bokulich-lab nf-ducken issues

bokulich-lab / nf-ducken

Workflow to process amplicon meta-analysis data, from NCBI accession IDs to taxonomic diversity metrics.

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Small changes plus final Jekyll fix

#123 lina-kim closed 3 months ago
0
Remove unnecessary sample_id values in input channels

#122 lina-kim opened 3 months ago
0
Give user option to split pre-denoised samples by name/accession instead of number

#121 lina-kim opened 4 months ago
0
Set up static GitHub Pages-based documentation

#120 lina-kim opened 4 months ago
0
Configure different parameter sets for ITS-based Cutadapt runs

#119 lina-kim opened 4 months ago
0
Add iterative Cutadapt runs for ITS

#118 lina-kim opened 4 months ago
0
Make feature classification step optional

#117 lina-kim opened 4 months ago
0
Set up workflow profiles for execution on local, slurm, parallel, etc.

#116 lina-kim opened 5 months ago
0
Run CHECK_FASTQ_TYPE() in parallel with trimming/denoising, not through

#115 lina-kim opened 5 months ago
0
Output more feature table-based visualizations

#114 lina-kim closed 5 months ago
0
Incorporate input metadata table into visualizations e.g. taxa barplot

#113 lina-kim opened 5 months ago
0
Offer more visualizations based on feature tables

#112 lina-kim closed 5 months ago
0
Fix manifest generator script

#111 lina-kim closed 5 months ago
0
nf-ducken tutorial: v1.0

#110 lina-kim closed 5 months ago
0
BUG: make_manifest.py mismatch in --r1/2_suffix vs --suffix

#109 lina-kim closed 5 months ago
0
Make OTU clustering optional

#108 lina-kim closed 5 months ago
1
Make taxonomy-based collapse optional

#107 lina-kim opened 6 months ago
0
Directory restructure

#106 lina-kim closed 6 months ago
2
FIX: Wait for all the outputs of Cutadapt before applying MultiQC

#105 ChristosMatzoros closed 6 months ago
3
Suggest users use local versions of reference files/databases instead of hardcoding wget links

#104 lina-kim opened 6 months ago
0
Make closed OTU clustering optional

#103 lina-kim closed 5 months ago
0
FIX: Adding sra-tools dependency to the fondue conda recipes

#102 ChristosMatzoros closed 6 months ago
3
Fix: MultiQC conda environment creation issue

#101 ChristosMatzoros closed 6 months ago
1
BUG: Error with the creation of MultiQC conda environment

#100 ChristosMatzoros closed 6 months ago
1
FIX: Resolve fondue Conda env

#99 lina-kim closed 6 months ago
4
Fix q2-fondue Conda environment

#98 lina-kim closed 5 months ago
3
Update Cutadapt to take multiple primers

#97 lina-kim closed 7 months ago
0
ENH: Added capability to start the pipeline with an already created input artifact

#96 ChristosMatzoros closed 6 months ago
2
ENH: Capability to start the pipeline with an already created input artifact

#95 ChristosMatzoros closed 6 months ago
0
ENH: Adding a parameter for optional validation through nextflow

#94 ChristosMatzoros closed 7 months ago
3
BUG: Removing the validateParams execution from the imported validation library

#93 ChristosMatzoros closed 7 months ago
0
ENH: Optional validation through the paramsValidator.nf

#92 ChristosMatzoros closed 7 months ago
0
BUG: Execution of the validation function inside the imported library for validation

#91 ChristosMatzoros closed 7 months ago
0
BUG: Remove conda environments directories after workflow completion

#90 ChristosMatzoros closed 7 months ago
3
Automatically remove local Conda environments generated by Nextflow run

#89 lina-kim closed 7 months ago
2
ENH: Export more ouputs of plugins to the outDir(/stats/) directory.

#88 ChristosMatzoros closed 8 months ago
1
Removing dependency of outdir and tracedir

#87 ChristosMatzoros closed 8 months ago
0
Allow detection of pre-trimmed samples

#86 lina-kim opened 9 months ago
0
Improve accuracy of taxonomic classification using full-length reference sequences

#85 lina-kim opened 9 months ago
0
Add automated rarefaction and/or user-input parameters

#84 lina-kim opened 9 months ago
1
Manage optimal sample-primer classification out of Cutadapt

#83 lina-kim closed 5 months ago
2
Validate input parameters

#82 ChristosMatzoros closed 9 months ago
3
Build environments specific to osx-arm64 machines

#81 lina-kim opened 9 months ago
0
Split process execution into separate workflows

#80 ChristosMatzoros closed 9 months ago
2
Incorporate Conda environment creation in workflow

#79 lina-kim closed 9 months ago
2
Incorporating MultiQC action

#78 ChristosMatzoros closed 9 months ago
1
Fix pipeline DAG

#77 lina-kim closed 10 months ago
0
Incorporate MultiQC statistics process

#76 ChristosMatzoros closed 10 months ago
0
Nicely integrate q2-fondue with automated Conda or Docker-based executions

#75 lina-kim opened 10 months ago
1
Split process execution into separate workflows by input type

#74 lina-kim closed 9 months ago
0