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bokulich-lab
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nf-ducken
Workflow to process amplicon meta-analysis data, from NCBI accession IDs to taxonomic diversity metrics.
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Split process execution into separate workflows by input type
#74
lina-kim
closed
11 months ago
0
Clean up documentation for initial release
#73
lina-kim
opened
12 months ago
0
Incorporated Cutadapt for primer removal and binning
#72
lina-kim
closed
12 months ago
1
Clean up references using Nextflow input repeaters
#71
lina-kim
opened
12 months ago
0
Incorporate anywhere/adapter-based Cutadapt primer removal
#70
lina-kim
opened
12 months ago
1
Wrap Nextflow workflow into QIIME 2 plugin
#69
lina-kim
opened
12 months ago
0
Fixes skipped processes for nonlocal refs
#68
lina-kim
closed
1 year ago
0
Fix entrypoints for missing references
#67
lina-kim
closed
1 year ago
0
Double-check process launches (esp. intermediate) dependent on empty-param flags
#66
lina-kim
closed
10 months ago
1
Calculate phylogenetic core metrics
#65
lina-kim
opened
1 year ago
0
Filter tables after taxonomy classification to remove non-target sequences / contaminants / macrofungi
#64
lina-kim
opened
1 year ago
0
Add option for named outputDir
#63
lina-kim
closed
10 months ago
1
Incorporate primer removal with cutadapt
#62
lina-kim
closed
12 months ago
1
Expose all user-input FastQC parameters to user
#61
lina-kim
opened
1 year ago
0
Expose mutually exclusive parameters in Cutadapt to user
#60
lina-kim
opened
1 year ago
0
Automate identification of primers within samples
#59
lina-kim
opened
1 year ago
0
Automatically fix unnecessary features in pipeline DAG
#58
lina-kim
closed
11 months ago
1
Add DAG to README
#57
lina-kim
closed
1 year ago
0
Incorporate FastQC into workflow for quality control
#56
lina-kim
closed
1 year ago
0
Optimise FASTQ splitting; includes recommendations and/or automation
#55
lina-kim
opened
1 year ago
0
Update QIIME 2 container
#54
lina-kim
closed
1 year ago
0
Add phylogenetic tree construction
#53
lina-kim
opened
1 year ago
0
Update README and/or documentation to include DAG
#52
lina-kim
closed
1 year ago
1
Incorporate primer-based binning prior to primer removal
#51
lina-kim
closed
12 months ago
2
Incorporate FastQC into workflow for quality control
#50
lina-kim
closed
1 year ago
2
Incorporate process statistics with MultiQC
#49
lina-kim
closed
11 months ago
1
Automate rerun of paired-end reads as single-end based on QC
#48
lina-kim
opened
1 year ago
0
Automate recognition of input read types: single-end or paired-end
#47
lina-kim
opened
1 year ago
0
Automate filename format recognition
#46
lina-kim
opened
1 year ago
0
ENH: Redirect tmpdirs to local
#45
lina-kim
closed
1 year ago
0
FIX: Combine artifacts to generate a single taxonomy and feature table output
#44
lina-kim
closed
1 year ago
0
DOC: Update README for new requirements
#43
lina-kim
closed
1 year ago
0
FIX: allow more permissive characters in make_manifest.py
#42
lina-kim
closed
1 year ago
0
Optimize VSEARCH parameters
#41
lina-kim
opened
2 years ago
0
Combine output feature tables into single output
#40
lina-kim
closed
1 year ago
1
Update default containers to use QIIME 2022.11
#39
lina-kim
closed
1 year ago
0
Incorporate other VSEARCH application methods: open reference and de novo clustering, de novo chimera filtering, ref-based chimera filtering
#38
lina-kim
opened
2 years ago
0
Integrate CI
#37
lina-kim
opened
2 years ago
0
Add test suite for workflow
#36
lina-kim
opened
2 years ago
0
Log split_manifest outputs to contribute to a final meta-log at end of workflow
#35
lina-kim
opened
2 years ago
1
Completely ignore references to samples starting with special characters (#)
#34
lina-kim
closed
2 years ago
2
Optimize artifact splitting for feature classification
#33
lina-kim
opened
2 years ago
0
Optimize artifact splitting for VSEARCH
#32
lina-kim
opened
2 years ago
0
Add workflow output detailing original command run
#31
lina-kim
closed
1 year ago
1
Expose all user-input parameters in q2-fondue to user
#30
lina-kim
opened
2 years ago
0
Allow artifact splitting prior to running DADA2
#29
lina-kim
closed
2 years ago
0
Allow split FASTQs starting with special characters (#) to be imported by IMPORT_FASTQ
#28
lina-kim
opened
2 years ago
0
Expose all user-input parameters in q2-feature-classifier to user
#27
lina-kim
closed
2 years ago
1
Expose all user-input parameters in VSEARCH to user
#26
lina-kim
closed
2 years ago
0
Optimize memory/CPU usage per process
#25
lina-kim
opened
2 years ago
0
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