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add workflow: fetch_sra_bams_for_genbank_accession #475

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add workflow: fetch_sra_bams_for_genbank_accession #475

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@tomkinsc tomkinsc commented Jul 6, 2023

WIP

tomkinsc added 30 commits May 19, 2023 18:42
@tomkinsc
WIP commit of fetch_sra_runs_for_genbank_accession task and associate…
d6eeae2 
…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
pluralize output of fetch_sra_bams_for_genbank_accession workflow
720a47e
@tomkinsc
update ncbi-tools docker image 2.10.8 -> 2.11
74d0b79
@tomkinsc
pin ncbi-tools docker image to 2.11.0
076fbc1
@tomkinsc
update retrieval of SRA accessions given a GenBank accession
42d4355
@tomkinsc
bump ncbi-tools 2.11.0 -> 2.11.1
f1cb9dc
@tomkinsc
add workflow to fetch sequences from GenBank: fetch_fasta_for_genbank…
2e4099c 
…_accessions
@tomkinsc
update NCBI esearch parameter name ("-q" -> "-query") to reflect API …
b1bf8ef 
…change
@tomkinsc
pin broadinstitute/qiime2=latest
c26c920
@tomkinsc
pin docker image to latest in other tasks of tasts_16S_amplicon.wdl
b9d683f
@tomkinsc
bump womtool and cromwell 61->85
cb69a63
@tomkinsc
do not quit commands in tasks_16S_amplicon on pipefail
cc9524b 
This is an attempt at troubleshooting the "No such image" (docker) error occurring on GitHub Actions (see: chanzuckerberg/miniwdl#232 (comment) )
@tomkinsc
condense GitHub actions script flags
d277bdd
@tomkinsc
bump setup-buildx-action GitHub action version v1->v2
6015636
@tomkinsc
pin quay.io/broadinstitute/qiime2 to specific build hash
50e402c 
pin quay.io/broadinstitute/qiime2 to specific build hash; extend module checking scripts to allow for image pinning by hash
@tomkinsc
chmod 644 two qiime-related WDLs
3f42c91
@tomkinsc
increase default mem for nextstrain_build_subsample task 50->96GB
4c8bd10
@tomkinsc
WIP config to reduce verbosity of cromwell logging
4164239
@tomkinsc
list on dockstore: fetch_sra_bams_for_genbank_accession, fetch_fasta_…
e274a4f 
…for_genbank_accessions
@tomkinsc
cleanup cromwell test dir on failure or exit (unless KEEP_OUTPUT=true)
64a7d73
@tomkinsc
bugfix
a986189
@tomkinsc
only disable miniwdl post-execution output chown on macOS
ea4f193
@tomkinsc
add docker action for tests-cromwell; cruft removal;
f3b9eb2
@tomkinsc
delay cd to test_dir until after jar copy
8eed3b5
@tomkinsc
roll back version of ncbi-tools pin
1bb6e03
@tomkinsc
Merge branch 'master' into ct-fetch-sra-bams-for-genbank-accession
a624343
@tomkinsc
(debugging) roll back cromwell test config
9a05bff
@tomkinsc
roll back cromwell 85 -> 61
8e1d45e
@tomkinsc
DRY: use Fetch_SRA_to_BAM to fetch (and reheader) SRA bams
e42bf47
@tomkinsc
Merge branch 'master' into ct-fetch-sra-bams-for-genbank-accession
8ba6bbc
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@tomkinsc