CWL Workflow: heatmap-prepare.cwl

Workflow: heatmap-prepare.cwl

Fetched 2023-01-09 02:00:04 GMT

Verified with cwltool version 3.1.20221201130942

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

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This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

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

Inputs

ID	Type	Title	Doc
bam_file	File[]	BAM files	Array of input BAM files
total_reads	Integer[]	Total reads numbers	Array of total reads number for downstream normalization
fragment_size	Integer[]	Fragment sizes	Array of fragment sizes

Steps

ID	Runs	Label	Doc
make_tag_directory	homer-make-tag-directory.cwl (CommandLineTool)		Tool runs makeTagDirectory that basically parses through the alignment file and splits the tags into separate files based on the chromosomes. Multiple alignment files are not supported. Alignment file's format is restricted to be only BAM. Output is placed in a folder with the name derived from the input BAM file's basename. Skipped arguments: Rely on the default value: -format - format will be autodetected -precision - the default value is used Not required general functionality: -d -single -force5th -t -flip -tbp Not required GC-bias options: -genome -checkGC -normGC -normFixedOligo -minNormRatio -maxNormRatio -iterNorm -filterReads Not required HiC options: -removePEbg -restrictionSite -removeSpikes -bowtiePE -directional

Outputs

ID	Type	Label	Doc
tag_folder	Directory[]	Tag directories	Array of tag directories