Comments (4)
VADR annotation has been added in #73 and version 3.4.0. Hopefully that helps with your downstream needs @fanninpm!
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@Codes1985 that's great to know! I wonder if staphb have a Conda channel since I don't seem to be getting anywhere with trying to update VADR in Bioconda. Bioconda MacOSX builds are the bane of my existence... I usually skip them for my own tools. I wonder if I can get away with adding an OSX skip in my PR.
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Thanks @fanninpm for letting me know about VADR now supporting Influenza genome annotation.
It looks like the Bioconda package hasn't been updated in a while and v1.5.1 is the latest. I'll see if I can get it updated based on the changes in bioconda/bioconda-recipes#44370
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Just to follow up on this, I pulled the VADR singularity image from staphb, and I'm running it as a post-processing step after nf-flu finishes. So far it has been working well, and we are using it as part of our QC regime prior to uploading our data to GISAID.
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Related Issues (20)
- Error running newly installed pipeline HOT 1
- [BUG]: Conda and Mamba profiles broken in 3.3.0 HOT 1
- [BUG]: no H/N subtypes assigned in subtyping reports with user-specified sequences HOT 1
- [BUG]: The fasta sequence does not match the REF allele at OQ234674.1:1946 HOT 3
- Emit concatenated, re-named .fastq files into subdirectory within the nf-flu results directory HOT 1
- [BUG]: Error executing process > 'NF_FLU:ILLUMINA:SUBTYPING_REPORT (1)' HOT 3
- [BUG]: cat: can't open 'GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/*.fa': No such file or directory HOT 3
- [BUG]: Mixed IAV and IBV run analysis reports all samples as IBV only HOT 4
- Optional dehosting
- Update README and docs for running nf-flu test profiles for Nanopore and Illumina platforms HOT 1
- [BUG]: ComputeError on SUBTYPING_REPORT HOT 4
- Read samplesheet.csv with fields as strong rather than inferred types
- Compatibility with cloud storage paths HOT 2
- Clair3 not variant calling ends of each segment HOT 4
- [BUG]: pull is only supported for shub URIs HOT 1
- Ability to output consensus sequences based on quality metrics (i.e., breadth and depth of coverage)
- [BUG]: nf-flu improperly labels segment ID for PB1 and PB2 for Influenza B HOT 3
- Better top reference selection from IRMA consensus seqs with high numbers of ambiguous bases
- [BUG]: CAT_ILLUMINA_FASTQ can mistakenly append 1:N:0:./2:N:0:. to quality score lines
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