Local processes to nf-core/modules
d4straub opened this issue · 1 comments
d4straub commented
Several processes are using tools that are maybe interesting also in other pipeline and could be made available in nf-core/modules, such as:
- modules/local/canu.nf
- modules/local/dfast.nf
- modules/local/medaka.nf
- modules/local/miniasm.nf
- modules/local/nanopolish.nf
- modules/local/porechop.nf
Other processes use local modules because the nf-core modules were not applicable:
- modules/local/pycoqc.nf -> only accepts fast5 summary files, no raw fast5 files
- modules/local/nanoplot.nf -> only accepts accepts only .fastq.gz, not .fq.gz
- modules/local/minimap_align.nf -> inout path does not match nf.core module, might be possible to fix in bacass
- modules/local/unicycler.nf -> only allows short read assembly (but not hybrid and long)
Daniel-VM commented
[UPDATE] some locals have now an nf-core version and have been refactor into nf-core modules (#86):
| Tool | Previous version | New version |
|---|---|---|
| Canu | 2.1.1 | 2.2 |
| Minimap2 | 2.21 | 2.2 |
| Miniasm | 0.3 | - |
| Racon | 1.4.20-1 | - |
| Nanoplot (patch) | 1.38.0 | 1.41.6 |
| Porechop | 0.2.4 | 0.2.4 |
Still working on the remaining 👍🏾