modules/faqcs

Perform adapter and quality trimming on sequencing reads with reporting

trimmingquality controlfastqfaqcs

https://github.com/nf-core/modules/[...]/modules/nf-core/faqcs

Description

Perform adapter and quality trimming on sequencing reads with reporting

Input

name:type

description

pattern

`meta:map`

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

]

`reads: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`

`meta:map`

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

]

`*.trimmed.fastq.gz:file`

The trimmed/modified fastq reads

*trimmed.fastq.gz

`stats`

`meta:map`

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

]

`*.stats.txt:file`

trimming/qc text stats file

*.stats.txt

`debug`

`meta:map`

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

]

`./debug:directory`

trimming/qc files from —debug option

./debug

`statspdf`

`meta:map`

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

]

`*_qc_report.pdf:file`

trimming/qc pdf report file

*_qc_report.pdf

`reads_fail`

`meta:map`

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

]

`*.discard.fastq.gz:file`

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

*discard.fastq.gz

`reads_unpaired`

`meta:map`

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

]

`*.trimmed.unpaired.fastq.gz:file`

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

*trimmed.unpaired.fastq.gz

`log`

`meta:map`

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

]

`*.log:file`

fastq log file

*.log

`versions`

`versions.yml: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

modules/faqcs

Description

Input

meta:map

reads:file

Output

reads

meta:map

*.trimmed.fastq.gz:file

stats

meta:map

*.stats.txt:file

debug

meta:map

./debug:directory

statspdf

meta:map

*_qc_report.pdf:file

reads_fail

meta:map

*.discard.fastq.gz:file

reads_unpaired

meta:map

*.trimmed.unpaired.fastq.gz:file

log

meta:map

*.log:file

versions

versions.yml:file

Tools

faqcs GPLv3 License

`meta:map`

`reads:file`

`reads`

`meta:map`

`*.trimmed.fastq.gz:file`

`stats`

`meta:map`

`*.stats.txt:file`

`debug`

`meta:map`

`./debug:directory`

`statspdf`

`meta:map`

`*_qc_report.pdf:file`

`reads_fail`

`meta:map`

`*.discard.fastq.gz:file`

`reads_unpaired`

`meta:map`

`*.trimmed.unpaired.fastq.gz:file`

`log`

`meta:map`

`*.log:file`

`versions`

`versions.yml:file`

faqcs
GPLv3 License