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34 Open 12 Closed
34 Open 12 Closed
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Issues list

Adjust channels and operators to allow input sequences to begin filtering without bottleneck rework
#48 opened Nov 20, 2024 by jackscanlan
Make filtering processes output channel of rejected sequences enhancement New feature or request
#47 opened Nov 20, 2024 by jackscanlan
Download known COI pseudogenes as test data for filters validation
#45 opened Nov 11, 2024 by jackscanlan
Add nf-schema validation of parameters enhancement New feature or request
#44 opened Nov 7, 2024 by jackscanlan Validation
MATCH_BOLD fails to cache on -resume bug Something isn't working low priority
#43 opened Nov 6, 2024 by jackscanlan
Add dynamic resources to all processes that handle the combined sequences (eg. REMOVE_CONTAM) high priority rework
#39 opened Nov 2, 2024 by jackscanlan Minimum viable internal pipeline
Change PRUNE_GROUPS to remove identical sequences, retaining all sequence variation (not including length) by default rework
#37 opened Nov 1, 2024 by jackscanlan
Does IDTAXA require 'balanced' sampling across species? validation
#36 opened Nov 1, 2024 by jackscanlan
Check if PHMM-based alignment necessarily outputs an MSA validation
#35 opened Oct 31, 2024 by jackscanlan
4
Output database .fasta as unaligned by default; add parameter to align as a final step enhancement New feature or request
#34 opened Oct 31, 2024 by jackscanlan
1
Replace NCBI API querying in PARSE_TARGETS with taxdump .rds info from GET_NCBI_TAXONOMY rework
#31 opened Oct 29, 2024 by jackscanlan
Add dynamic retry with backoff to PARSE_TARGETS in case of HTTPS 500 error in NCBI servers rework
#30 opened Oct 29, 2024 by jackscanlan
Allow pipeline to gracefully allow no matches for GenBank/BOLD etc. and simply format internal sequences rework
#29 opened Oct 29, 2024 by jackscanlan
Allow user Genbank queries instead of known marker enhancement New feature or request
#28 opened Oct 29, 2024 by jackscanlan
.fasta output header options enhancement New feature or request
#27 opened Oct 28, 2024 by jackscanlan
Additional filtering based on intraspecific sequence outliers (inverse of REMOVE_CONTAM) enhancement New feature or request high priority
#26 opened Oct 27, 2024 by jackscanlan Minimum viable internal pipeline
1
Add more detailed database summaries enhancement New feature or request
#25 opened Oct 16, 2024 by jackscanlan
Add option to use lineage string and/or taxid for grouping sequences in PRUNE_GROUPS enhancement New feature or request
#24 opened Oct 16, 2024 by jackscanlan
Check SUMMARISE_TAXA is working correctly validation
#23 opened Oct 16, 2024 by jackscanlan
Fetch GenBank flat file and parse, rather than .fasta format + taxid rework
#22 opened Oct 16, 2024 by jackscanlan
Replace PHMM filtering code rework
#20 opened Oct 16, 2024 by jackscanlan
2
Add ability to download BOLD database with BOLD user account details enhancement New feature or request
#18 opened Oct 16, 2024 by jackscanlan
Add explicit version tracking of software and databases enhancement New feature or request
#17 opened Oct 16, 2024 by jackscanlan
Add ability to merge two or more finished databases, removing redundancy enhancement New feature or request
#16 opened Oct 16, 2024 by jackscanlan
Add ability to build PHMM from an input .fasta enhancement New feature or request
#15 opened Oct 16, 2024 by jackscanlan
ProTip! What’s not been updated in a month: updated:<2024-10-25.