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[TheiaCoV] iVar Consensus Pipefail fix #629
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Added set -euo pipefail to variants task.
Switch o and u for consistency
Added optional inputs for compute variables for stats and coverage for primer trimming
Corrected disk size naming variable for stats n coverage prim trim
Michal-Babins
changed the title
Mb ivar pipe fail dev
Theiacov Ivar Consensus Pipefail fix
Sep 20, 2024
Michal-Babins
changed the title
Theiacov Ivar Consensus Pipefail fix
[TheiaCov] Ivar Consensus Pipefail fix
Sep 20, 2024
Michal-Babins
changed the title
[TheiaCov] Ivar Consensus Pipefail fix
[TheiaCoV] Ivar Consensus Pipefail fix
Sep 20, 2024
Michal-Babins
changed the title
[TheiaCoV] Ivar Consensus Pipefail fix
[TheiaCoV] iVar Consensus Pipefail fix
Sep 20, 2024
Update md5 sum for variant call and consensus for ivar consensus tests.
Update md5 check sum for variant call and consensus
Remove buffer space
Updated docs for ivar consensus optional inputs exposing compute params.
sage-wright
reviewed
Sep 23, 2024
sage-wright
approved these changes
Sep 26, 2024
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This PR closes #598
🗑️ This dev branch should be deleted after merging to main.
🧠 Summary
The Ivar Consensus workflow was facing a silent error due to a pipefail on input files that were very large.
The changes in this PR do the following:
set -euo pipefail
to both the ivar consensus task and the ivar variant calling task.cpu
,memory
,disk_size
, anddocker
parameters for the following tasks in the ivar consensus wf:3.Improve error handling so that tasks will now fail correctly instead of producing silent errors.
⚡ Impacted Workflows/Tasks
This PR may lead to different results in pre-existing outputs: No
This PR uses an element that could cause duplicate runs to have different results: No
🛠️ Changes
⚙️ Algorithm
set -euo pipefail
has been added to the task_ivar_consensus.wdl and to task_ivar_variant_call.wdl➡️ Inputs
The following optional inputs have been added to the ivar consensus workflow:
⬅️ Outputs
🧪 Testing
This PR was tested on the input data that originally brought up this bug by Marc Perry from UCSC. The following set of rsv fastq inputs: RSV00100_A & RSV00122_A, these inputs can be exported from the ucsc-rsv data table found here.
This data was first tested with the workflow defaults, which lead to the correct failures being flagged on terra.
Then the data was tested with the following parameters adjusted for the ivar consensus task on the TheiaCov Illumina PE wf:
ivar_consensus_memory: 16
ivar_variant_memory: 16
To further confirm the updates did not cause any breaking changes, the workflow was tested with defaults against WNV and MPXV validation data from the theiagen validation illumina pe data set.
Suggested Scenarios for Reviewer to Test
Please test with simple inputs with defualt and one with large files >=1.5GB per fastq with the following adjustments:
ivar_consensus_memory: 16
ivar_variant_memory: 16
I can provide the source to the large datasets.
🔬 Final Developer Checklist
🎯 Reviewer Checklist