Bug #14622

Annotate l7g CWL pipeline

Added by Ben Carr 7 months ago. Updated 7 months ago.

Status:
New
Priority:
Normal
Assigned To:
Target version:
-
Start date:
Due date:
% Done:

0%

Estimated time:
Billable:
Estimatedhours:
Hours:
Totalhours:
Resolution:
Story points:
-

Description

Old Ticket:
Tiling workflow documentation is out of date. It can be auto-generated partly directly from the cwl workflows.

----
SWZ:

CWL annotated:
[...]

CWL: Not annotated yet, and not experimental
[...]

I would like you to annotate the ones in the following folders as noted by the main workflows (and those cwl they call) called in the AD overview documents:

/cwl-version/filter/cwl
/cwl-version/clean/cwl
/cwl-version/convert2fastj/gvcf_version/cwl
/cwl-version/tilelib/cwl
/cwl-version/checks/check-sglf/cwl
/cwl-version/cgf3/cwl
/cwl-version/checks/check-cgf/gvcf/cwl/
/cwl-version/npy/cwl

Also please spellcheck and check for existing typos.
----
BHCC:

Quote Edit Delete
As of 20181212 the Following is Annotated :

./cgf3/cwl/createcgf.cwl
./cgf3/cwl/getdirs20.cwl
./cgf3/cwl/tiling_convert2cgf.cwl
./cgf3/cwl/getdirs.cwl
./checks/check-cgf/gvcf/cwl/validate-conversion-gvcf-cgf-chrom_workflow.cwl
./checks/check-cgf/gvcf/cwl/gather_validate-conversion-gvcf-cgf.cwl
./checks/check-cgf/gvcf/cwl/validate-conversion-gvcf-cgf-chrom.cwl
./checks/check-sglf/cwl/sglf-sanity-check.cwl
./tagset/l7g-tagset.cwl
./tagset/tagset.cwl
./convert2fastj/gvcf_version/cwl/tiling_convert2fastj_gvcf.cwl
./convert2fastj/gvcf_version/cwl/convertgvcf.cwl
./convert2fastj/gvcf_version/cwl/getdirs.cwl
./clean/cwl/tiling_clean_gvcf.cwl
./clean/cwl/getdirs.cwl
./clean/cwl/cleangvcf.cwl
./filter/cwl/filter.cwl
./filter/cwl/getCollections.cwl
./filter/cwl/tiling_filtergvcf.cwl
./tilelib/cwl/getpaths_chunk.cwl
./tilelib/cwl/tiling_createsglf_chunk-scatter_v2.cwl
./tilelib/cwl/merge-tilelib.cwl
./tilelib/cwl/createsglf_chunkv2.cwl
./npy/cwl/tiling_npy-wf.cwl
./npy/cwl/cwl_steps/tiling_create-npy.cwl
./npy/cwl/cwl_steps/tiling_consol-npy.cwl

BHCC:
Te branch we are working on is

14386-cwl-docum
I have reviewed the list for typographical errors, including grep'ing out all labels and running them through spellcheck. The only place where camel case was used is where it is used by convention for clarity (NumPy) of the package or object.

Things needed to be addressed:
Check spelling one more time
make sure every label starts with a capital
Remove any unnecessary Camel Case
Use the YML files as a guide, as variable names do not always reflect what is going on
Remove and Doc blocks that do not add anything beyond what the label covers.
Shorten any labels as much as possible, the more concise the better
Don't include the type of code C++ / bash unless absolutely necessary
Will likely need a new ticket for the automated generation of figures and may need to run view.cwl locally to make that work. Will test automated generation once the labels are merged to master as vew.cwl only currently works off GitHub-master.
We should consider renaming the "gff" in the variable names of the following scripts:

./filter/cwl/filter.cwl
./filter/cwl/tiling_filtergvcf.cwl
./convert2fastj/gvcf_version/cwl/tiling_convert2fastj_gvcf_named.cwl
./convert2fastj/gvcf_version/cwl/tiling_convert2fastj_gvcf.cwl
./convert2fastj/gvcf_version/cwl/convertgvcf.cwl

to reflect gVCF status

History

#1 Updated by Ben Carr 7 months ago

The new branch we are working on for annotation is:

14622-annotate-cwl

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