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22 Open 33 Closed
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Issues list

percolate biosample attributes to sample table in Terra
#532 opened Apr 5, 2024 by dpark01
@tomkinsc
update / make new Terra-friendly genbank prep workflow
#531 opened Apr 2, 2024 by dpark01
1
update nextclade 2 -> 3
#530 opened Apr 2, 2024 by dpark01
workflow-ify lab data model maintenance scripts enhancement New feature or request
#496 opened Oct 26, 2023 by dpark01
@tomkinsc
add workflow for megablast reads to LCA tab file
#491 opened Sep 28, 2023 by golu099
Fetch_SRA_to_BAM retrieves incorrect run_date
#479 opened Aug 10, 2023 by dpark01
Expose kraken2 --minimum-hit-groups param
#472 opened May 8, 2023 by tomkinsc
Add task to convert Illumina-formatted sample sheet to tab-delimited version with extra columns
#471 opened May 5, 2023 by tomkinsc
Detect when i5 indices need to be rev-comp'ed
#469 opened Apr 20, 2023 by tomkinsc
Specify (short) input names in call to MultiQC
#466 opened Apr 19, 2023 by tomkinsc
2
rename amplicon16S_analysis to classify_qiime2_multi
#463 opened Apr 13, 2023 by dpark01
@golu099
task illumina_demux does not tolerate spaces in input filenames
#460 opened Mar 29, 2023 by dpark01
WDL task samplesheet_rename_ids does not accept Illumina-style csv sample sheets
#305 opened Jun 14, 2021 by tomkinsc
tsv_join wdl task fails on gzipped tsv input
#202 opened Jan 27, 2021 by dpark01
docker error on augur_from_assemblies call-draft_augur_tree: "This node is not a swarm manager..."
#177 opened Dec 2, 2020 by mark-fathom
7
output reads per million
#166 opened Oct 19, 2020 by tomkinsc
purge supplementary alignments prior to indel realignment in refbased assembly
#165 opened Oct 15, 2020 by tomkinsc
ensure preservation of RX tag; UMI-aware ref-based assembly
#164 opened Oct 15, 2020 by tomkinsc
2
BEAST WDL emit checkpoint and/or logs/trees in case of premature termination
#130 opened Jun 24, 2020 by dpark01
1
convert more coverage stats to samtools
#119 opened Jun 17, 2020 by dpark01
new Genbank download WDL
#109 opened Jun 10, 2020 by dpark01
@cmloreth
remux_plus
#49 opened Apr 24, 2020 by dpark01
1
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