name: "fcs_fcsadaptor"
description: Run NCBI's FCS adaptor on assembled genomes
keywords:
  - assembly
  - genomics
  - quality control
  - contamination
  - NCBI
tools:
  - "fcs":
      description: |
        The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign
        organisms in genome assemblies to prepare your data for submission. Therefore, the
        submission process to NCBI is faster and fewer contaminated genomes are submitted.
        This reduces errors in analyses and conclusions, not just for the original data submitter
        but for all subsequent users of the assembly.
      homepage: "https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/"
      documentation: "https://github.com/ncbi/fcs/wiki/FCS-adaptor"
      tool_dev_url: "https://github.com/ncbi/fcs"
      doi: ""
      licence: "United States Government Work"
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - assembly:
      type: file
      description: assembly fasta file
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - cleaned_assembly:
      type: file
      description: Cleaned assembly in fasta format
      pattern: "*.{cleaned_sequences.fa.gz}"
  - adaptor_report:
      type: file
      description: Report of identified adaptors
      pattern: "*.{fcs_adaptor_report.txt}"
  - log:
      type: file
      description: Log file
      pattern: "*.{fcs_adaptor.log}"
  - pipeline_args:
      type: file
      description: Run arguments
      pattern: "*.{pipeline_args.yaml}"
  - skipped_trims:
      type: file
      description: Skipped trim information
      pattern: "*.{skipped_trims.jsonl}"
authors:
  - "@d4straub"