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nf-core / rnafusion

RNA-seq analysis pipeline for detection of gene-fusions
https://nf-co.re/rnafusion
MIT License
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error when using whitelist parameter #462

Closed ahwanpandey closed 6 months ago

ahwanpandey commented 7 months ago

Description of the bug

I get an error when running the pipeline with the whitelist parameter. The contents of the whitelist.txt file is exactly how it is shown in the documentation i.e.

GENE1--GENE2
GENE3--GENE4

line 39 as indicated by the terminal output message is as follows

    32          if (params.whitelist)  {
    33              ch_whitelist = ch_fusion_list.fusions.combine(Channel.value(file(params.whitelist, checkIfExists:true)))
    34                              .map { meta, fusions, whitelist -> [ meta, [fusions, whitelist] ] }
    35
    36              CAT_CAT(ch_whitelist) // fusioninspector takes care of possible duplicates
    37              ch_versions = ch_versions.mix(CAT_CAT.out.versions)
    38
    39              ch_fusion_list.fusions = CAT_CAT.out.file_out
    40          }

Command used and terminal output

N E X T F L O W  ~  version 23.04.1
Launching `/researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion/3_0_1/main.nf` [deadly_babbage] DSL2 - revision: 620ccd6098

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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnafusion v3.0.1
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Core Nextflow options
  runName                           : deadly_babbage
  containerEngine                   : singularity
  launchDir                         : /researchers/ahwan.pandey/Projects/RNAseq/Project_DG/LGSC_Tania/analysis_15_04_2020_3/run_output
  workDir                           : /researchers/ahwan.pandey/Projects/RNAseq/Project_DG/LGSC_Tania/analysis_15_04_2020_3/run_output/work
  projectDir                        : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion/3_0_1
  userName                          : apandey
  profile                           : singularity
  configFiles                       :

Input/output options
  input                             : /researchers/ahwan.pandey/Projects/RNAseq/Project_DG/LGSC_Tania/analysis_15_04_2020_3/nfcore_rnafusion_samplesheet.csv
  outdir                            : /researchers/ahwan.pandey/Projects/RNAseq/Project_DG/LGSC_Tania/analysis_15_04_2020_3/run_output
  genomes_base                      : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references
  ensembl_version                   : 102
  starfusion_build                  : true
  read_length                       : 150
  all                               : true
  arriba_ref                        : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/arriba
  arriba_ref_blacklist              : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz
  arriba_ref_cytobands              : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv
  arriba_ref_known_fusions          : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz
  arriba_ref_protein_domains        : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3
  ensembl_ref                       : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/ensembl
  fusioncatcher_limitSjdbInsertNsj  : 2000000
  fusioncatcher_ref                 : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/fusioncatcher/human_v102
  fusioninspector_limitSjdbInsertNsj: 1000000
  fusionreport_ref                  : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/fusion_report_db
  hgnc_ref                          : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/hgnc/hgnc_complete_set.txt
  hgnc_date                         : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/hgnc/HGNC-DB-timestamp.txt
  starfusion_ref                    : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/starfusion/ctat_genome_lib_build_dir
  starindex_ref                     : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/star
  tools_cutoff                      : 1
  whitelist                         : /researchers/ahwan.pandey/Projects/RNAseq/Project_DG/LGSC_Tania/analysis_15_04_2020_3/whitelist.txt

Read trimming options
  fastp_trim                        : true
  adapter_fasta                     : /researchers/ahwan.pandey/references/Contaminants/RNAseq/contaminants.fa

Alignment compression options
  cram                              : []

Reference genome options
  genome                            : GRCh38
  fasta                             : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/ensembl/Homo_sapiens.GRCh38.102.all.fa
  fai                               : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/ensembl/Homo_sapiens.GRCh38.102.all.fa.fai
  gtf                               : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/ensembl/Homo_sapiens.GRCh38.102.gtf
  chrgtf                            : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf
  transcript                        : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/ensembl/Homo_sapiens.GRCh38.102.cdna.all.fa.gz
  refflat                           : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf.refflat
  rrna_intervals                    : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion_refs/output/references/ensembl/Homo_sapiens.GRCh38.102.interval_list

Institutional config options
  custom_config_base                : /researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion/3_0_1/../configs/
  config_profile_description        : Peter MacCallum Cancer Centre (PeterMac) Rosalind HPC cluster profile
  config_profile_contact            : Richard Lupat (@rlupat)
  config_profile_url                : https://www.petermac.org/

Max job request options
  max_cpus                          : 40
  max_memory                        : 300 GB
  max_time                          : 14d

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

* The pipeline
  https://doi.org/10.5281/zenodo.151721952

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

* Software dependencies
  https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md

[-        ] process > NFCORE_RNAFUSION:RNAFUSION:... -
ERROR ~ argument type mismatch

 -- Check script '/researchers/ahwan.pandey/Tools/omics_tools/nf-core/nf-core-rnafusion/3_0_1/./workflows/../subworkflows/local/fusioninspector_workflow.nf' at line: 39 or see '.nextflow.log' file for more details

Relevant files

nextflow.log.zip

System information

No response