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

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

Fetched 2023-01-09 02:36:24 GMT

Verified with cwltool version 3.1.20221201130942

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

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Inputs/Outputs

This workflow is Open Source and may be reused according to the terms of: MIT License

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	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	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/8aabde14169421a7115c5cd48c4740b3a7bd818f/v1.0/quant/split-bams-by-strand-and-index.cwl