Modules#10

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djfeistel wants to merge 391 commits into

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Commits on Jul 1, 2025

AMD-13092: modified C_TEST1_20.miraConvert_input.tar.gz input for local/modules/mira/convert/tests
rouzbahani
committed

Commits on Jul 8, 2025

AMD-11675: small input for Cyclone pipeline-level nf-test
rouzbahani
committed

Commits on Jul 10, 2025

AMD-11675: input sample sheet for pipeline-level nf-test
rouzbahani
committed

Commits on Jul 11, 2025

Commits on Jul 12, 2025

AMD-11675: added FULL2 datasets for Cyclone pipeline-level nf-test
rouzbahani
committed

Commits on Jul 14, 2025

AMD-11433: inputs for modules/local/fasta_junction_make_refs/tests
rouzbahani
committed

Commits on Jul 15, 2025

Commits on Jul 16, 2025

Commits on Jul 17, 2025

phylophoenix griphin data
astoicame
committed

Commits on Jul 18, 2025

Commits on Jul 21, 2025

phoenix data
astoicame
committed

Commits on Jul 23, 2025

Commits on Jul 29, 2025

Commits on Jul 30, 2025

phylophoenix test data
astoicame
committed

Commits on Jul 31, 2025

haplotypesheet has been cut down to just fewer rows for faster bayesian heuristics
arunbodd
committed

Commits on Aug 4, 2025

added seqtk inputs for various subworkflows
arunbodd
committed

Commits on Aug 7, 2025

Update test_phoenix_scaffolds_samplesheet.csv
astoicame
authored

Commits on Aug 8, 2025

Commits on Aug 9, 2025

Commits on Aug 13, 2025

test
Linen
committed
snpeff db for tb
Linen
committed

Commits on Aug 14, 2025

AMD-14514: inputs for local samtools,seqtk, haplotype assignment
daveJacobson-quh7
committed

Commits on Aug 15, 2025

Commits on Aug 21, 2025

Commits on Aug 25, 2025

mira convert test data
astoicame
committed

Commits on Aug 26, 2025

AMD-15708 inputs for modules/local/csv_fasta_converter/tests
rouzbahani
committed

Commits on Sep 10, 2025

update snpeff for tb
Linen
committed
update snpeff for tb
Linen
committed

Commits on Sep 17, 2025

Commits on Sep 19, 2025

Commits on Sep 25, 2025

Commits on Sep 26, 2025

adding test data for GAMBIT_QUERY
djfeistel
committed

Commits on Sep 30, 2025

additional neissflow data
daveJacobson-quh7
authored

Commits on Oct 17, 2025

Commits on Oct 21, 2025

Commits on Oct 23, 2025

Commits on Oct 29, 2025

update samplesheet paths for phoenix
Linen
committed

Commits on Oct 30, 2025

Add files via upload
yyr4
authored

Commits on Nov 5, 2025

Commits on Nov 6, 2025

adding bowtie index
ay97L
committed

Commits on Nov 20, 2025

adding test data for updated qc_report module
Slucking3
committed

Commits on Nov 24, 2025

update tb asset
Linen
committed
update tb asset
Linen
committed

Commits on Nov 25, 2025

small mlst files for neissflow
daveJacobson-quh7
authored

Commits on Nov 26, 2025

local raxml files
daveJacobson-quh7
authored

Commits on Dec 16, 2025

AMD-19650: nf-test data for penguin module for TTL uploaded
rouzbahani
committed

Commits on Dec 17, 2025

Commits on Dec 19, 2025

Commits on Jan 2, 2026

phylophoenix data
astoicame
committed

Commits on Jan 5, 2026

phoenix test data
astoicame
committed

Commits on Jan 12, 2026

Commits on Jan 15, 2026

Commits on Jan 20, 2026

Adding phylophoenix validate_directies tar.gz

lekalle
authored and
lekalle
committed
staging phylophoenix validate_directories samplesheet

lekalle
authored and
lekalle
committed
updated phylophoenix validate_directories staged file

lekalle
authored and
lekalle
committed
Updated PhyloPhoenix validate_directories samplesheet

lekalle
authored and
lekalle
committed

Commits on Jan 21, 2026

Updated snvphyl subworkflow test data

lekalle
authored and
lekalle
committed

Commits on Jan 22, 2026

Commits on Jan 23, 2026

Commits on Jan 26, 2026

bspb files
Linen
committed

Commits on Jan 29, 2026

bspb data
Linen
committed
bspb test bakta database
anochmohan
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bspb data
Linen
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bspb data
Linen
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Merge branch 'modules' of https://github.com/CDCgov/oamd-bio-test-data into modules
Linen
committed

