Made profile a required setting and documented them properly.

Author: viklund

README.md

@@ -11,7 +11,7 @@ mv ./nextflow ~/bin
 export NXF_WORK=$SNIC_NOBACKUP/work
 
 # Pull worfklow from this repo, run manta, normalize, and variant effect predictor:
-nextflow run NBISweden/wgs-structvar --project <uppmax_project_id> --bam <bamfile.bam> --steps manta,normalize,vep
+nextflow run -profile milou NBISweden/wgs-structvar --project <uppmax_project_id> --bam <bamfile.bam> --steps manta,normalize,vep
 
 # Monitor log file
 tail -f .nextflow.log
@@ -32,6 +32,29 @@ used for that dataset. If you have access to the structural variants in the
 swegen dataset you can add that file to the pipeline and thereby have the
 ability to filter population specific variants.
 
+### Profiles for running on Uppmax HPC clusters
+
+It is possible to run the pipeline in a few different ways. Either as a
+single-node job or letting nextflow distribute the tasks using the SLURM
+queing engine. There is also some slight differences in module usage depending
+on which HPC system is used.
+
+specify the profile to use with the `-profile` option to NextFlow:
+
+<dl>
+  <dt>-profile milou</dt>
+  <dd>Run on the milou cluster using the queueing system (for example,
+  directly from the login node).
+  <dt>-profile miloulocal</dt>
+  <dd>Run on milou but only on the local node. Use this in a batch job on one
+  node, reserve it for 48 hours and everything should be ok.
+  <dt>-profile bianca</dt>
+  <dd>The same as `milou` but on the Bianca system</dd>
+  <dt>-profile biancalocal</dt>
+  <dd>The same as `miloulocal` but on the Bianca system</dd>
+</dl>
+
+
 ### Masking
 
 #### Artifact masking
@@ -54,7 +77,7 @@ filters put the `bed` files in the `mask_cohort/` subdirectory and add the
 ```bash
 cp some_bed_file.bed <path-to-wgs-structvar>/mask_cohort/
 
-nextflow run <path-to-wgs-structvar>/main.nf --project <uppmax_project_id> --bam <bamfile.bam> --steps manta,normalize,vep,mask_cohort
+nextflow run -profile biancalocal <path-to-wgs-structvar>/main.nf --project <uppmax_project_id> --bam <bamfile.bam> --steps manta,normalize,vep,mask_cohort
 ```
 
 You can configure the location of the cohort mask files with the
@@ -80,8 +103,11 @@ Options:
                     with a run id to more easily keep track of the run (otherwise
                     it\'s autogenerated).
     --project       Uppmax project to log cluster time to
-       OR
-    -profile local  Run locally, only for very small datasets
+    -profile <profile>
+                    Where profile can be any of milou, localmilou, bianca,
+                    localbianca and devel. The local<x> are for running the
+                    entire workflow on a single node on the cluster, without
+                    the local prefix the slurm queueing system is used.
   Optional
     --help          Show this message and exit
     --fastq         Input fastqfile (default is bam but with fq as fileending)

main.nf

@@ -447,8 +447,11 @@ def usage_message() {
     log.info '                    with a run id to more easily keep track of the run (otherwise'
     log.info '                    it\'s autogenerated).'
     log.info '    --project       Uppmax project to log cluster time to'
-    log.info '       OR'
-    log.info '    -profile local  Run locally, only for very small datasets'
+    log.info '    -profile <profile>'
+    log.info '                    Where profile can be any of milou, localmilou, bianca,'
+    log.info '                    localbianca and devel. The local<x> are for running the'
+    log.info '                    entire workflow on a single node on the cluster, without'
+    log.info '                    the local prefix the slurm queueing system is used.'
     log.info '  Optional'
     log.info '    --help          Show this message and exit'
     log.info '    --fastq         Input fastqfile (default is bam but with fq as fileending)'

nextflow.config

@@ -29,7 +29,7 @@ params {
 }
 
 profiles {
-    standard {
+    milou {
         includeConfig 'config/standard.config'
         includeConfig 'config/milou.config'
     }
@@ -44,8 +44,7 @@ profiles {
         includeConfig 'config/milou.config'
     }
 
-    // Pass -profile local to run locally on UPPMAX
-    local {
+    localmilou {
         includeConfig 'config/milou.config'
         process.executor = 'local'
         process.errorStrategy = { $params.runfile != "" ? 'ignore' : 'terminate' }