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:false ]

`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:false ]

`*.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:false ]

`*.stats.txt`
`:file`

trimming/qc text stats file

*.stats.txt

`debug`

`meta`
`:map`

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

`./debug`
`:directory`

trimming/qc files from —debug option

./debug

`statspdf`

`meta`
`:map`

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

`*_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:false ]

`*.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:false ]

`*.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:false ]

`*.log`
`:file`

fastq log file

*.log

`versions_faqcs`

`${task.process}`
`:string`

The name of the process

`faqcs`
`:string`

The name of the tool

`FaQCs --version 2>&1 | sed 's/^.*Version: //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`faqcs`
`:string`

The name of the tool

`FaQCs --version 2>&1 | sed 's/^.*Version: //'`
`:eval`

The expression to obtain the version of the tool

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_faqcs`

`${task.process}`
`:string`

`faqcs`
`:string`

`FaQCs --version 2>&1 | sed 's/^.*Version: //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`faqcs`
`:string`

`FaQCs --version 2>&1 | sed 's/^.*Version: //'`
`:eval`

Tools

faqcs
GPLv3 License

maintainers

get in touch

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_faqcs

${task.process}:string

faqcs:string

FaQCs --version 2>&1 | sed 's/^.*Version: //':eval

Topics

versions

${task.process}:string

faqcs:string

FaQCs --version 2>&1 | sed 's/^.*Version: //':eval

Tools

faqcs GPLv3 License

maintainers

get in touch

`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_faqcs`

`${task.process}`
`:string`

`faqcs`
`:string`

`FaQCs --version 2>&1 | sed 's/^.*Version: //'`
`:eval`

`versions`

`${task.process}`
`:string`

`faqcs`
`:string`

`FaQCs --version 2>&1 | sed 's/^.*Version: //'`
`:eval`

faqcs
GPLv3 License