falco

fastqc

sequencing

Description

A C++ drop-in replacement of FastQC to assess the quality of sequence read data

Input arguments

Name	Type & Properties	Description
--input	file required multiple	input fastq files

Name

Type & Properties

--input

file

required

multiple

Run arguments

Name	Type & Properties	Description
--nogroup	boolean_true	Disable grouping of bases for reads >50bp. All reports will show data for every base in the read. WARNING: When using this option, your plots may end up a ridiculous size. You have been warned!
--contaminents	file	Specifies a non-default file which contains the list of contaminants to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored. Default: https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt
--adapters	file	Specifies a non-default file which contains the list of adapter sequences which will be explicity searched against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored. Default: https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt
--limits	file	Specifies a non-default file which contains a set of criteria which will be used to determine the warn/error limits for the various modules. This file can also be used to selectively remove some modules from the output all together. The format needs to mirror the default limits.txt file found in the Configuration folder. Default: https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt
--subsample -s	integer	[Falco only] makes falco faster (but possibly less accurate) by only processing reads that are a multiple of this value (using 0-based indexing to number reads).
--bisulfite -b	boolean_true	[Falco only] reads are whole genome bisulfite sequencing, and more Ts and fewer Cs are therefore expected and will be accounted for in base content.
--reverse_complement -r	boolean_true	[Falco only] The input is a reverse-complement. All modules will be tested by swapping A/T and C/G

Name

Type & Properties

--nogroup

boolean_true

--contaminents

file

--adapters

file

--limits

file

--subsample

-s

integer

--bisulfite

-b

boolean_true

--reverse_complement

-r

boolean_true

Output arguments

Name	Type & Properties	Description
--outdir -o	file required output	Create all output files in the specified output directory. FALCO-SPECIFIC: If the directory does not exists, the program will create it.
--format -f	string	Bypasses the normal sequence file format detection and forces the program to use the specified format. Validformats are bam, sam, bam_mapped, sam_mapped, fastq, fq, fastq.gz or fq.gz.
--data_filename -D	file output	[Falco only] Specify filename for FastQC data output (TXT). If not specified, it will be called fastq_data.txt in either the input file's directory or the one specified in the --output flag. Only available when running falco with a single input.
--report_filename -R	file output	[Falco only] Specify filename for FastQC report output (HTML). If not specified, it will be called fastq_report.html in either the input file's directory or the one specified in the --output flag. Only available when running falco with a single input.
--summary_filename -S	file output	[Falco only] Specify filename for the short summary output (TXT). If not specified, it will be called fastq_report.html in either the input file's directory or the one specified in the --output flag. Only available when running falco with a single input.

Name

Type & Properties

--outdir

-o

file

required

output

--format

-f

string

--data_filename

-D

file

output

--report_filename

-R

file

output

--summary_filename

-S

file

output

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
outdir: "$id.$key.outdir.output"  
data_filename: "$id.$key.data_filename"  
report_filename: "$id.$key.report_filename"  
summary_filename: "$id.$key.summary_filename"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/falco/main.nf \  
  -params-file params.yaml

falco

Input arguments

Run arguments

Output arguments

Run this component

Relationships

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