Merge pull request #49 from NBISweden/release/v0.2

Release v0.2

Author: viklund

.gitignore

@@ -1 +1,7 @@
 .nextflow.*
+results*
+slurm-*
+CEP-1-7*
+test_data
+.cache
+.nextflow

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)

bin/uppmax_make_test_data.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+module load bioinfo-tools
+module load samtools
+
+set -x
+
+CHR="1 2"
+FN="1-2"
+
+BASEDIR=/proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-1-7/03-BAM
+BASEFILE=CEP-1-7.clean.dedup.recal
+
+OUT="$BASEFILE.chr$FN"
+
+if [ ! -f $OUT.bam ]; then
+    samtools view -bh "$BASEDIR/$BASEFILE.bam" $CHR > $OUT.bam
+fi
+
+if [ ! -f $OUT.bam.bai ]; then
+    samtools index $OUT.bam
+fi
+
+if [ ! -f $OUT.fq.gz ]; then
+    samtools bam2fq $OUT.bam | gzip - > $OUT.fq.gz
+fi

data/RMNISTHS_30xdownsample.chr17-20kb.bam

@@ -0,0 +1,18 @@
+digraph {
+    annotate [label="vep OR snpEFF"];
+    bamfile -> manta -> annotate [style=bold,color=red];
+    bamfile -> fermikit -> annotate [style=bold];
+    bamfile -> tiddit -> annotate [style=dotted];
+    bamfile -> CNVnator -> annotate [style=dotted];
+
+    {manta; fermikit} -> mask [style=bold];
+    {tiddit; CNVnator} -> mask [style=dotted];
+
+    mask -> intersect [label="manta",style=bold];
+    mask -> intersect [label="fermikit",style=bold];
+
+    intersect -> intersect_deletions -> annotate [style=bold];
+    intersect -> intersect_insertions -> annotate [style=bold];
+    intersect -> intersect_duplications -> annotate [style=bold];
+
+}