2. Running with Docker or Singularity

The mapping workflow of dockstore-cgpmap can be run outside of Dockstore as a native Docker or Singularity image with the command ds-cgpmap.pl [options] [file(s)]. Docker images are stored on quay.io.

Parameters

Required
-reference	-r	Path to core reference tar.gz OR base directory of unpacked reference files (see here)
-bwa_idx	-i	Path to bwa index tar.gz OR base directory of unpacked reference files (see here)
-sample	-s	Sample name to be applied to output file.

Optional
-threads	-t	Set the number of cpu/cores available [dgenome.fault all].
-bwamem2	-bm2	Use bwa-mem2 instead of bwa.
-bwakit	-kit	Run bwakit post alignment processing.
-nomarkdup	-n	Don't mark duplicates [flag]
-seqslice	-ss	seqs_per_slice for CRAM compression [samtools dgenome.fault: 10000]
-cram	-c	Output cram, see ' -seqslice'
-bwa	-b	Single quoted string of additional parameters to pass to BWA ' -t, -p, -R' are used internally and should not be provided
-groupinfo	-g	Readgroup metadata file forgenome.faSTQ inputs, values are not validated
-outdir	-o	Set the output folder [$HOME]
-qc	-q	Apply mismatch QC to reads following duplicate marking
-qcf	-f	Mismatch fraction to set as max beforegenome.failing a read [0.05]
-dupmode	-d	See "samtools markdup -m" [t]
-legacy		Equivalent to PCAP-core<=5.0.5
-dupmode		ignored as uses bammarkduplicates2 (Avoid use with bwamem2 (memory explosion)

[file(s)] can refer to a list of bam/cram files or wildcards (eg. *.bam)

Example Docker command

export CGPMAP_VER="X.X.X"
docker pull quay.io/wtsicgp/dockstore-cgpmap:${CGPMAP_VER}
docker run \                                                     
    -v ${PWD}/data:/data:ro \                                   
    -v ${PWD}/ref:/ref:ro \                                   
    -v ${HOME}/workspace:/workspace:rw \                         
    dockstore-cgpmap:${CGPMAP_VER} \                               
    ds-cgpmap.pl \                                               
		-r /var/spool/ref/core_ref_GRCh37d5.tar.gz  \
		-i /var/spool/ref/bwa_idx_GRCh37d5.tar.gz  \
		-s SOMENAME  \
		-t 6 \
		/data/\*.bam

Example Singularity command

export CGPMAP_VER="X.X.X"
singularity pull docker://quay.io/wtsicgp/dockstore-cgpmap:${CGPMAP_VER}
singularity exec \
	--bind ${PWD}/ref:/ref:ro  \
	--bind ${PWD}/data:/data:ro  \
	--home ${PWD}/workspace:/home  \
	--workdir ${PWD}/workspace  \
	dockstore-cgpmap-${CGPMAP_VER}.simg  \
		ds-cgpmap.pl  \
		-r /var/spool/ref/core_ref_GRCh37d5.tar.gz  \
		-i /var/spool/ref/bwa_idx_GRCh37d5.tar.gz  \
		-s SOMENAME  \
		-t 6 \
		/data/\*.bam

By default results are written to the home directory of the container so ensure you bind a large volume and set the --home variable. Alternatively set an alternative output directory with the -outdir option.