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broadinstitute
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viral-pipelines
viral-ngs: complete pipelines
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enable merge_group builds in github actions CI
#503
dpark01
closed
9 months ago
0
fix mem high watermark reporting
#502
tomkinsc
closed
9 months ago
0
create generalized version of enterics visualization WDL
#501
schaluva
closed
9 months ago
0
WDL for creating Enterics Visualizations
#500
schaluva
closed
9 months ago
0
add masked_positions and masked_positions_file arguments to task polyphonia_detect_cross_contamination
#499
lakras
closed
9 months ago
0
expose numberOfNegativeControls in illumina_demux
#498
tomkinsc
closed
10 months ago
0
add check_terra_env task
#497
tomkinsc
closed
10 months ago
0
workflow-ify lab data model maintenance scripts
#496
dpark01
opened
10 months ago
0
Add task for terra backend env exploration
#495
tomkinsc
closed
10 months ago
2
mark downsample_bams task as volatile (nondeterministic)
#494
tomkinsc
closed
10 months ago
0
allow docker image pinning to be skipped with #skip-global-version-pin annotation
#493
tomkinsc
closed
11 months ago
0
pass through sbt template if optional defaults_yaml is not provided and author_list string is empty
#492
tomkinsc
closed
11 months ago
0
add workflow for megablast reads to LCA tab file
#491
golu099
opened
11 months ago
0
genbank workflow no longer accepts author.sbt file
#490
dpark01
closed
11 months ago
1
Fetch_SRA_to_BAM - tolerate no isolate defined
#489
dpark01
closed
1 year ago
0
dnanexus CI fix 4
#488
dpark01
closed
1 year ago
0
dnanexus build fixes pt 3
#487
dpark01
closed
1 year ago
0
dnanexus build fixes
#486
dpark01
closed
1 year ago
0
dnanexus CI build fixes
#485
dpark01
closed
1 year ago
0
sc2 nextstrain: reduce temp file sizes
#484
dpark01
closed
1 year ago
0
Subsampler and augur workflow
#483
dpark01
closed
11 months ago
0
bump pangolin
#482
dpark01
closed
1 year ago
0
bugfix output location of fasta in download_annotations; pass NCBI API key to tasks: download_fasta, download_annotations
#481
tomkinsc
opened
1 year ago
0
hotfix for bug in output path
#480
dpark01
closed
1 year ago
0
Fetch_SRA_to_BAM retrieves incorrect run_date
#479
dpark01
opened
1 year ago
0
extend beast task and workflow to glob and output *.ops, *.rates, and *.root files
#478
tomkinsc
closed
1 year ago
0
move transposed parameter_meta block outside command block scope to where it belongs
#477
tomkinsc
closed
1 year ago
0
Update LICENSE copyright year
#476
tomkinsc
closed
1 year ago
0
add workflow: fetch_sra_bams_for_genbank_accession
#475
tomkinsc
opened
1 year ago
0
GitHub actions update
#474
tomkinsc
closed
1 year ago
0
Update genbank.WDL so author_list input is optional
#473
tomkinsc
closed
1 year ago
0
Expose kraken2 --minimum-hit-groups param
#472
tomkinsc
opened
1 year ago
0
Add task to convert Illumina-formatted sample sheet to tab-delimited version with extra columns
#471
tomkinsc
opened
1 year ago
0
parameterize disk size for illumina_demux task
#470
tomkinsc
closed
1 year ago
0
Detect when i5 indices need to be rev-comp'ed
#469
tomkinsc
opened
1 year ago
0
max_records_in_ram param 2000000 -> 10000000 for Nova S2
#468
tomkinsc
closed
1 year ago
0
omit --dirs from the MultiQC invocation to only show sample names in report
#467
tomkinsc
closed
1 year ago
0
Specify (short) input names in call to MultiQC
#466
tomkinsc
opened
1 year ago
2
de novo assembly & scaffold mem default 31 -> 63 GB
#465
tomkinsc
closed
1 year ago
0
tweaks to demux_only and demux_metag
#464
dpark01
closed
1 year ago
0
rename amplicon16S_analysis to classify_qiime2_multi
#463
dpark01
opened
1 year ago
0
syntax bugfixes
#462
dpark01
closed
1 year ago
0
Enhancing documentation for viral-pipelines
#461
golu099
closed
1 year ago
3
task illumina_demux does not tolerate spaces in input filenames
#460
dpark01
opened
1 year ago
0
Integration of taxonomic classifier trainer wdl
#459
golu099
opened
1 year ago
3
pushing training classifier WDL
#458
golu099
closed
1 year ago
1
parameterize more assembly knobs
#457
dpark01
closed
1 year ago
0
Update pangolin, nextclade, and vadr docker images
#456
dpark01
closed
1 year ago
1
parameterize and update defaults for VM shapes in nextstrain tasks
#455
dpark01
closed
1 year ago
1
samtools ampliconstats needs bed in certain order
#454
dpark01
closed
1 year ago
0
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