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31 Open 23 Closed
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Issues list

Allow propagation of denoising info through to merging output DSL2 Prioritize for DSL2 implementation good first issue Good for newcomers
#63 opened Feb 1, 2025 by cjfields
Add back custom tax ranks DSL2 Prioritize for DSL2 implementation good first issue Good for newcomers
#62 opened Feb 1, 2025 by cjfields
Add a stop step after merging + chimera detection DSL2 Prioritize for DSL2 implementation
#61 opened Jan 29, 2025 by cjfields
Screening sequences using Infernal or HMMER
#60 opened Jan 26, 2025 by cjfields
Implement variable amplicon (ITS) subworkflow
#59 opened Jan 26, 2025 by cjfields
Add priors support
#58 opened Jan 26, 2025 by cjfields
1
Add phangorn
#57 opened Jan 26, 2025 by cjfields
Add cutadapt as alternate trimming subworkflow
#56 opened Jan 26, 2025 by cjfields
3 tasks
Switch Illumina test data
#55 opened Jan 14, 2025 by cjfields
DECIPHER: Alignment larger than the maximum allowable size
#54 opened Jan 13, 2025 by Charmy0619
4
Implement binned error model from DADA2
#53 opened Jan 7, 2025 by cjfields
1
Refactor trimming and filtering DSL2 Prioritize for DSL2 implementation
#49 opened Oct 28, 2024 by cjfields
1
PacBio initial read counts and cutadapt-based trimming details missing from read tracking bug Something isn't working DSL2 Prioritize for DSL2 implementation high priority Needs fixin'!
#48 opened Aug 23, 2024 by cjfields
Update fluidigm-run.py to include sample sheet for PacBio DSL2 Prioritize for DSL2 implementation
#47 opened Jul 18, 2024 by NeginValizadegan
1
Add options for priors DSL2 Prioritize for DSL2 implementation
#46 opened Jun 15, 2024 by cjfields
3
Address pooling when doing chimera detection DSL2 Prioritize for DSL2 implementation
#45 opened Jun 15, 2024 by cjfields
Initial trimming steps DSL2 Prioritize for DSL2 implementation
#44 opened Mar 11, 2024 by cjfields
4 tasks
v2
@cjfields
Initial QC steps DSL2 Prioritize for DSL2 implementation
#43 opened Mar 11, 2024 by cjfields
3 of 5 tasks
v2
DSL1 is no longer supported high priority Needs fixin'!
#41 opened Nov 9, 2023 by cjfields
Documentation cleanup
#40 opened Jun 19, 2023 by cjfields
1
Set up Dockstore
#39 opened Dec 22, 2022 by cjfields
1 of 4 tasks
@cjfields @ziyaadparker
1
Shoreline data without primers appear to be in either orientation low priority needs documentation Not necessarily a fix, but should be documented for clarity
#36 opened Apr 19, 2022 by cjfields
5
Reorganizing output directories DSL2 Prioritize for DSL2 implementation
#35 opened Feb 28, 2022 by cjfields
1
Generation of large matrices and data frames takes forever
#34 opened Feb 14, 2022 by cjfields
2
Overall name changes DSL2 Prioritize for DSL2 implementation
#33 opened Jan 24, 2022 by cjfields
3
ProTip! Updated in the last three days: updated:>2025-01-30.