
+- Use trimming (trim = true)
+- Take the fusions identified by at least 2 fusion detection tools to the fusioninspector analysis (fusioninspector_filter = true)

pipeline/rnafusion.config

@@ -9,5 +9,6 @@
  */
 
 profiles {
+  hasta { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/hasta.config" }
   munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/munin.config" }
-}
+}