BCCDC-PHL fluviewer-nf issues

BCCDC-PHL / fluviewer-nf

Nextflow pipeline for influenza A whole genome sequence analysis

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Add `genoflu_version` field to the GenoFLU tsv output

#47 dfornika opened 3 weeks ago
0
Remove unnecessary `genotype_key.xlsx` file

#46 dfornika closed 4 weeks ago
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Remove `defaults` from all conda `environment.yml` files

#45 dfornika closed 4 weeks ago
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Remove genotype key and defaults channels

#44 jpalmer37 closed 4 weeks ago
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Bump genoflu version

#43 jpalmer37 closed 4 weeks ago
0
Update snp calling module

#42 jpalmer37 opened 2 months ago
0
Update AA mutation calling module

#41 jpalmer37 opened 2 months ago
1
Version conflict between Matplotlib et numpy

#40 EricFournier3 closed 2 months ago
1
Add support for apptainer containers

#39 jpalmer37 opened 3 months ago
0
Remove automatic Nextclade dataset updates and improve provenance tracking

#38 jpalmer37 opened 4 months ago
1
Revert automated Nextclade dataset retrieval in favour of fixed datasets and regimented updates

#37 jpalmer37 opened 4 months ago
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Update README

#36 dfornika closed 4 months ago
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Add support for singularity/apptainer containers

#35 dfornika opened 4 months ago
1
Fix blastx version in provenance

#34 dfornika closed 4 months ago
0
Update README prior to tagging next release

#33 dfornika closed 4 months ago
0
Formatting of `tool_version` value for `blastx` tool in `snp_calling` process

#32 dfornika closed 4 months ago
0
Update Nextclade version and default datasets

#31 jpalmer37 closed 4 months ago
2
Update Nextclade version and associated default datasets

#30 jpalmer37 closed 4 months ago
0
Bump FluViewer version to v0.1.11-6

#29 dfornika closed 4 months ago
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Bump FluViewer version (again)

#28 dfornika closed 4 months ago
0
Bump fluviewer version

#27 dfornika closed 4 months ago
0
Bump FluViewer version

#26 dfornika closed 4 months ago
0
Fix clade calling

#25 dfornika closed 4 months ago
0
fix fluviewer log & error copying approach

#24 jpalmer37 closed 4 months ago
1
Add separate read normalization step

#23 dfornika closed 4 months ago
0
Bump FluViewer version

#22 dfornika closed 4 months ago
0
Bump FluViewer version

#21 dfornika closed 4 months ago
0
Pin setuptools to avoid conflict with spades

#20 dfornika closed 4 months ago
0
Incompatibility between `spades=3.15.3` and `setuptools=70.*` in FluViewer environment

#19 dfornika closed 4 months ago
0
Collect QC stats from FluViewer in MultiQC report

#18 dfornika opened 4 months ago
0
`clade_calling` process is failing

#17 dfornika closed 4 months ago
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Add bbnorm process upstream of fluviewer

#16 dfornika closed 4 months ago
0
Add support for samplesheet input

#15 dfornika closed 4 months ago
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Add support for `--samplesheet_input`

#14 dfornika closed 4 months ago
0
Fix output file handling in fluviewer process

#13 jpalmer37 closed 4 months ago
2
add db and fastq_input parameter checks

#12 jpalmer37 closed 4 months ago
0
changed outdir schema for all processes

#11 jpalmer37 closed 4 months ago
0
New fluviewer conda environment complaining about missing pip

#10 jpalmer37 closed 4 months ago
1
Make test workflow more stringent

#9 dfornika opened 5 months ago
0
Adopt BCCDC-PHL/FluViewer

#8 dfornika closed 4 months ago
2
Consider adopting BCCDC-PHL/FluViewer

#7 dfornika closed 4 months ago
0
Remove `--versioned_outdir` param

#6 dfornika closed 5 months ago
0
Work on testing pipeline

#5 dfornika closed 5 months ago
4
Move responsibility for higher-level output directory structure outside pipeline

#4 dfornika closed 4 months ago
0
Behavior when `--db` param isn't included

#3 dfornika closed 4 months ago
0
Add testing pipeline

#2 dfornika closed 5 months ago
1
Add a GitHub Actions-based testing workflow

#1 dfornika closed 5 months ago
0