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Currently we have separate instructions in the user guide, the novice tutorial, the cwltool README, and probably other places
mr-c updated
11 months ago
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See https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update for full description of each task (requires gitlab login)
- assembly accession number: GCF_024516045.1
…
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Treat the path to samtools (used in analyze_bam.py) the same way as the other external tool dependencies e.g.,
```
emboss_tool:
label: Path to install directory of EMBOSS needle/water exe…
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There are three tools in OpenMS that are reusing the name of an option. First use is always as an value and the second one as a group/section. This causes the XML to be not as precise as maybe assumed…
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# OGS remapping (@mpoelchau)
- review OGS and remap if necessary
- remap 1 manual annotation
# Change old content
- [x] back up and deprecate old Apollo2
- [x] back up and deprecate old fasta…
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On second look, I think our integration with Bioconda has actually broken. We seem to use an `--experimental-solver` option that has been removed. We need to adapt to the change, or force a version of…
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If I want to provide an array of max. two strings, how am I supposed to do that?
1) Purely JSON Schema:
```yaml
inputs:
example:
schema:
type: array
maxItems: 2
items…
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# OGS remapping (@mpoelchau)
- remap OGS
- remap manual annotations
# Change old content
- [ ] back up and deprecate old Apollo2
- [ ] back up and deprecate old fasta files in BLAST
- [ ] bac…
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# Change old content
- [x] back up and deprecate old Apollo2
- [x] back up and deprecate old fasta files in BLAST
- [x] back up and deprecate old fasta files in Hmmer
- [x] Monica needs to revie…
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# remapping
- [x] manual annotation remapping - @mpoelchau
# Change old content
- [x] back up and deprecate old Apollo2
- [x] back up and deprecate old fasta files in BLAST
- [x] back up and …