Closed kapsakcj closed 1 year ago
@cimendes FYI I think we will need to update the spatyper
parsing code to account scenarios where more than one match is found (example: different hits from different contigs)
One of the samples I tested with had 2 hits in the output spatyper TSV, leading to parsing issues with the spatyper_repeats
and spatyper_type
output strings
Sample is SAMEA2238216
in my sandbox workspace within the staph_illumina_pe
data table, also uploaded the TSV here:
SAMEA2238216.tsv.txt
Let's be careful with pushing commits now, because we have 2 non-Theiagen labs that may be using this dev branch for testing. Only push commits when we're confident they will run properly in Terra, please!
retested in Terra successfully after the recent changes to spatyper results parsing:
SE - https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/curtis_sandbox/job_history/78fe80bb-929c-47ba-8ea0-70ca8635c290 PE - https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/curtis_sandbox/job_history/6ca6c9a8-8190-4633-90aa-71b858cc9915
Successful testing in Terra following the merge of PR #218 (addition of agrvate
to S aureus subworkflow)
Paired end (1 failure is related to data and expected, failure not related to code changes): https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/curtis_sandbox/job_history/c276ff93-3a08-411b-af42-d36c1b0ec2f4
Tested on Terra with a different set of saureus and everything worked as expected: https://job-manager.dsde-prod.broadinstitute.org/jobs/2bae52ca-80e2-42c2-9ce9-fa7a317352f6
setting as a draft for now, will provide further details soonStill have a good bit of code to edit and needs testing in Terra before we set this as "ready to review"EDIT: I think we need to adjust the spatyper output parsing code. Set this PR back to draft state until that is resolved.I think we're almost wrapped up with code additions and testing in Terra. The only other thing would be to add the toolagravate
, which we already have a WDL task for, but it would need updating and testing. I propose we delay that the addition of that toolAdded
agrvate
in PR #218 ,will mark this PR as ready for review once that is merged and the CI has been fixedPR is finally ready for review
Summary
This PR adds 3 Staphylococcus aureus-specific tools to the merlin_magic subworkflow as well as TheiaProk_Illumina_SE and TheiaProk_Illumina_PE workflows.
staphopia_sccmec
- "staphopia-sccmec
reads Staphopia results or assembly to assign a SCCmec type."spatyper
- "Computational method for finding spa types."agrvate
- "Rapid identification of Staphylococcus aureus agr locus type and agr operon variants"Changes for
staphopia_sccmec
andspatyper
.github/workflows/miniwdl-check.yml
and.github/workflows/pytest-workflows.yml
actions/checkout@v3
andactions/upload-artifact@v3
to prevent warningstasks/species_typing/task_spatyper.wdl
?
fromcpu
inputecho
for versioningFile spatyper_tsv
String spatyper_repeats
String spatyper_type
String spatyper_docker
cpu
now uses input variabletasks/species_typing/task_staphopiasccmec.wdl
hamming
- we opted to always generate the hamming distance TSVcpu
to1
since this doesn't need many threadsFile staphopiasccmec_results_tsv
File staphopiasccmec_hamming_distance_tsv
String staphopiasccmec_types_and_mecA_presence
String staphopiasccmec_docker
cpu
runtime attribute now uses input variabletasks/taxon_id/task_gambit.wdl
merlin_tag
toStaphylococcus aureus
tasks/utilities/task_broad_terra_tools.wdl
workflows/wf_merlin_magic.wdl
workflows/wf_theiaprok_illumina_pe.wdl
andworkflows/wf_theiaprok_illumina_se.wdl
Changes for
agrvate
tasks/species_typing/task_agrvate.wdl
disk_size
input var to50
, don't need much spaceecho
agrvate
command to always use mummer with-m
option since usearch is not available in the container (due to strict redistribution rules)cpu
now uses input variablecpu
tasks/utilities/task_broad_terra_tools.wdl
agrvate_docker_image
for when new versions are releasedTesting
Tested both PE and SE workflows on Terra with 4 Staphylococcus aureus Illumina samples. Both ran successfully and export_taxon_tables ran as expected as well.