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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Have you loaded the SQANTI3.env conda environment?
- [ ] I have loaded the SQANTI3.env conda environment
### …
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## Bug report
### Expected behavior and actual behavior
I would anticipate that passing arguments such as `--minimap2_args '-k15'` would result in the parameter `minimap2_args` being set to t…
cjw85 updated
1 month ago
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### Description of the bug
I am trying to run the scrnaseq nextflow workflow with the following error message:
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER ([])'
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Hello,
I have 6 trinity fasta files, one for each tissue. How do I use all of this information PASA to get the genome annotation?
Would I run one of the fastas to create the database and then loa…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Cercis/canadensis/genomes/ISC453364.gnm3.GWXB
- Cercis/canadensis/annotations/IS…
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[2024-10-28 04:01:14] INFO: GTDB-Tk v2.4.0
[2024-10-28 04:01:14] INFO: gtdbtk classify_wf --genome_dir new_genome_data/ --skip_ani_screen --out_dir classify_wf_out --cpus 16
[2024-10-28 04:01:14] IN…
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The URL starting with 'ftp' is no longer accessible which causes a problem in get_genome and get_annotation in genome.smk.
To specify to use the URL starting with 'http' instead of 'ftp', 'url' param…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Chamaecrista/fasciculata/genomes/ISC494698.gnm1.8Q19
- Chamaecrista/fasciculata…
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Version: `isosceles v0.2.1`
Running `prepare_transcripts` with bulk ONT reads aligned to chr1 of GRCh38 with minimap2:
```
BAM
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### Description of feature
Can sarek be used for variant calling in plant genome? And if possible, what should be done?