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!
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!
------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ // \ |) | } { | | | _, _/ | \ |__ `-.,--,.,.,' nf-core/viralrecon v2.6.0-g3731dd3Core 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`