This PR exposes the absolute coverage of the second-most prevalent genus detected by MIDAS in a sample. It also makes MIDAS a default module so that contamination is more easily identifiable.
:clipboard: Workflow/Task Steps
The MIDAS task performs the following steps:
orders the MIDAS report by the relative abundance column
identifies the most prevalent genus by relative abundance
identifies the second-most prevalent genus by relative abundance
flags if the relative abundance of the second-most prevalent genus is above 0.01 (1%)
In addition to these steps, the task will now also:
report the absolute coverage of the second-most prevalent genus as shown in the "coverage" column below.
species_id
count_reads
coverage
relative_abundance
Salmonella_enterica_58156
3309
89.88006645
0.855888033
Salmonella_enterica_58266
501
11.60606061
0.110519371
Salmonella_enterica_53987
99
2.232896237
0.021262881
Citrobacter_youngae_61659
46
0.995216227
0.009477003
Escherichia_coli_58110
5
0.123668877
0.001177644
This PR also makes the MIDAS module default in TheiaProk_Illumina_PE_PHB and TheiaProk_Illumina_SE_PHB. However, the workflow can be turned off by setting call_midas to false to conserve compute resources and time.
Finally, this PR adds the string input workflow_series to the TheiaProk PE and SE workflows with the default value of "theiaprok" for consistency with the TheiaProk ONT workflow. This input is passed to read_qc_trim_pe and read_qc_trim_se, respectively, to ensure that the MIDAS task is only run for the TheiaProk workflows.
sage-wright
commented
7 months ago
Closes https://github.com/theiagen/public_health_bioinformatics/issues/247
:hammer_and_wrench: Changes Being Made
Impacted Workflows/Tasks
./tasks/taxon_id/task_midas.wdl ./tasks/quality_control/task_qc_check.wdl ./tasks/utilities/task_broad_terra_tools.wdl ./workflows/theiaprok/wf_theiaprok_illumina_se.wdl ./workflows/theiaprok/wf_theiaprok_illumina_pe.wdl ./workflows/utilities/wf_read_QC_trim_se.wdl ./workflows/utilities/wf_read_QC_trim_pe.wdl
:brain: Context and Rationale
This PR exposes the absolute coverage of the second-most prevalent genus detected by MIDAS in a sample. It also makes MIDAS a default module so that contamination is more easily identifiable.
:clipboard: Workflow/Task Steps
The MIDAS task performs the following steps:
In addition to these steps, the task will now also:
This PR also makes the MIDAS module default in TheiaProk_Illumina_PE_PHB and TheiaProk_Illumina_SE_PHB. However, the workflow can be turned off by setting
call_midastofalseto conserve compute resources and time.Finally, this PR adds the string input
workflow_seriesto the TheiaProk PE and SE workflows with the default value of "theiaprok" for consistency with the TheiaProk ONT workflow. This input is passed to read_qc_trim_pe and read_qc_trim_se, respectively, to ensure that the MIDAS task is only run for the TheiaProk workflows.Inputs
No workflow inputs
Outputs
midas_secondary_genus_coverage
Impacted Outputs
:test_tube: Testing
Locally
No local testing was performed
Terra
TheiaProk_Illumina_PE_PHB testing on 55 enteric samples: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Scribner_Sandbox/job_history/27465535-a7d4-42a4-a979-c880ea737019
Scenarios for Reviewer to Test
TheiaProk_Illumina_SE_PHB still needs testing
:microscope: Quality checks
Pull Request (PR) checklist: