Comments (1)
Updating java / nextflow resolved these issues. Closing. It does give me a "warning" about this, but it still allows work and the changes I've made while using the multiqc config and the -c for the pangolin update file.
from viralrecon.
Related Issues (20)
- Allow viralrecon to take gtf as input annotation file
- primer_set is not taking param
- Artic v5 mismatched primer names in artic-ncov2019 repo cause certain amplicons to be erroneously filtered/removed
- Add QIAseq DIRECT SARS-CoV-2 Kit amplicons
- Argument input-fasta is missing in NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:NEXTCLADE_RUN" HOT 4
- Problem installing viralrecon
- Adding "aggregate" and "plot" methods in the freyja subworkflow HOT 4
- Error running version 2.6.0 with Nanopore data in process NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION
- Unable to download the python script HOT 3
- Split authors in generated RO crate
- Adding "--grouplineages" parameter in the nf-core/viralrecon HOT 3
- Make cutadapt primer's position ext.arg
- Properly deal with multiqc in the config files before the next release HOT 3
- Temp file problem in VARIANTS_IVAR:BCFTOOLS_SORT HOT 1
- Allow skipping `freyja boot` HOT 1
- `MOSDEPTH_AMPLICON` doesn't run in `dev` branch HOT 1
- Non-SCV2 amplicon run returns consensus genomes with no low-coverage masking HOT 5
- nf-core/viralrecon run halted due to R version clash HOT 6
- Error when running illumina command
- ivariant filtering problem using 'tsv file' generated by 'ivar variant' command. HOT 7
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