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bump viral-ngs and nextclade docker images#648

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dpark01 merged 1 commit into
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bump-viral-ngs
Mar 4, 2026
Merged

bump viral-ngs and nextclade docker images#648
dpark01 merged 1 commit into
masterfrom
bump-viral-ngs

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@dpark01

@dpark01 dpark01 commented Mar 4, 2026

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  • viral-ngs 3.0.7 to 3.0.8
  • nextclade 3.18.1 to 3.19.0

Copilot AI review requested due to automatic review settings March 4, 2026 21:47
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dpark01 enabled auto-merge March 4, 2026 21:47

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Pull request overview

Updates pinned container image versions used by WDL workflows and module requirements, aligning pipeline execution environments with newer viral-ngs and nextclade releases.

Changes:

  • Bump broadinstitute/viral-ngs from 3.0.73.0.8 across WDL task docker references and module requirements.
  • Bump nextstrain/nextclade from 3.18.13.19.0 in module requirements and Nextstrain WDL tasks.

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated no comments.

Show a summary per file
File Description
requirements-modules.txt Updates pinned module image versions for viral-ngs and nextclade.
pipes/WDL/tasks/tasks_utils.wdl Updates viral-ngs docker tags used by utility tasks.
pipes/WDL/tasks/tasks_terra.wdl Updates viral-ngs docker tags used by Terra helper tasks.
pipes/WDL/tasks/tasks_taxon_filter.wdl Updates viral-ngs docker tags for taxon filtering tasks.
pipes/WDL/tasks/tasks_reports.wdl Updates viral-ngs docker tags for reporting/metrics tasks.
pipes/WDL/tasks/tasks_read_utils.wdl Updates viral-ngs docker tags for read utility tasks.
pipes/WDL/tasks/tasks_nextstrain.wdl Updates nextclade docker tags and viral-ngs tags used by Nextstrain-related tasks.
pipes/WDL/tasks/tasks_ncbi.wdl Updates viral-ngs docker tags used by NCBI-related tasks.
pipes/WDL/tasks/tasks_metagenomics.wdl Updates viral-ngs docker tags for metagenomics tasks.
pipes/WDL/tasks/tasks_megablast.wdl Updates viral-ngs docker tags used by megablast tasks.
pipes/WDL/tasks/tasks_intrahost.wdl Updates viral-ngs docker tags for intrahost tasks.
pipes/WDL/tasks/tasks_interhost.wdl Updates viral-ngs docker tags for interhost tasks.
pipes/WDL/tasks/tasks_demux.wdl Updates viral-ngs docker tags for demux tasks.
pipes/WDL/tasks/tasks_assembly.wdl Updates viral-ngs docker tags for assembly/alignment tasks.

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@dpark01
dpark01 merged commit 90f53de into master Mar 4, 2026
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@dpark01
dpark01 deleted the bump-viral-ngs branch March 4, 2026 22:21
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2 participants