Comments (1)
This should be fixed in #202 @charlesfoster. I submitted a PR to create a multi-tool container that contains ASCIIGenome and BEDTools. The interval size adjustment will now be chucked through bedtools slop
as an additional step to santise the intervals and to make sure they don't cross chromosomal boundaries. Be great if you can test this when that PR is merged.
nextflow pull nf-core/viralrecon
nextflow run nf-core/viralrecon -r dev <YOUR_PARAMETERS>
from viralrecon.
Related Issues (20)
- epi2me-labs/wf-cnv failed during analysis HOT 7
- 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 1
- nf-core/viralrecon run halted due to R version clash HOT 1
- Error when running illumina command
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from viralrecon.