Comments (4)
peterk87
commented on July 18, 2024
Hi @ayooluwaB, would you be able to share the results privately? I'm very interested in what's going on as I've tested the pipeline with both IAV and IBV samples and it has worked as expected. Have you looked at the IRMA results and reports? I'm not sure what could be going on.
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peterk87
commented on July 18, 2024
Hi @ayooluwaB just confirming that dehosting with a Kraken2 human seq index resolved your issue. I've added a TODO to add optional Kraken2 dehosting to the pipeline (#50).
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ayooluwaB
commented on July 18, 2024
Hi @peterk87, this is correct. I believe an optional dehosting step would be very beneficial.
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peterk87
commented on July 18, 2024
Great! I'll close this issue and leave #50 to tackle in a future PR.
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Related Issues (20)
- [BUG]: Error executing process > 'NF_FLU:ILLUMINA:SUBTYPING_REPORT' HOT 8
- 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
- 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
- VADR Annotation HOT 3
- [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
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