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Graph	Name	Retrieved From	View
	rnaseq-se-dutp.cwl Runs RNA-Seq dUTP BioWardrobe basic analysis with strand specific single-end data file.	https://github.com/Barski-lab/workflows.git Path: workflows/rnaseq-se-dutp.cwl Branch/Commit ID: dcf683418d101917852b1711a91af817d4ea5d03
	align_merge_sas	https://github.com/ncbi/pgap.git Path: task_types/tt_align_merge_sas.cwl Branch/Commit ID: cabb1a9a95244e93294727be8cf5816c38992cb0
	count-lines2-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff
	Single-Cell RNA-Seq Dimensionality Reduction Analysis Single-Cell RNA-Seq Dimensionality Reduction Analysis Removes noise and confounding sources of variation by reducing dimensionality of gene expression data from the outputs of “Single-Cell RNA-Seq Filtering Analysis” or “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipelines. The results of this workflow are primarily used in “Single-Cell RNA-Seq Cluster Analysis” or “Single-Cell WNN Cluster Analysis” pipelines.	https://github.com/datirium/workflows.git Path: workflows/sc-rna-reduce.cwl Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
	Filter differentially expressed genes from DESeq for Tag Density Profile Analyses Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.	https://github.com/datirium/workflows.git Path: workflows/filter-deseq-for-heatmap.cwl Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
	retrieve sequence and perform pairwise alignment (sub-workflow process) \"Perform pairwise alignment of protein sequences for pairs identified by structural similarity search. Step 1: retrieve sequence from blastdbcmd result Step 2: makeblastdb: ../Tools/14_makeblastdb.cwl Step 3: blastdbcmd: ../Tools/15_blastdbcmd.cwl Step 4: seqretsplit: ../Tools/16_seqretsplit.cwl Step 5: needle (Global alignment): ../Tools/17_needle.cwl Step 6: water (Local alignment): ../Tools/17_water.cwl\"	https://github.com/yonesora56/plant2human.git Path: Workflow/11_retrieve_sequence_wf.cwl Branch/Commit ID: 11b46d8d8c0db462edbd2657fc62cf31bc93ecee
	count-lines14-wf.cwl	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/count-lines14-wf.cwl Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
	Detect Docm variants	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/docm_cle.cwl Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
	Bismark Methylation PE 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-pe.cwl Branch/Commit ID: ebbf23764ede324cabc064bd50647c1f643726fa
	ValidationWorkflowMissing This is a placeholder for a missing acceptance workflow.	https://github.com/gammasim/workflows.git Path: workflows/ValidationWorkflowMissing.cwl Branch/Commit ID: bf4d4a44a543bcc04f4508ce020751c71550acf5