Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	snaptools_create_snap_file.cwl	https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git Path: steps/snaptools_create_snap_file.cwl Branch/Commit ID: 4b2af54638bc471ee3e14e5f49546a2b6860804e
	revsort.cwl Reverse the lines in a document, then sort those lines.	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/revsort.cwl Branch/Commit ID: 78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf
	1st-workflow.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/1st-workflow.cwl Branch/Commit ID: aec33fcfa3459a90cbba8c88ebb991be94d21429
	Subsample BAM file creating a tagAlign and pseudoreplicates This workflow creates a subsample from a BAM file creating a tagAlign and pseudoreplicates	https://github.com/ncbi/cwl-ngs-workflows-cbb.git Path: workflows/File-formats/subample-pseudoreplicates.cwl Branch/Commit ID: e541470bc9d0b064bc4ed7dd2b45d8ec67760613
	exome alignment and germline variant detection, with optitype for HLA typing	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/germline_exome_hla_typing.cwl Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
	wf_full_IDR_pipeline_1input_scatter.cwl The main workflow that: produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each). runs the 'rescue ratio' statistic runs the 'consistency ratio' statistic	https://github.com/YeoLab/merge_peaks.git Path: cwl/wf_full_IDR_pipeline_1input_scatter.cwl Branch/Commit ID: aedc0a14d4ba109ee65678a3201a52c5bb6ad473
	tt_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: f2bd4687f06f85ea848b6f1ce04ec97f48525334
	Hello World Outputs a message using echo	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/hello-workflow.cwl Branch/Commit ID: 9f3b9e7b74d5a904b12674dfd1300b56a48c3d33
	bam to trimmed fastqs and biscuit alignments	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
	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: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c