Workflow: split-bams-by-strand-and-index.cwl

Fetched 2023-01-10 19:53:04 GMT

Split reads in a BAM file by strands and index forward and reverse output BAM files

children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
input_bam_files File[]
input_basenames String[]
bamtools_forward_filter_file File

JSON filter file for forward strand used in bamtools (see bamtools-filter command)

bamtools_reverse_filter_file File

JSON filter file for reverse strand used in bamtools (see bamtools-filter command)

Steps

ID Runs Label Doc
index_plus_bam
../map/samtools-index.cwl (CommandLineTool)
split-bam-plus
bamtools-filter.cwl (CommandLineTool)

Description: filters BAM file(s).

Usage: bamtools filter [-in <filename> -in <filename> ... | -list <filelist>] [-out <filename> | [-forceCompression]] [-region <REGION>] [ [-script <filename] | [filterOptions] ]

Input & Output:

-in <BAM filename> the input BAM file(s) [stdin]

-list <filename> the input BAM file list, one

line per file

-out <BAM filename> the output BAM file [stdout]

-region <REGION> only read data from this

genomic region (see documentation for more

details)

-script <filename> the filter script file (see

documentation for more details)

-forceCompression if results are sent to stdout

(like when piping to another tool),

default behavior is to leave output

uncompressed. Use this flag to override

and force compression



General Filters:

-alignmentFlag <int> keep reads with this *exact*

alignment flag (for more detailed queries,

see below)

-insertSize <int> keep reads with insert size

that matches pattern

-mapQuality <[0-255]> keep reads with map quality

that matches pattern

-name <string> keep reads with name that

matches pattern

-queryBases <string> keep reads with motif that

matches pattern

-tag <TAG:VALUE> keep reads with this

key=>value pair



Alignment Flag Filters:

-isDuplicate <true/false> keep only alignments that are

marked as duplicate? [true]

-isFailedQC <true/false> keep only alignments that

failed QC? [true]

-isFirstMate <true/false> keep only alignments marked as

first mate? [true]

-isMapped <true/false> keep only alignments that were

mapped? [true]

-isMateMapped <true/false> keep only alignments with

mates that mapped [true]

-isMateReverseStrand <true/false> keep only alignments with mate

on reverese strand? [true]

-isPaired <true/false> keep only alignments that were

sequenced as paired? [true]

-isPrimaryAlignment <true/false> keep only alignments marked as

primary? [true]

-isProperPair <true/false> keep only alignments that

passed PE resolution? [true]

-isReverseStrand <true/false> keep only alignments on

reverse strand? [true]

-isSecondMate <true/false> keep only alignments marked as

second mate? [true]

-isSingleton <true/false> keep only singletons [true]



Help:

--help, -h shows this help text

index_minus_bam
../map/samtools-index.cwl (CommandLineTool)
split-bam-minus
bamtools-filter.cwl (CommandLineTool)

Description: filters BAM file(s).

Usage: bamtools filter [-in <filename> -in <filename> ... | -list <filelist>] [-out <filename> | [-forceCompression]] [-region <REGION>] [ [-script <filename] | [filterOptions] ]

Input & Output:

-in <BAM filename> the input BAM file(s) [stdin]

-list <filename> the input BAM file list, one

line per file

-out <BAM filename> the output BAM file [stdout]

-region <REGION> only read data from this

genomic region (see documentation for more

details)

-script <filename> the filter script file (see

documentation for more details)

-forceCompression if results are sent to stdout

(like when piping to another tool),

default behavior is to leave output

uncompressed. Use this flag to override

and force compression



General Filters:

-alignmentFlag <int> keep reads with this *exact*

alignment flag (for more detailed queries,

see below)

-insertSize <int> keep reads with insert size

that matches pattern

-mapQuality <[0-255]> keep reads with map quality

that matches pattern

-name <string> keep reads with name that

matches pattern

-queryBases <string> keep reads with motif that

matches pattern

-tag <TAG:VALUE> keep reads with this

key=>value pair



Alignment Flag Filters:

-isDuplicate <true/false> keep only alignments that are

marked as duplicate? [true]

-isFailedQC <true/false> keep only alignments that

failed QC? [true]

-isFirstMate <true/false> keep only alignments marked as

first mate? [true]

-isMapped <true/false> keep only alignments that were

mapped? [true]

-isMateMapped <true/false> keep only alignments with

mates that mapped [true]

-isMateReverseStrand <true/false> keep only alignments with mate

on reverese strand? [true]

-isPaired <true/false> keep only alignments that were

sequenced as paired? [true]

-isPrimaryAlignment <true/false> keep only alignments marked as

primary? [true]

-isProperPair <true/false> keep only alignments that

passed PE resolution? [true]

-isReverseStrand <true/false> keep only alignments on

reverse strand? [true]

-isSecondMate <true/false> keep only alignments marked as

second mate? [true]

-isSingleton <true/false> keep only singletons [true]



Help:

--help, -h shows this help text

Outputs

ID Type Label Doc
bam_plus_files File[]

BAM files containing only reads in the forward (plus) strand.

bam_minus_files File[]

BAM files containing only reads in the reverse (minus) strand.

Permalink: https://w3id.org/cwl/view/git/ebd63f705d0fde7290e42c8300d5420c25cfbfe3/v1.0/quant/split-bams-by-strand-and-index.cwl