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Graph	Name	Retrieved From	View
	Single-Cell Differential Abundance Analysis Single-Cell Differential Abundance Analysis Compares the composition of cell types between two tested conditions	https://github.com/datirium/workflows.git Path: workflows/sc-rna-da-cells.cwl Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
	Bismark Methylation SE Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).	https://github.com/datirium/workflows.git Path: workflows/bismark-methylation-se.cwl Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e
	scatter-wf2.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl Branch/Commit ID: 7dec97bb8f0bc2d9e9eb710faf41f2e98cc7cdda
	secret_wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/secret_wf.cwl Branch/Commit ID: dbc4c4c2ad30ed31367b4fbcc3bb4084fdcabaa2
	kmer_cache_store	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: f10de890d1d2271299931349fa8aea660acef4ee
	Hello World Outputs a message using echo	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/hello-workflow.cwl Branch/Commit ID: 55ccde7c2fe3e7899136ce8606a341e292d7050a
	kmer_seq_entry_extract_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl Branch/Commit ID: c28cfb9882dedd3c522160f933cff1050ae24100
	Varscan Workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/varscan_germline.cwl Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
	exome alignment with qc	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/exome_alignment.cwl Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6
	Subworkflow that runs cnvkit in single sample mode and returns a vcf file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cnvkit_single_sample.cwl Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca