sigven/cacao

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

cacao's Issues

`Error in makeGroupOptions(sharedData, group, allLevels)`

Hi Sigve,

Having this error in hereditary mode:

python cacao_wflow.py test/slice.sorted.bam data test grch37 hereditary \ 
   SmallCellNET__PRJ180596_CW-DNA029841T
2018-11-21 23:31:08 - cacao-run - INFO - Start
2018-11-21 23:31:08 - cacao-run - INFO - Validating input files and command-line parameters
2018-11-21 23:31:08 - cacao-run - INFO - Running cacao workflow - assessment of coverage at actionable and pathogenic loci
2018-11-21 12:31:16 - cacao-get-track - INFO - Determination of BED region file - considering genome assembly, cancer mode, and chromosome naming convention
2018-11-21 12:31:17 - cacao-coverage-assessment - INFO - Determination of coverage in target regions with https://github.com/brentp/mosdepth: pathogenic loci in hereditary cancer
2018-11-21 12:31:17 - cacao-coverage-assessment - INFO - command: mosdepth --no-per-base --by /workdir/tracks/cancer_hereditary_pathogenic_loci.grch37.bed --mapq 0 --threads 0 SmallCellNET__PRJ180596_CW-DNA029841T_hereditary /workdir/query.bam
2018-11-21 12:31:29 - cacao-coverage-assessment - INFO - Decompressing BED file (SmallCellNET__PRJ180596_CW-DNA029841T_hereditary.regions.bed.gz) with coverage pr. loci
2018-11-21 12:31:30 [INFO] ------
2018-11-21 12:31:30 [INFO] Assigning callability levels across loci
2018-11-21 12:31:31 [INFO] ------
2018-11-21 12:31:31 [INFO] Writing JSON file with CACAO report contents
2018-11-21 12:31:32 [INFO] ------
2018-11-21 12:31:32 [INFO] Rendering HTML report with rmarkdown
Quitting from lines 171-197 (cacao_report.Rmd)
Error in makeGroupOptions(sharedData, group, allLevels) :
  Can't form options with zero-length group vector
Calls: <Anonymous> ... eval -> <Anonymous> -> <Anonymous> -> makeGroupOptions
Execution halted
2018-11-21 23:31:32 - cacao-run - INFO - Finished

Attaching the BAM file:

Archive.zip

Run on the SGE cluster without Docker support

Hi Sigve,

How could I run cacao on the SGE cluster without Docker support?

Regards,
Ya

Option to include/switch reference data and a global preview table

Hi Sigve

Thanks for another awesome framework. We (@umccr) are very much interested to incorporate this into our reporting.

I have looked at the github repo/code and tested it locally - it works great. We have a couple of questions/comments:

1. Would it be possible to feed our own reference (bed) files?

We are interested in using some of the reference data from Hartwig. Looking at the codebase, it shouldn't be a problem as the data directory is passed as an argument and this directory contains reference data to be used for the analysis. However, this might impact the annotations that the framework reads in from the .tsv(s) in `cacao_utils.R for specific clinical genomic tracks?

There is an optional flag --target, which according to my understanding refers to the targeted region in the input sample?

2. Would it make sense to have one global table (that checks coverage for specific genes), stratified by callability - instead of having to go through multiple tracks?

This probably links back to point 1 i.e. feeding in one specific bed track (in this case) which could be joint set of various loci sources such as CIViC, CGI and OncoKb and then reading in the (optional annotations as in the code base) for this data - if this idea aligns well with your original idea of the framework?

3. It would be useful if we could include an option to limit hereditary cancer - pathogenic loci table to cancer predisposition genes that is also used/referenced here https://github.com/sigven/cpsr?

Sorry about the long commentary and thanks for your time.

Cheers,
Sehrish