name: faqcs
description: Perform adapter and quality trimming on sequencing reads with reporting
keywords:
  - trimming
  - quality control
  - fastq
  - faqcs
tools:
  - faqcs:
      description: |
        FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.
      homepage: https://github.com/LANL-Bioinformatics/FaQCs
      documentation: https://github.com/LANL-Bioinformatics/FaQCs
      tool_dev_url: https://github.com/LANL-Bioinformatics/FaQCs
      doi: "https://doi.org/10.1186/s12859-014-0366-2"
      licence: ["GPLv3 License"]

## TODO nf-core: Add a description of all of the variables used as input
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.

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"
  - reads:
      type: file
      description: The trimmed/modified fastq reads
      pattern: "*trimmed.fastq.gz"
  - reads_fail:
      type: file
      description: Reads that failed the preprocessing (Optional with --discard args setting)
      pattern: "*discard.fastq.gz"
  - reads_unpaired:
      type: file
      description: Reads without matching mates in paired-end files (Optional)
      pattern: "*trimmed.unpaired.fastq.gz"
  - stats:
      type: file
      description: trimming/qc text stats file
      pattern: "*.stats.txt"
  - txt:
      type: file
      description: trimming/qc text txt files from --debug option
      pattern: "*.txt"
  - statspdf:
      type: file
      description: trimming/qc pdf report file
      pattern: "*_qc_report.pdf"
  - log:
      type: file
      description: fastq log file
      pattern: "*.log"
authors:
  - "@mjcipriano"
  - "@sateeshperi"
  - "@hseabolt"