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Graph	Name	Retrieved From	View
	bam-filtering BAM filtering	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/subworkflows/bam_filtering.cwl Branch/Commit ID: e1fd26587a78afc376c10bf6db36abd2c840768e
	io-any-wf-1.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/io-any-wf-1.cwl Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
	Single-Cell Label Integration Analysis Single-Cell Label Integration Analysis Harmonizes conflicting annotations in single-cell genomics studies.	https://github.com/datirium/workflows.git Path: workflows/sc-triangulate.cwl Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
	BAM to BEDPE Comvert BAM to BEDPE and compress the output	https://github.com/ncbi/cwl-ngs-workflows-cbb.git Path: workflows/File-formats/bamtobedpe-gzip.cwl Branch/Commit ID: 33123d6a92bf0038951820d0d2c9cf501ae2ebf6
	running cellranger mkfastq and count	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl Branch/Commit ID: d2c2f2eb846ae2e9cdcab46e3bb88e42126cb3f5
	allele-vcf-alignreads-se-pe.cwl Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.	https://github.com/datirium/workflows.git Path: subworkflows/allele-vcf-alignreads-se-pe.cwl Branch/Commit ID: b141f7e73005227d6d02fa03a47151836dd4109b
	xenbase-sra-to-fastq-pe.cwl	https://github.com/datirium/workflows.git Path: subworkflows/xenbase-sra-to-fastq-pe.cwl Branch/Commit ID: 9a2c389364674221fab3f0f6afdda799e6aa3247
	bam-bedgraph-bigwig.cwl Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.	https://github.com/datirium/workflows.git Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 4dcc405133f22c63478b6091fb5f591b6be8950f
	count-lines1-wf-noET.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/count-lines1-wf-noET.cwl Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
	kfdrc_qc_wf.cwl	https://github.com/kids-first/kf-alignment-workflow.git Path: workflows/kfdrc_qc_wf.cwl Branch/Commit ID: f6902dad01403ba2739724c3677007955270c185