Adding a new hostile task as the human reads removal (dehosting) tool for TheiaCoV_ONT_PHB, and an optional dehosting tool for TheiaCoV_Illumina_PE_PHB.
The current dehosting tool ncbi-scrub only works with illumina paired end reads, whereas hostile works with both illumina and oxford nanopore (ONT) reads. Therefore, we are implementing hostile for dehosting of reads in the TheiaCoV_ONT_PHB workflow.
For TheiaCoV_Illumina_PE_PHB, we are giving users the option to use hostile if so preferred.
:clipboard: Workflow/Task Steps
The hostile task takes as input the variable seq_method to determine if working with or ONT reads. By default, these are set in the TheiaCoV_Illumina_PE_PHB and TheiaCoV_ONT_PHB workflows as ILLUMINA and OXFORD_NANOPORE, respectively.
Inputs
TheiaCoV_ONT_PHB: Inputs remain the same
TheiaCoV_Illumina_PE_PHB: Added an optional input dehosting_tool which takes in the options ncbi_scrub (default) or hostile
Outputs
Remain the same
Impacted Outputs
:test_tube: Testing
Locally
Works as expected locally for the TheiaCoV_ONT_PHB and TheiaCoV_Illumina_PE_PHB workflows
NOTE: Merge https://github.com/theiagen/public_health_bioinformatics/pull/202 before merging this branch!!
:hammer_and_wrench: Changes Being Made
Adding a new
hostile
task as the human reads removal (dehosting) tool forTheiaCoV_ONT_PHB
, and an optional dehosting tool forTheiaCoV_Illumina_PE_PHB
.Impacted Workflows/Tasks
task_hostile
wf_read_QC_trim_pe
TheiaCoV_Illumina_PE_PHB
wf_read_QC_trim_ont
TheiaCoV_ONT_PHB
:brain: Context and Rationale
The current dehosting tool
ncbi-scrub
only works with illumina paired end reads, whereashostile
works with both illumina and oxford nanopore (ONT) reads. Therefore, we are implementinghostile
for dehosting of reads in theTheiaCoV_ONT_PHB
workflow.For
TheiaCoV_Illumina_PE_PHB
, we are giving users the option to use hostile if so preferred.:clipboard: Workflow/Task Steps
The
hostile
task takes as input the variableseq_method
to determine if working with or ONT reads. By default, these are set in theTheiaCoV_Illumina_PE_PHB
andTheiaCoV_ONT_PHB
workflows asILLUMINA
andOXFORD_NANOPORE
, respectively.Inputs
TheiaCoV_ONT_PHB
: Inputs remain the sameTheiaCoV_Illumina_PE_PHB
: Added an optional inputdehosting_tool
which takes in the optionsncbi_scrub
(default) orhostile
Outputs
Remain the same
Impacted Outputs
:test_tube: Testing
Locally
Works as expected locally for the
TheiaCoV_ONT_PHB
andTheiaCoV_Illumina_PE_PHB
workflowsTerra
Works as expected for
TheiaCoV_ONT_PHB
: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/f84b2815-6ef5-4ba2-9da6-ba27e49b0a9f SARS-CoV-2 andTheiaCoV_Illumina_PE_PHB
: Withdehosting_tool
set tohostile
: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/d731282a-07c6-4aca-8015-f15c5c7dd2c8 Influenza Withdehosting_tool
blank or the defaultncbi_scrub
: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/8c8e1e82-cf14-4ad2-a872-011d03248bc2 influenzaScenarios for Reviewer to Test
Test for pathogens other than SARS-CoV-2 and Influenza, and with samples rich in human reads.
:microscope: Quality checks
Pull Request (PR) checklist: