custom schemes

[rebeelouise]

Hello!

I am trying to run this on a custom primer scheme for another coronavirus, not SC2.

Data is nanopore data.

1st thing, the data is now being outputted as pod5 as opposed to fast5_pass/fail. - does this matter?

2nd thing is what parameters do I need to get this to run the custom scheme. I have provided the paths to the reference fasta, the primer bed file and the suffix for the right and left primers.

If anyone could point me in the right direction that would be great, as so far, no good!

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| | | _, _/ | \ |___ `-.,--, .,._,'
nf-core/viralrecon v2.6.0-g3731dd3

Core Nextflow options
revision : master
runName : exotic_chandrasekhar
containerEngine : docker
launchDir : /home/van_hohenheim
workDir : /home/van_hohenheim/work
projectDir : /home/van_hohenheim/.nextflow/assets/nf-core/viralrecon
userName : van_hohenheim
profile : docker
configFiles : /home/van_hohenheim/.nextflow/assets/nf-core/viralrecon/nextflow.config

Input/output options
platform : nanopore
outdir : user/rebee/projects/viral_recon_MHV

Reference genome options
fasta : /mnt/c/primer_schemes/MHVCoV-400/MHVCoV-400.reference.fasta
primer_bed : /mnt/c/primer_schemes/MHVCoV-400/MHVCoV-400.scheme.bed
primer_left_suffix : _F
primer_right_suffix : _R

Nanopore options
fastq_dir : /mnt/c/data/artic/20241025_MHV_OC43_RPR/20241025_1638_MN46757_FAY84222_db1155b0/fastq_pass/
fast5_dir : /mnt/c/data/artic/20241025_MHV_OC43_RPR/20241025_1638_MN46757_FAY84222_db1155b0/pod5/
sequencing_summary : /mnt/c/data/artic/20241025_MHV_OC43_RPR/20241025_1638_MN46757_FAY84222_db1155b0/sequencing_summary_FAY84222_db1155b0_ef1fbc1a.txt
artic_scheme : /mnt/c/primer_schemes/MHVCoV-400/

Nanopore/Illumina options
nextclade_dataset_name: MHV

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/viralrecon for your analysis please cite:

• The pipeline
  https://doi.org/10.5281/zenodo.3901628

• The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

• Software dependencies
  https://github.com/nf-core/viralrecon/blob/master/CITATIONS.md

---

[- ] NFCORE_VIRALRECON:NANOPORE:PYCOQC -
[- ] NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -
[- ] NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:COLLAPSE_PRIMERS -
[- ] NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:NEXTCLADE_DATASETGET -
[- ] NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:SNPEFF_BUILD -
ERROR ~ A process input channel evaluates to null -- Invalid declaration val scheme_version

-- Check script '.nextflow/assets/nf-core/viralrecon/./workflows/nanopore.nf' at line: 308 or see '.nextflow.log' file for more details`