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Issues list

Automate filename format recognition enhancement New feature or request nice to have Stretch goal if time
#46 opened Jan 30, 2023 by lina-kim Microbiota Vault 🪁
Optimize artifact splitting for DADA2 analysis-needed Less implementation, more analysis nice to have Stretch goal if time
#21 opened May 25, 2022 by lina-kim
Determine appropriate chimera-checking method for DADA2 and VSEARCH analysis-needed Less implementation, more analysis nice to have Stretch goal if time
#23 opened Jun 1, 2022 by lina-kim
2
Optimize memory/CPU usage per process analysis-needed Less implementation, more analysis nice to have Stretch goal if time
#25 opened Jun 8, 2022 by lina-kim
Allow split FASTQs starting with special characters (#) to be imported by IMPORT_FASTQ bug Something isn't working
#28 opened Jun 24, 2022 by lina-kim
Expose all user-input parameters in q2-fondue to user core-function Related to core functionality quick-fix Low-hanging fruit
#30 opened Jul 4, 2022 by lina-kim
Optimize artifact splitting for VSEARCH analysis-needed Less implementation, more analysis nice to have Stretch goal if time
#32 opened Jul 7, 2022 by lina-kim
Optimize artifact splitting for feature classification analysis-needed Less implementation, more analysis nice to have Stretch goal if time
#33 opened Jul 12, 2022 by lina-kim
Log split_manifest outputs to contribute to a final meta-log at end of workflow enhancement New feature or request quick-fix Low-hanging fruit
#35 opened Jul 26, 2022 by lina-kim
1
Add test suite for workflow testing Improvements or additions to testing
#36 opened Jul 29, 2022 by lina-kim Beta release 1.0b 🪄
@ChristosMatzoros
Integrate CI testing Improvements or additions to testing
#37 opened Aug 2, 2022 by lina-kim
Incorporate other VSEARCH application methods: open reference and de novo clustering, de novo chimera filtering, ref-based chimera filtering core-function Related to core functionality
#38 opened Aug 3, 2022 by lina-kim
Consider solutions to process heterogeneous read types i.e. datasets with SE + PE reads enhancement New feature or request nice to have Stretch goal if time
#10 opened Apr 6, 2022 by lina-kim
Optimize VSEARCH parameters analysis-needed Less implementation, more analysis nice to have Stretch goal if time
#41 opened Oct 19, 2022 by lina-kim
Automate recognition of input read types: single-end or paired-end enhancement New feature or request nice to have Stretch goal if time
#47 opened Jan 30, 2023 by lina-kim Microbiota Vault 🪁
Automate rerun of paired-end reads as single-end based on QC enhancement New feature or request nice to have Stretch goal if time
#48 opened Jan 30, 2023 by lina-kim Microbiota Vault 🪁
Add phylogenetic tree construction core-function Related to core functionality
#53 opened May 12, 2023 by lina-kim
Optimise FASTQ splitting; includes recommendations and/or automation analysis-needed Less implementation, more analysis enhancement New feature or request nice to have Stretch goal if time
#55 opened May 19, 2023 by lina-kim
Automate identification of primers within samples enhancement New feature or request nice to have Stretch goal if time
#59 opened Jun 2, 2023 by lina-kim
Expose mutually exclusive parameters in Cutadapt to user enhancement New feature or request quick-fix Low-hanging fruit
#60 opened Jun 7, 2023 by lina-kim
Expose all user-input FastQC parameters to user quick-fix Low-hanging fruit
#61 opened Jun 8, 2023 by lina-kim
Filter tables after taxonomy classification to remove non-target sequences / contaminants / macrofungi analysis-needed Less implementation, more analysis enhancement New feature or request
#64 opened Nov 1, 2023 by lina-kim
Calculate phylogenetic core metrics core-function Related to core functionality
#65 opened Nov 1, 2023 by lina-kim
Wrap Nextflow workflow into QIIME 2 plugin core-function Related to core functionality
#69 opened Nov 9, 2023 by lina-kim
@ChristosMatzoros
Remove unnecessary sample_id values in input channels enhancement New feature or request nice to have Stretch goal if time quick-fix Low-hanging fruit
#122 opened May 24, 2024 by lina-kim
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