Updated README and usage instructions

Author: viklund

README.md

@@ -12,13 +12,15 @@ mv ./nextflow ~/bin
 ### Run the pipeline
 
 ```bash
-nextflow run NBISweden/wgs-structvar --project <uppmax_project_id> --bam <bamfile.bam> --run_all
+nextflow run NBISweden/wgs-structvar --project <uppmax_project_id> --bam <bamfile.bam> --steps manta,fermikit,vep
 ```
 
-This will run both manta and fermikit and create summary files for everything
-in the `results` subdirectory.
+This will run both manta and fermikit, annotate the results with variant
+effect predictor and create summary files for everything in the `results`
+subdirectory.
 
-It is recommended that you set the environment variable `NXF_WORK` to something like
+It is recommended that you set the environment variable `NXF_WORK` to
+something like
 
 ```bash
 export NXF_WORK=$SNIC_NOBACKUP/work
@@ -41,6 +43,56 @@ The pipeline will use the following mask files to remove known artifacts:
 * From [cc2qe/speedseq](https://github.com/cc2qe/speedseq): https://github.com/cc2qe/speedseq/raw/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed
 * From [lh3/varcmp](https://github.com/lh3/varcmp): https://github.com/lh3/varcmp/raw/master/scripts/LCR-hs37d5.bed.gz
 
+
+## Detailed usage
+
+### Command line options
+
+```
+Usage:
+    nextflow main.nf --bam <bamfile> [more options]
+
+Options:
+  Required
+    --bam           Input bamfile
+    --project       Uppmax project to log cluster time to
+  Optional:
+    (default values in parenthesis where applicable)
+    --help          Show this message and exit
+    --fastq         Input fastqfile (default is bam but with fq as fileending)
+                    Used by fermikit, will be created from the bam file if
+                    missing.
+    --steps         Specify what steps to run, comma separated (manta,vep):
+                Callers: manta, fermikit
+                Annotation: vep, snpeff
+    --outdir        Directory where resultfiles are stored (results)
+    --prefix        Prefix for result filenames ()
+```
+
+
+### Customization
+
+The file `nextflow.config` can be used to make some further customizations to
+the workflow.
+
+It's probably only the `params` scope of the config file that is of interest
+to customize.
+
+The first part has the default values for the command line parameters, see the
+usage message for information on them.
+
+The next section has the reference assembly to use, both as fasta and assembly
+name.
+
+The `modules` section contains all modules used by the workflow and their
+versions, change modules here not in the `main.nf` file.
+
+Finally the `runtime` section has the different runtimes for the different
+parts of the workflow. `fermikit` has it's own timespec since that is a very
+long running program, otherwise the workflow differentiates between `callers`
+and other supporting `simple` single-core jobs.
+
+
 ## External links
 
 * [NextFlow website](http://www.nextflow.io)

main.nf

@@ -360,13 +360,16 @@ def usage_message() {
     log.info '    --bam           Input bamfile'
     log.info '    --project       Uppmax project to log cluster time to'
     log.info '  Optional'
+    log.info '     (default values in parenthesis where applicable)'
     log.info '    --help          Show this message and exit'
+    log.info '                    Used by fermikit, will be created from the bam file if'
+    log.info '                    missing.'
     log.info '    --fastq         Input fastqfile (default is bam but with fq as fileending)'
     log.info '    --steps         Specify what steps to run, comma separated:'
-    log.info '                Callers: manta, fermikit (choose one or many)'
-    log.info '                Annotation: vep OR snpeff'
-    log.info '    --outdir        Directory where resultfiles are stored'
-    log.info '    --prefix        Prefix for result filenames'
+    log.info '                Callers: manta, fermikit
+    log.info '                Annotation: vep, snpeff'
+    log.info '    --outdir        Directory where resultfiles are stored (results)'
+    log.info '    --prefix        Prefix for result filenames (empty)'
     log.info ''
 }