Unable to run viralrecon using custom FASTA, GFF and Primer BED file for nanopore data #568
Description
Description of the bug
After @ewels provided some motivation here, I set out to test viralrecon using custom BED file, FASTA and GFF file for dengue data. However, it fails to run both using metagenomic or amplicon protocol. As described in the document, it appears that viralrecon is unable to take custom primer sets and only supports Artic primers
For Nanopore data, the pipeline only supports amplicon-based analysis obtained from primer sets created and maintained by the ARTIC Network.
Command used and terminal output
nextflow run nf-core/viralrecon --platform nanopore --protocol metagenomic -profile mam
ba --input samplesheet_nanopore.csv --outdir test_rohit --primer_bed primers.bed --primer_left_suffix '_L' --primer_right_suffix '_R' -resume --fasta denv2.
fasta --gff denv2.gff --fastq_dir fastq_pass/
N E X T F L O W ~ version 25.10.0
WARN: It appears you have never run this project before -- Option `-resume` is ignored
Launching `https://github.com/nf-core/viralrecon` [sad_euclid] DSL2 - revision: 395079f1d2 [master]
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
There is a problem with your Conda configuration!
You will need to set-up the conda-forge and bioconda channels correctly.
Please refer to https://bioconda.github.io/
The observed channel order is
[defaults]
but the following channel order is required:
[conda-forge, bioconda]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/viralrecon 3.0.0
------------------------------------------------------
Input/output options
input : samplesheet_nanopore.csv
platform : nanopore
protocol : metagenomic
outdir : test_rohit
Reference genome options
fasta : denv2.fasta
gff : denv2.gff
primer_bed : primers.bed
primer_left_suffix : _L
primer_right_suffix: _R
Nanopore options
fastq_dir : fastq_pass/
Generic options
trace_report_suffix: 2025-11-19_22-36-34
Core Nextflow options
revision : master
runName : sad_euclid
launchDir : /mnt/c/Users/rohit_satyam/Pictures
workDir : /mnt/c/Users/rohit_satyam/Pictures/work
projectDir : /home/rohit/.nextflow/assets/nf-core/viralrecon
userName : rohit
profile : mamba
configFiles : /home/rohit/.nextflow/assets/nf-core/viralrecon/nextflow.config
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* 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:VIRALRECON:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -
[- ] NFCORE_VIRALRECON:VIRALRECON:PREPARE_GENOME:UNTAR_KRAKEN2_DB -
[- ] NFCORE_VIRALRECON:VIRALRECON:PREPARE_GENOME:COLLAPSE_PRIMERS -
[- ] NFCORE_VIRALRECON:VIRALRECON:PREPARE_GENOME:SNPEFF_BUILD -
[- ] NFCORE_VIRALRECON:VIRALRECON:ARTIC_GUPPYPLEX -
[- ] NFCORE_VIRALRECON:VIRALRECON:KRAKEN2_KRAKEN2 -
[- ] NFCORE_VIRALRECON:VIRALRECON:NANOPLOT -
ERROR ~ A process input channel evaluates to null -- Invalid declaration `val model`
-- Check script '/home/rohit/.nextflow/assets/nf-core/viralrecon/workflows/viralrecon.nf' at line: 923 or see '.nextflow.log' file for more details
nextflow run nf-core/viralrecon --platform nanopore --protocol amplicon -profile mamba --input samplesheet_nanopore.csv --outdir test_rohit --primer_bed primers.bed --prim
er_left_suffix '_L' --primer_right_suffix '_R' -resume --fasta denv2.fasta --gff denv2.gff --fastq_dir fastq_pass/
N E X T F L O W ~ version 25.10.0
Launching `https://github.com/nf-core/viralrecon` [cheesy_hodgkin] DSL2 - revision: 395079f1d2 [master]
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
There is a problem with your Conda configuration!
You will need to set-up the conda-forge and bioconda channels correctly.
Please refer to https://bioconda.github.io/
The observed channel order is
[defaults]
but the following channel order is required:
[conda-forge, bioconda]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/viralrecon 3.0.0
------------------------------------------------------
Input/output options
input : samplesheet_nanopore.csv
platform : nanopore
protocol : amplicon
outdir : test_rohit
Reference genome options
fasta : denv2.fasta
gff : denv2.gff
primer_bed : primers.bed
primer_left_suffix : _L
primer_right_suffix: _R
Nanopore options
fastq_dir : fastq_pass/
Generic options
trace_report_suffix: 2025-11-19_22-28-57
Core Nextflow options
revision : master
runName : cheesy_hodgkin
launchDir : /mnt/c/Users/rohit_satyam/Pictures
workDir : /mnt/c/Users/rohit_satyam/Pictures/work
projectDir : /home/rohit/.nextflow/assets/nf-core/viralrecon
userName : rohit
profile : mamba
configFiles : /home/rohit/.nextflow/assets/nf-core/viralrecon/nextflow.config
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* 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:VIRALRECON:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -
[- ] NFCORE_VIRALRECON:VIRALRECON:PREPARE_GENOME:UNTAR_KRAKEN2_DB -
[- ] NFCORE_VIRALRECON:VIRALRECON:PREPARE_GENOME:COLLAPSE_PRIMERS -
[- ] NFCORE_VIRALRECON:VIRALRECON:PREPARE_GENOME:SNPEFF_BUILD -
[- ] NFCORE_VIRALRECON:VIRALRECON:ARTIC_GUPPYPLEX -
[- ] NFCORE_VIRALRECON:VIRALRECON:KRAKEN2_KRAKEN2 -
[- ] NFCORE_VIRALRECON:VIRALRECON:NANOPLOT -
ERROR ~ A process input channel evaluates to null -- Invalid declaration `val model`
-- Check script '/home/rohit/.nextflow/assets/nf-core/viralrecon/workflows/viralrecon.nf' at line: 923 or see '.nextflow.log' file for more detailsRelevant files
barcode01.zip
files.zip
.nextflow.log
System information
Windows 11 Subsystem linux
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Address sizes: 48 bits physical, 48 bits virtual
Byte Order: Little Endian
CPU(s): 16
On-line CPU(s) list: 0-15
Vendor ID: AuthenticAMD
Model name: AMD Ryzen 7 6800H with Radeon Graphics
CPU family: 25
Model: 68
Thread(s) per core: 2
Core(s) per socket: 8
Socket(s): 1
Stepping: 1