Invalid declaration val medaka_model_string

[alethomas]

Description of the bug

When using the pipeline I'm experiencing an error and I can't figure out the problem (see text of attached log file).

Command used and terminal output

nextflow run nf-core/viralrecon -qs 4 -revision 2.4.1 -profile docker --input results/benchmarking/nf-core-viralrecon/nanopore/sample-sheets/1_ont/sample_sheet.csv --sequencing_summary data/RAW/ONT_batch1/sequencing_summary.txt --fastq_dir resources/benchmarking/data/nf-core-viralrecon/1_ont/fastq_pass --fast5_dir resources/benchmarking/data/nf-core-viralrecon/1_ont/fast5_pass --platform nanopore --genome 'MN908947.3' --primer_set_version 3 --outdir results/benchmarking/nf-core-viralrecon/nanopore/nanopolish/1_ont  > logs/nf-core-nf_core_viralrecon_nanopore/nanopolish/1_ont.log 2>&1

Relevant files

N E X T F L O W  ~  version 21.10.6
Pulling nf-core/viralrecon ...
 downloaded from https://github.com/nf-core/viralrecon.git
Launching `nf-core/viralrecon` [fabulous_bhabha] - revision: 42e38bba3d [2.4.1]

  nf-core/viralrecon v2.4.1
------------------------------------------------------
Core Nextflow options
  revision                   : 2.4.1
  runName                    : fabulous_bhabha
  containerEngine            : docker
  launchDir                  : /local/master-snakemake-workflow-sars-cov2
  workDir                    : /local/master-snakemake-workflow-sars-cov2/work
  projectDir                 : /home/alex/.nextflow/assets/nf-core/viralrecon
  userName                   : alex
  profile                    : docker
  configFiles                : /home/alex/.nextflow/assets/nf-core/viralrecon/nextflow.config

Input/output options
  input                      : results/benchmarking/nf-core-viralrecon/nanopore/sample-sheets/1_ont/sample_sheet.csv
  platform                   : nanopore
  outdir                     : results/benchmarking/nf-core-viralrecon/nanopore/nanopolish/1_ont

Reference genome options
  genome                     : MN908947.3
  fasta                      : https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta
  gff                        : https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz
  primer_bed                 : https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed
  primer_set_version         : 3

Nanopore options
  fastq_dir                  : resources/benchmarking/data/nf-core-viralrecon/1_ont/fastq_pass
  fast5_dir                  : resources/benchmarking/data/nf-core-viralrecon/1_ont/fast5_pass
  sequencing_summary         : data/RAW/ONT_batch1/sequencing_summary.txt
  artic_scheme               : nCoV-2019

Nanopore/Illumina options
  nextclade_dataset          : https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-01-18T12_00_00Z.tar.gz
  nextclade_dataset_name     : sars-cov-2
  nextclade_dataset_reference: MN908947
  nextclade_dataset_tag      : 2022-01-18T12:00:00Z

!! 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
------------------------------------------------------
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PYCOQC                              -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:GUNZIP_GFF           -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:COLLAPSE_PRIMERS     -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:UNTAR                -

[-        ] process > NFCORE_VIRALRECON:NANOPORE:PYCOQC                              -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:GUNZIP_GFF           -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:COLLAPSE_PRIMERS     -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:UNTAR                -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:PREPARE_GENOME:SNPEFF_BUILD         -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:INPUT_CHECK:SAMPLESHEET_CHECK       -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:MULTIQC_TSV_NO_SAMPLE_NAME          -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:MULTIQC_TSV_NO_BARCODES             -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:MULTIQC_TSV_BARCODE_COUNT           -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:ARTIC_GUPPYPLEX                     -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:MULTIQC_TSV_GUPPYPLEX_COUNT         -
[-        ] process > NFCORE_VIRALRECON:NANOPORE:NANOPLOT                            -
A process input channel evaluates to null -- Invalid declaration `val medaka_model_string`

 -- Check script '/home/alex/.nextflow/assets/nf-core/viralrecon/./workflows/nanopore.nf' at line: 310 or see '.nextflow.log' file for more details

System information

Nextflow version: 21.10.6
Hardware: Server
Executor: local via shell and Snakemake
Container engine: Docker/Conda
OS: Ubuntu 20.04.2 LTS
Version of nf-core/viralrecon: 2.4.1

[drpatelh]

Hi @alethomas ! Apologies for the late response. This will be fixed in the upcoming release via cb7efb7