add support for Contig Mapping File

[aclum]

There are a few things we need to confirm are working properly so we can support NMDC workflows that start with an input assembly file. That is, workflows that start with a contigs file, instead of reads. In this case we need to

• [ ] execute pre_qc_execute from a customized inputs.json generated by workflow automation
• [ ] make sure that mapping file is output from the workflow in the wdl task and workflow outputs block
• [ ] make sure the output renamed contig file is the input to the other wdl structural_annotation tasks.

see related task on the automation side https://github.com/microbiomedata/nmdc_automation/issues/35

cc @mhuntemann @scanon

[aclum]

@hubin-keio is there someone else on the LANL side that can work on this?

[aclum]

If you need to look at the original code that our pre_qc task comes from it is here https://code.jgi.doe.gov/img/img-pipelines/img-annotation-pipeline/-/tree/main/bin/qc/pre-annotation?ref_type=heads

[aclum]

This is required for rerunning annotation post re-iding (if assemblies came from JGI), 16 JGI 1000 soil projects and 87 JGI NEON projects.

[ssarrafan]

@mbthornton-lbl will be continuing to work on this in the next sprint per Slack message. Moving over.

[kaijli]

Currently testing addition of map file task to master branch of mg_annotation (new branch called mapping). Tried adding it to wdl v 1.0 branch but ran into gm_license issues (branched called map_file).

[kaijli]

Branch is ready for merge, pull request created, test results sent to @aclum

[aclum]

@kaijli is there an update here? Based on the last discussion the annotation identifiers should be used.

[aclum]

Per @kaijli in testing.

[ssarrafan]

Moving to next sprint to complete testing

[kaijli]

https://github.com/microbiomedata/mg_annotation/pull/28 merged with master branch