Added alignment_software & alignment_software_version field in analysis_protocol Fixes #1533

[arschat]

Release notes

For analysis_protocol.json schema:

• Added alignment_software optional field
• Added alignment_software_version optional field

Why are these changes needed?

This field is needed to record the specific software used in order to align fastq files to a reference genome. Is one of the upcoming Tier 1 metadata proposed from HCA Integration Teams & HCA Bionetworks.

[arschat]

@hannes-ucsc Hello Hannes! My initial thought was to accompany the aligner with the genome assembly version, and since genome assembly version field is recorded in the analysis file, I modeled it that way. I can see the pros of modeling it in the analysis protocol, and if you agree on separating alignment_software and genome_assembly_version I will proceed with the proposed change.

[hannes-ucsc]

and if you agree on separating alignment_software and genome_assembly_version I will proceed with the proposed change

Did you mean "alignment_software and alignment_software_version"?

And with "proposed change" you mean moving alignment_software and alignment_software_version to analysis_protocol schema?

[arschat]

Exactly. If you agree on separating alignment_software and alignment_software_version from genome_assembly_version I will proceed with moving the two new fields in the analysis_protocol type. Sorry for not being clear before.

[hannes-ucsc]

Great, that's the approach I find most reasonable.

[hannes-ucsc]

Note https://github.com/HumanCellAtlas/dcp2/blob/main/docs/dcp2_operating_procedures.rst step 9

9. Start another cycle by requesting a review from the reviewers currently on the PR, even those that already approved the PR or just commented on it. Proceed to step 3.

[arschat]

Applied dependencies keyword instead of dependentRequired as discussed above, and fixed update_log.csv. Please review!