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Upgrade to nextclade v3 & update default dataset tags #375

Merged
merged 24 commits into from
Apr 4, 2024
Merged

Upgrade to nextclade v3 & update default dataset tags #375

merged 24 commits into from
Apr 4, 2024

Commits on Mar 5, 2024

  1. added new WDL task for nextclade v3. tested w miniwdl. not added to w… 

    …orkflows yet
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  2. added common miniwdl output directories to .gitignore

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    kapsakcj committed Mar 5, 2024
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Commits on Mar 6, 2024

  1. update sars-cov-2 nextclade defaults; removed unnecessary nextclade_d… 

    …ataset_reference inputs and outputs from organism_param subworkflow
    @kapsakcj
    kapsakcj committed Mar 6, 2024
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  2. updates to nextclade v3 task

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    kapsakcj committed Mar 6, 2024
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  3. update theiacov_fasta to use nextclade v3 task. tested successfully w… 

    …ith miniwdl and sc2 sample
    @kapsakcj
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  4. update nextclade defaults for non-sc2 organisms. Have not tested at a… 

    …ll, need to test in Terra
    @kapsakcj
    kapsakcj committed Mar 6, 2024
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  5. update to nextclade 3.3.1 and implement --verbosity flag for nextclad… 

    …e commands
    @kapsakcj
    kapsakcj committed Mar 6, 2024
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  6. updated WDL task for adding samples to nextclade ref tree. tested fin… 

    …e with miniwdl and a Flu HA FASTA
    @kapsakcj
    kapsakcj committed Mar 6, 2024
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  7. update Sample_to_ref_tree_PHB workflow: removed old inputs and made a… 

    …ssembly_fasta input singular
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    kapsakcj committed Mar 6, 2024
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Commits on Mar 7, 2024

  1. updated theiacov_fasta_batch, ilmn pe, ilmn se, and ont to use nextcl… 

    …ade v3. need to test on Terra still (have not tested with miniwdl)
    @kapsakcj
    kapsakcj committed Mar 7, 2024
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Commits on Mar 21, 2024

  1. update theiacov_clearlabs to use nextclade_v3. did not test with mini… 

    …wdl so will need to test in Terra
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    kapsakcj committed Mar 21, 2024
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Commits on Mar 22, 2024

  1. Merge remote-tracking branch 'origin/main' into cjk-nextclade-v3

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    kapsakcj committed Mar 22, 2024
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  2. fix import path for organism_paramteters subwf in theiacov_clearlabs … 

    …workflow
    @kapsakcj
    kapsakcj committed Mar 22, 2024
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  3. shellcheck lied to me. reverting last commit

    @kapsakcj
    kapsakcj committed Mar 22, 2024
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  4. update theiacov_fasta CI

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    kapsakcj committed Mar 22, 2024
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  5. update theiacov_clearlabs CI

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    kapsakcj committed Mar 22, 2024
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  6. update theiacov_ont CI

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    kapsakcj committed Mar 22, 2024
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  7. re-enable theiacov_illumina_pe and se CI workflows; update them for n… 

    …extclade_v3 and a slew of other updates from previous PRs that were missed since the CI was disabled
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    kapsakcj committed Mar 22, 2024
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Commits on Mar 28, 2024

  1. Merge remote-tracking branch 'origin/main' into cjk-nextclade-v3

    @kapsakcj
    kapsakcj committed Mar 28, 2024
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  2. update CI

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    kapsakcj committed Mar 28, 2024
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Commits on Apr 4, 2024

  1. nextclade_v3 task: removed unused pcr_primers_csv input; added back i… 

    …nput_ref optional input. tested successfully with miniwdl
    @kapsakcj
    kapsakcj committed Apr 4, 2024
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  2. nextclade_addToRefTree task and wf change: remove input-pcr-primers o… 

    …ption and add input-ref option
    @kapsakcj
    kapsakcj committed Apr 4, 2024
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  3. Merge remote-tracking branch 'origin/main' into cjk-nextclade-v3

    @kapsakcj
    kapsakcj committed Apr 4, 2024
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  4. corrected input file type for input-ref

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    kapsakcj committed Apr 4, 2024
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