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Graph	Name	Retrieved From	View
	allele-vcf-rnaseq-se.cwl Allele specific RNA-Seq (using vcf) single-read workflow	https://github.com/datirium/workflows.git Path: workflows/allele-vcf-rnaseq-se.cwl Branch/Commit ID: a9551ece898f619167db58e4b74a6cae2d7f7d13
	steplevel-resreq.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/steplevel-resreq.cwl Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
	count-lines11-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl Branch/Commit ID: fd6e054510e2bb65eed4069a3a88013d7ecbb99c
	xenbase-rnaseq-se.cwl XenBase workflow for analysing RNA-Seq single-end data	https://github.com/datirium/workflows.git Path: workflows/xenbase-rnaseq-se.cwl Branch/Commit ID: a9551ece898f619167db58e4b74a6cae2d7f7d13
	Bismark Methylation - pipeline for BS-Seq data analysis 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: 564156a9e1cc7c3679a926c479ba3ae133b1bfd4
	scatter-valuefrom-inputs-wf1.cwl	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/scatter-valuefrom-inputs-wf1.cwl Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
	cond-wf-010_nojs.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/conditionals/cond-wf-010_nojs.cwl Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
	rnaseq-se-dutp-mitochondrial.cwl RNA-Seq strand specific mitochondrial workflow for single-read experiment based on BioWardrobe's basic analysis.	https://github.com/datirium/workflows.git Path: workflows/rnaseq-se-dutp-mitochondrial.cwl Branch/Commit ID: e284e3f6dff25037b209895c52f2abd37a1ce1bf
	step_valuefrom5_wf_with_id_v1_0.cwl	https://github.com/common-workflow-language/cwl-utils.git Path: testdata/step_valuefrom5_wf_with_id_v1_0.cwl Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51
	timelimit3-wf.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/timelimit3-wf.cwl Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5