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update viral-core 2.3.0 -> 2.3.1 #527

Merged
merged 21 commits into from
Mar 19, 2024
Merged

update viral-core 2.3.0 -> 2.3.1 #527

merged 21 commits into from
Mar 19, 2024

Commits on Mar 12, 2024

  1. update viral-core 2.3.0 -> 2.3.1 

    update viral-core 2.3.0 -> 2.3.1
    @tomkinsc
    tomkinsc committed Mar 12, 2024
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  2. bump nextstrain/base build-20230905T192825Z -> build-20240223T221827Z

    @tomkinsc
    tomkinsc committed Mar 12, 2024
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  3. change Seq.ungap("-") to Seq.replace("-","") 

    https://github.com/biopython/biopython/blob/master/DEPRECATED.rst#bioseqsequngap
    @tomkinsc
    tomkinsc committed Mar 12, 2024
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  4. specify docker.io for nextstrain images

    @tomkinsc
    tomkinsc committed Mar 12, 2024
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  5. roll back nextstrain/base image version

    @tomkinsc
    tomkinsc committed Mar 12, 2024
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  6. roll back nextstrain/base to build-20230905T192825Z

    @tomkinsc
    tomkinsc committed Mar 12, 2024
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  7. docker image prune between miniwdl calls to reduce disk space usage o… 

    …n github actions runner
    @tomkinsc
    tomkinsc committed Mar 12, 2024
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  8. try specifying nextstrain/base image by hash rather than tag

    @tomkinsc
    tomkinsc committed Mar 12, 2024
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Commits on Mar 13, 2024

  1. bump python version in GitHub Actions build to 3.10 for all build jobs

    @tomkinsc
    tomkinsc committed Mar 13, 2024
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Commits on Mar 15, 2024

  1. update nextstrain/base tag

    @tomkinsc
    tomkinsc committed Mar 15, 2024
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  2. pin nextstrain/base image to build-20240209T204939Z 

    pin nextstrain/base image to build-20240209T204939Z until a tagged release of the image includes a version of augur with the bugfix included in nextstrain/augur#1439
    @tomkinsc
    tomkinsc committed Mar 15, 2024
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  3. viral-classify pinned to version 2.2.4.1

    @tomkinsc
    tomkinsc committed Mar 15, 2024
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Commits on Mar 18, 2024

  1. restore bin of viral-classify image to 2.2.4.0

    @tomkinsc
    tomkinsc committed Mar 18, 2024
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  2. debugging: disable exit on pipefail in kraken2 task

    @tomkinsc
    tomkinsc committed Mar 18, 2024
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  3. update nextstrain/base image to build-20240318T173028Z 

    update nextstrain/base image to build-20240318T173028Z, which should include a version of augur incorporating the bugfix from nextstrain/augur#1439
    @tomkinsc
    tomkinsc committed Mar 18, 2024
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  4. update nextstrain/base tags

    @tomkinsc
    tomkinsc committed Mar 18, 2024
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  5. list files in cromwell execution directory

    @tomkinsc
    tomkinsc committed Mar 18, 2024
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  6. wildcard stderr and stdout output 

    wildcard stderr and stdout output, since cromwell output files can be called stderr.background and stdout.background rather than simply stderr and stdout
    @tomkinsc
    tomkinsc committed Mar 18, 2024
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  7. change cromwell docker cmd so we wait to remove docker images until d… 

    …ocker cid file indicates completion

wait to remove docker images until docker cid file indicates completion
see:
broadinstitute/cromwell#3370 (comment)
    @tomkinsc
    tomkinsc committed Mar 18, 2024
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  8. prune docker images between cromwell tests to save space

    @tomkinsc
    tomkinsc committed Mar 18, 2024
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  9. restore pipefail condition for kraken2 command block

    @tomkinsc
    tomkinsc committed Mar 18, 2024
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