ERROR: Use of uninitialized value $item in sprintf at /opt/wtsi-cgp/bin/ds-cgpwgs.pl line 255.

[leiendeckerlu]

Hi there,

I tried to run the dockstore-cgpwgs:2.0.0 container like this:

singularity exec ./dockstore-cgpwgs-2.0.0.simg ds-cgpwgs.pl \
-r /groups/ob/Software/docker/ftp.sanger.ac.uk/pub/cancer/dockstore/human/core_ref_GRCh37d5.tar.gz \
-a /groups/ob/Software/docker/ftp.sanger.ac.uk/pub/cancer/dockstore/human/VAGrENT_ref_GRCh37d5_ensembl_75.tar.gz \
-si /groups/ob/Software/docker/ftp.sanger.ac.uk/pub/cancer/dockstore/human/SNV_INDEL_ref_GRCh37d5.tar.gz \
-cs /groups/ob/Software/docker/ftp.sanger.ac.uk/pub/cancer/dockstore/human/CNV_SV_ref_GRCh37d5_brass6+.tar.gz \
-cr 350000 \
-sc /groups/ob/Software/docker/ftp.sanger.ac.uk/pub/cancer/dockstore/human/SUBCL_ref_GRCh37d5.tar.gz \
-t /groups/ob/Software/docker/MCC_1T/MCC_1T.bam \
-tidx /groups/ob/Software/docker/MCC_1T/MCC_1T.bam.bai \
-n /groups/ob/Software/docker/MCC_1N/MCC_1N.bam \
-nidx /groups/ob/Software/docker/MCC_1N/MCC_1N.bam.bai \
-o ./cgpwgs_MCC1_out \
-c 14 \
-e /groups/ob/Software/docker/ignore_contigs_GRCh37d5.txt

And got the following error output:

https://gist.github.com/leiendeckerlu/c72d1589dd2595bd5e0c2f2c23dbb247

Any idea whats going wrong here?

Thank you!

[keiranmraine]

Hi,

Looks like we've failed to document -qc/-qcset in the command line help.

see here for files:

https://github.com/cancerit/dockstore-cgpwgs/blob/develop/examples/cgpwgs/bam_bai_pu_pl.json#L22-L24

(also need to make checks for these more robust and give informative error messages, historical assumption of CWL use is making us miss these)

[zhouyangyu]

Please merge PR #32 to help users avoid this issue in the future.