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"