Description

Perform adapter and quality trimming on sequencing reads with reporting

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

reads{:bash}

:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

Output

name:type
description
pattern

reads{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.trimmed.fastq.gz{:bash}

:file

The trimmed/modified fastq reads

*trimmed.fastq.gz

stats{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.stats.txt{:bash}

:file

trimming/qc text stats file

*.stats.txt

debug{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

./debug{:bash}

:directory

trimming/qc files from —debug option

./debug

statspdf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_qc_report.pdf{:bash}

:file

trimming/qc pdf report file

*_qc_report.pdf

reads_fail{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.discard.fastq.gz{:bash}

:file

Reads that failed the preprocessing (Optional with —discard args setting)

*discard.fastq.gz

reads_unpaired{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.trimmed.unpaired.fastq.gz{:bash}

:file

Reads without matching mates in paired-end files (Optional)

*trimmed.unpaired.fastq.gz

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.log{:bash}

:file

fastq log file

*.log

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

faqcs
GPLv3 License

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.

github.com/LANL-Bioinformatics/FaQCs 10.1186/s12859-014-0366-2
maintainers
Github user mjcipriano
Github user sateeshperi
Github user hseabolt
get in touch
Ask a question on Slack Open an issue on GitHub