Repository navigation
Enhancements & fixes
- Removed fixed nextflow version for test download
- Fix FASTA file name for test_full profile
- Upgraded to the nf-core template v4.1.0
- Slack / Teams functionality now moved to Nextflow plugins (nf-slack, nf-teams)
- Add check for BAM/CRAM headers in nf-test
- Preserve PG lines from original BAM/CRAM files and processing steps in final alignment outputs
- Add Hifi_trimmer trimming statistics to the MultiQC report
- Add MultiQC report per datatype
- Support PacBio PiMmS and Ampli-Fi data
Parameters
| Old parameter | New parameter |
|---|---|
--outfmt |
--alignment_format |
NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.
Software dependencies
Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
| Dependency | Old version | New version |
|---|---|---|
hifi-trimmer |
2.2.0 | 5.0.1 |
multiqc |
1.33 | 1.35 |
samtools |
1.22.1, 1.23, and 1.23.1 | 1.22.1, 1.23, 1.23.1, and 1.24 |
gawk |
5.3.0 | 5.3.1 |
blobtk depth |
0.7.1 | 0.8.0 |
NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.