Commits on Jan 30, 2026

bspb sra test files
anochmohan
committed

Commits on Feb 1, 2026

Merge remote-tracking branch 'refs/remotes/origin/modules' into modules
astoicame
committed

Commits on Feb 2, 2026

Commits on Feb 3, 2026

bspb data
Linen
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Merge branch 'modules' of https://github.com/CDCgov/oamd-bio-test-data into modules
Linen
committed
bspb data
Linen
committed

Commits on Feb 4, 2026

test busco db
Linen
committed

Commits on Feb 5, 2026

Phoenix Pushing new test file

lekalle
authored and
lekalle
committed
bspb data
astoicame
committed

Commits on Feb 6, 2026

mock kraken1 db for bspb
Linen
committed

Commits on Feb 18, 2026

Commits on Feb 23, 2026

Phoenix: Adding data for V2.2.0 modules

lekalle
authored and
lekalle
committed

Commits on Feb 26, 2026

initial viralrecon local test data
daveJacobson-quh7
authored

Commits on Mar 11, 2026

added snpeff_cache archive with revised structure
tstark-cdc
committed

Commits on Mar 18, 2026

updating data for single_sample qc for cyclone
djfeistel
committed

Commits on Mar 19, 2026

aggregate summary data for viralrecon
daveJacobson-quh7
authored
Phoenix: Updated samplesheets

lekalle
authored and
lekalle
committed

Commits on Mar 20, 2026

Rename snpeff_cache directory to mtb_NC_000962_3
smagala
committed

Commits on Mar 23, 2026

Commits on Mar 24, 2026

greater depth for req. for freyja subwf
daveJacobson-quh7
authored

Commits on Mar 25, 2026

Commits on Mar 26, 2026

aquascope aggregate outputs
daveJacobson-quh7
authored

Commits on Mar 31, 2026

Commits on Apr 6, 2026

Commits on Apr 9, 2026

Commits on Apr 10, 2026

Commits on Apr 13, 2026

Commits on Apr 14, 2026

Commits on Apr 20, 2026

fai for sarscov2
daveJacobson-quh7
authored

Commits on Apr 21, 2026

Phoenix: Updating test data

lekalle
authored and
lekalle
committed
Phoenix: Updating nf-test data

lekalle
authored and
lekalle
committed
Phoenix: Updating nf-test data

lekalle
authored and
lekalle
committed
Phoenix: Updating nf-test data

lekalle
authored and
lekalle
committed

Commits on Apr 24, 2026

Commits on Apr 30, 2026

adding test data for new mycosnp module
Slucking3
committed

Commits on May 7, 2026

Phoenix: add sample_files/test.tar.gz fixture for createandupdatereadme test

lekalle
authored and
lekalle
committed
aquascope freyja filtering
Nicholas-Lowe-CDC
committed
Phoenix V2.2.0 test data

lekalle
authored and
lekalle
committed

Commits on May 11, 2026

Phoenix: Updating test data

lekalle
authored and
lekalle
committed

Commits on May 20, 2026

Commits on May 27, 2026

Commits on May 29, 2026

Phoenix Updating test data

lekalle
authored and
lekalle
committed

Commits on Jun 3, 2026

test data for new qc metrics
Nicholas-Lowe-CDC
committed

Commits on Jun 9, 2026

Phoenix: Updating updater files

lekalle
authored and
lekalle
committed

Commits on Jul 1, 2026

Commits on Jul 6, 2026

chromsizes for talos qc report
daveJacobson-quh7
authored

Commits on Jul 14, 2026

Add legion allele_phylogeny test data (all-public GCA cgMLST barometer profile)
zsb3
committed

Commits on Jul 17, 2026

Commits on Jul 18, 2026

Phoenix: adding nf-test files

lekalle
authored and
lekalle
committed

Commits on Jul 22, 2026