samtools/samtools_fastq

fastq

bam

sam

cram

Description

Converts a SAM, BAM or CRAM to FASTQ format.

Inputs

Name	Type & Properties	Description
--input	file required	input SAM/BAM/CRAM file

Name

Type & Properties

--input

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	output FASTQ file

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--no_suffix -n	boolean_true	By default, either '/1' or '/2' is added to the end of read names where the corresponding READ1 or READ2 FLAG bit is set. Using -n causes read names to be left as they are.
--suffix -N	boolean_true	Always add either '/1' or '/2' to the end of read names even when put into different files.
--use_oq -O	boolean_true	Use quality values from OQ tags in preference to standard quality string if available.
--singleton -s	file	write singleton reads to FILE.
--copy_tags -t	boolean_true	Copy RG, BC and QT tags to the FASTQ header line, if they exist.
--copy_tags_list -T	string	Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist. TAGLIST can be blank or `` to indicate all tags should be copied to the output. If using ``, be careful to quote it to avoid unwanted shell expansion.
--read1 -1	file output	Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. If the -s option is used, only paired reads will be written to this file.
--read2 -2	file output	Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. If the -s option is used, only paired reads will be written to this file.
--output_reads -o	file output	Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. This is equivalent to -1 FILE -2 FILE.
--output_reads_both 0	file output	Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE instead of outputting them.
--filter_flags -f	integer	Only output alignments with all bits set in INT present in the FLAG field. INT can be specified in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0' (i.e. /^0[0-7]+/). Default: `0`.
--excl_flags -F	string	Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0' (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and supplementary alignments. Default: `0x900`.
--incl_flags --rf	string	Only output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with '0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of flag names. Default: `0`.
--excl_flags_all -G	integer	Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0' (i.e. /^0[0-7]+/). Default: `0`.
--aux_tag -d	string	Only output alignments containing an auxiliary tag matching both TAG and VAL. If VAL is omitted then any value is accepted. The tag types supported are i, f, Z, A and H. "B" arrays are not supported. This is comparable to the method used in samtools view --tag. The option may be specified multiple times and is equivalent to using the --aux_tag_file option.
--aux_tag_file -D	string	Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE. The format of the file is one line per value. This is equivalent to specifying --aux_tag multiple times.
--casava -i	boolean_true	Add Illumina Casava 1.8 format entry to header, for example: `1:N:0:ATCACG`.
--compression -c	integer	set compression level when writing gz or bgzf fastq files.
--index1 --i1	file	write first index reads to FILE.
--index2 --i2	file	write second index reads to FILE.
--barcode_tag	string	Auxiliary tag to find index reads in. Default: `BC`.
--quality_tag	string	Auxiliary tag to find index quality in. Default: `QT`.
--index_format	string	string to describe how to parse the barcode and quality tags. For example: * `i14i8`: the first 14 characters are index 1, the next 8 characters are index 2. * `n8i14`: ignore the first 8 characters, and use the next 14 characters for index 1. If the tag contains a separator, then the numeric part can be replaced with '' to mean 'read until the separator or end of tag', for example: `ni*`.

Name

Type & Properties

--no_suffix

-n

boolean_true

--suffix

-N

boolean_true

--use_oq

-O

boolean_true

--singleton

-s

file

--copy_tags

-t

boolean_true

--copy_tags_list

-T

string

--read1

-1

file

output

--read2

-2

file

output

--output_reads

-o

file

output

--output_reads_both

file

output

--filter_flags

-f

integer

--excl_flags

-F

string

--incl_flags

--rf

string

--excl_flags_all

-G

integer

--aux_tag

-d

string

--aux_tag_file

-D

string

--casava

-i

boolean_true

--compression

-c

integer

--index1

--i1

file

--index2

--i2

file

--barcode_tag

string

--quality_tag

string

--index_format

string

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
read1: "$id.$key.read1"  
read2: "$id.$key.read2"  
output_reads: "$id.$key.output_reads"  
output_reads_both: "$id.$key.output_reads_both"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/samtools/samtools_fastq/main.nf \  
  -params-file params.yaml

samtools/samtools_fastq

Inputs

Outputs

Options

Run this component

Relationships

Used by

Uses