Unmapped variable "ch_spades_hmm"

hkunerth commented 1 year ago

Description of the bug

I'm trying to run TaxTriage and have encountered a bug involving the channels passed to the SPades module. The TaxTriage workflow trying to run SPADES_ILLUMINA but this channel hasn't been assigned.

It looks like there is a config variable called spades_hmm that defaults to null. I don't need to run SPades with a custom hmm, if that's useful.

Thanks!

Command used and terminal output

nextflow run ./main.nf --input data/Samplesheet.csv --db data/databases/minikraken2_v2_8GB_201904_UPDATE --outdir tmp --remove_taxids "9606" --max_memory 8GB --max_cpus 3 -profile singularity -with-report --skip-assembly

N E X T F L O W  ~  version 21.10.6
Launching `./main.nf` [nasty_babbage] - revision: ac98c18eda

WARN: Found unexpected parameters:
* --max_time: 240.h
* --config_profile_name: null
* --config_profile_url: null
* --config_profile_contact: null
* --config_profile_description: null
* --custom_config_base: https://raw.githubusercontent.com/nf-core/configs/master
* --custom_config_version: master
* --enable_conda: false
* --show_hidden_params: false
* --validate_params: true
* --help: false
* --monochrome_logs: false
* --plaintext_email: false
* --email_on_fail: null
* --publish_dir_mode: copy
* --tracedir: tmp/pipeline_info
* --skip-assembly: true
* --max_cpus: 3
* --max_memory: 8GB
* --max_multiqc_email_size: 25.MB
* --igenomes_ignore: false
* --igenomes_base: s3://ngi-igenomes/igenomes
* --genome: null
* --skip_variants: null
* --skip_consensus: null
* --subsample: null
* --top_hits_counts: null
* --spades_hmm: null
* --low_memory: null
- Ignore this warning: params.schema_ignore_params = "max_time,config_profile_name,config_profile_url,config_profile_contact,config_profile_description,custom_config_base,custom_config_version,enable_conda,show_hidden_params,validate_params,help,monochrome_logs,plaintext_email,email_on_fail,publish_dir_mode,tracedir,skip-assembly,max_cpus,max_memory,max_multiqc_email_size,igenomes_ignore,igenomes_base,genome,skip_variants,skip_consensus,subsample,top_hits_counts,spades_hmm,low_memory"

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/taxtriage v1.0dev
------------------------------------------------------
Core Nextflow options
  runName        : nasty_babbage
  containerEngine: singularity
  launchDir      : /panfs/jay/groups/32/mdh/kuner010/taxtriage
  workDir        : /panfs/jay/groups/32/mdh/kuner010/taxtriage/work
  projectDir     : /panfs/jay/groups/32/mdh/kuner010/taxtriage
  userName       : kuner010
  profile        : singularity
  configFiles    : /panfs/jay/groups/32/mdh/kuner010/taxtriage/nextflow.config

Input/output options
  input          : data/Samplesheet.csv
  db             : data/databases/minikraken2_v2_8GB_201904_UPDATE
  trim           : null
  outdir         : tmp
  remove_taxids  : 9606

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/taxtriage for your analysis please cite:

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

* Software dependencies
  https://github.com/nf-core/taxtriage/blob/master/CITATIONS.md
------------------------------------------------------
WARN: Access to undefined parameter `reference` -- Initialise it to a default value eg. `params.reference = some_value`
WARN: Access to undefined parameter `top_hits_count` -- Initialise it to a default value eg. `params.top_hits_count = some_value`
Top hits not specified, defaulting to 10 per rank level in taxonomy tree for database for kraken2
No assembly file given, downloading the standard ncbi one
WARN: Access to undefined parameter `assembly_file_type` -- Initialise it to a default value eg. `params.assembly_file_type = some_value`
/panfs/jay/groups/32/mdh/kuner010/taxtriage/data/Samplesheet.csv
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK       -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC                              -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES                      -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FASTQC                              -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:NANOPLOT                            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MOVE_NANOPLOT                       -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2                     -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:REMOVETAXIDSCLASSIFICATION          -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:TOP_HITS                            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_ASSEMBLY                   -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PULL_FASTA                          -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BWA_INDEX                 -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BWA_MEM                   -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:MINIMAP2_ALIGN            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_OXFORD   -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_ILLUMINA -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_STATS            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_CONSENSUS        -
empty
No such variable: ch_spades_hmm

 -- Check script './workflows/taxtriage.nf' at line: 318 or see '.nextflow.log' file for more details

Relevant files

No response

System information

N E X T F L O W ~ version 21.10.6 HPC slurm eventually, but was running locally here Singularity/apptainer NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" nf-core/taxtriage v1.0.0

Merritt-Brian commented 1 year ago

Looks like I simply need to add a default ch_spades_hmm if assembly is needed, for now, can you try it with --skip_assembly called?

I will work on adding a merge for fixing the default hmm

Merritt-Brian commented 1 year ago

Completed, you can now specify an optional ch_spades_hmm

jhuapl-bio / taxtriage