Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

add workflow: fetch_sra_bams_for_genbank_accession #475

Draft
wants to merge 30 commits into
base: master
Choose a base branch
from
Draft

add workflow: fetch_sra_bams_for_genbank_accession #475

wants to merge 30 commits into from

Commits on May 19, 2023

  1. WIP commit of fetch_sra_runs_for_genbank_accession task and associate… 

    …d workflow

WIP commit of fetch_sra_runs_for_genbank_accession task and associated workflow to retrieve reads from the NCBI Short Read Archive in unaligned BAM format, one file SRA run, associated with a given GenBank sequence accession. Accepts one GenBank accession, yields one or more bam files, one per SRA run associated with the accession. maps GenBank to biosample -> SRA SRS -> SRR
    @tomkinsc
    tomkinsc committed May 19, 2023
    Configuration menu
    Copy the full SHA
    d6eeae2 View commit details
    Browse the repository at this point in the history

Commits on Jun 1, 2023

  1. pluralize output of fetch_sra_bams_for_genbank_accession workflow

    @tomkinsc
    tomkinsc committed Jun 1, 2023
    Configuration menu
    Copy the full SHA
    720a47e View commit details
    Browse the repository at this point in the history

Commits on Jul 6, 2023

  1. update ncbi-tools docker image 2.10.8 -> 2.11

    @tomkinsc
    tomkinsc committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    74d0b79 View commit details
    Browse the repository at this point in the history

Commits on Jul 14, 2023

  1. pin ncbi-tools docker image to 2.11.0

    @tomkinsc
    tomkinsc committed Jul 14, 2023
    Configuration menu
    Copy the full SHA
    076fbc1 View commit details
    Browse the repository at this point in the history

Commits on Jul 17, 2023

  1. update retrieval of SRA accessions given a GenBank accession

    @tomkinsc
    tomkinsc committed Jul 17, 2023
    Configuration menu
    Copy the full SHA
    42d4355 View commit details
    Browse the repository at this point in the history

Commits on Jul 18, 2023

  1. bump ncbi-tools 2.11.0 -> 2.11.1

    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    f1cb9dc View commit details
    Browse the repository at this point in the history

  2. add workflow to fetch sequences from GenBank: fetch_fasta_for_genbank… 

    …_accessions
    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    2e4099c View commit details
    Browse the repository at this point in the history

  3. update NCBI esearch parameter name ("-q" -> "-query") to reflect API … 

    …change
    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    b1bf8ef View commit details
    Browse the repository at this point in the history

  4. pin broadinstitute/qiime2=latest

    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    c26c920 View commit details
    Browse the repository at this point in the history

  5. pin docker image to latest in other tasks of tasts_16S_amplicon.wdl

    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    b9d683f View commit details
    Browse the repository at this point in the history

  6. bump womtool and cromwell 61->85

    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    cb69a63 View commit details
    Browse the repository at this point in the history

  7. do not quit commands in tasks_16S_amplicon on pipefail 

    This is an attempt at troubleshooting the "No such image" (docker) error occurring on GitHub Actions (see: chanzuckerberg/miniwdl#232 (comment) )
    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    cc9524b View commit details
    Browse the repository at this point in the history

  8. condense GitHub actions script flags

    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    d277bdd View commit details
    Browse the repository at this point in the history

  9. bump setup-buildx-action GitHub action version v1->v2

    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    6015636 View commit details
    Browse the repository at this point in the history

  10. pin quay.io/broadinstitute/qiime2 to specific build hash 

    pin quay.io/broadinstitute/qiime2 to specific build hash; extend module checking scripts to allow for image pinning by hash
    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    50e402c View commit details
    Browse the repository at this point in the history

  11. chmod 644 two qiime-related WDLs

    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    3f42c91 View commit details
    Browse the repository at this point in the history

  12. increase default mem for nextstrain_build_subsample task 50->96GB

    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    4c8bd10 View commit details
    Browse the repository at this point in the history

  13. WIP config to reduce verbosity of cromwell logging

    @tomkinsc
    tomkinsc committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    4164239 View commit details
    Browse the repository at this point in the history

Commits on Jul 19, 2023

  1. list on dockstore: fetch_sra_bams_for_genbank_accession, fetch_fasta_… 

    …for_genbank_accessions
    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    e274a4f View commit details
    Browse the repository at this point in the history

  2. cleanup cromwell test dir on failure or exit (unless KEEP_OUTPUT=true)

    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    64a7d73 View commit details
    Browse the repository at this point in the history

  3. bugfix

    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    a986189 View commit details
    Browse the repository at this point in the history

  4. only disable miniwdl post-execution output chown on macOS

    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    ea4f193 View commit details
    Browse the repository at this point in the history

  5. add docker action for tests-cromwell; cruft removal;

    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    f3b9eb2 View commit details
    Browse the repository at this point in the history

  6. delay cd to test_dir until after jar copy

    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    8eed3b5 View commit details
    Browse the repository at this point in the history

  7. roll back version of ncbi-tools pin

    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    1bb6e03 View commit details
    Browse the repository at this point in the history

  8. Merge branch 'master' into ct-fetch-sra-bams-for-genbank-accession

    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    a624343 View commit details
    Browse the repository at this point in the history

  9. (debugging) roll back cromwell test config

    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    9a05bff View commit details
    Browse the repository at this point in the history

  10. roll back cromwell 85 -> 61

    @tomkinsc
    tomkinsc committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    8e1d45e View commit details
    Browse the repository at this point in the history

Commits on Jul 21, 2023

  1. DRY: use Fetch_SRA_to_BAM to fetch (and reheader) SRA bams

    @tomkinsc
    tomkinsc committed Jul 21, 2023
    Configuration menu
    Copy the full SHA
    e42bf47 View commit details
    Browse the repository at this point in the history

Commits on Jul 26, 2023

  1. Merge branch 'master' into ct-fetch-sra-bams-for-genbank-accession

    @tomkinsc
    tomkinsc authored Jul 26, 2023
    Configuration menu
    Copy the full SHA
    8ba6bbc View commit details
    Browse the repository at this point in the history