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73 lines
2.4 KiB
YAML
73 lines
2.4 KiB
YAML
name: faqcs
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description: Perform adapter and quality trimming on sequencing reads with reporting
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keywords:
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- trimming
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- quality control
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- fastq
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- faqcs
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tools:
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- faqcs:
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description: |
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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.
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homepage: https://github.com/LANL-Bioinformatics/FaQCs
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documentation: https://github.com/LANL-Bioinformatics/FaQCs
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tool_dev_url: https://github.com/LANL-Bioinformatics/FaQCs
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doi: "https://doi.org/10.1186/s12859-014-0366-2"
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licence: ["GPLv3 License"]
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## TODO nf-core: Add a description of all of the variables used as input
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- reads:
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type: file
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description: The trimmed/modified fastq reads
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pattern: "*trimmed.fastq.gz"
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- reads_fail:
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type: file
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description: Reads that failed the preprocessing (Optional with --discard args setting)
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pattern: "*discard.fastq.gz"
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- reads_unpaired:
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type: file
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description: Reads without matching mates in paired-end files (Optional)
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pattern: "*trimmed.unpaired.fastq.gz"
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- stats:
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type: file
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description: trimming/qc text stats file
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pattern: "*.stats.txt"
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- txt:
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type: file
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description: trimming/qc text txt files from --debug option
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pattern: "*.txt"
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- statspdf:
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type: file
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description: trimming/qc pdf report file
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pattern: "*_qc_report.pdf"
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- log:
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type: file
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description: fastq log file
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pattern: "*.log"
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authors:
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- "@mjcipriano"
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- "@sateeshperi"
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- "@hseabolt"
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