BCCDC-PHL / routine-assembly

Pipeline for performing routine genome assembly

Repository from Github https://github.comBCCDC-PHL/routine-assembly

BCCDC-PHL/routine-assembly Issues

Trial using sequera wave for container building
Closed 9 months ago
prokka and bakta fail with long sample IDs
Closed 10 months ago
Remove `--versioned_outdir` parameter
Closed 10 months ago
Prokka outputs not published
Closed 10 months ago
Add a pipeline diagram to the README
Closed a year ago
Indentation/formatting
Closed a year ago
Bump tool versions
Updated a year ago
Add GitHub Actions-based testing workflow
Closed a year ago
Build containers and push to registry
Closed a year ago
Pipeline fails when empty assembly produced
Closed 2 years ago2
Long and short reads aren't matched up correctly for hybrid assembly
Closed 2 years ago
Support mixed assembly modes with `--samplesheet_input`
Closed 2 years ago1
Intermittent failure of bakta
Closed 2 years ago
Consider dropping shovill and dragonflye in favor of using unicycler for all modes
Closed 2 years ago
Add long-read-only assembly mode
Closed 2 years ago
`--samplesheet_input` incompatible with `--hybrid` mode
Closed 2 years ago
Combine long-read QC pre/post filtering reports into single file
Closed 3 years ago
Some provenance data not correctly formatted
Closed 3 years ago
Add hybrid assembly mode
Closed 3 years ago
Add `process_name` to provenance entries
Closed 3 years ago
Add optional versioned output directory
Closed 3 years ago
Modify quast report parser to simply output csv with cleaned headers
Closed 3 years ago
Create separate quast, prokka and bakata outputs for shovill and unicycler assemblies
Closed 3 years ago1
Add read length-related fields to `fastp.csv` output
Closed 3 years ago
Create per-sample provenance record
Closed 3 years ago
Support 'SampleSheet' input mode
Closed 3 years ago
Add trimming stage
Closed 3 years ago
Remove `process.executor` setting from `nextflow.config`
Closed 4 years ago