Explore Workflows

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

Graph	Name	Retrieved From	View
	Nanopore assembly workflow Workflow for sequencing with ONT nanopore, from basecalled reads to (meta)assembly and binning Steps: - Read filtering - Kraken2 (taxonomic classification of FASTQ reads) - Flye (de novo assembly) - Medaka (assembly polishing) - metaQUAST (assembly quality reports) When Illumina reads are provided: - Assembly polishing with Pilon - Metabat2 binning - CheckM - BUSCO - GTDB-Tk	https://git.wur.nl/unlock/cwl.git Path: cwl/workflows/workflow_nanopore_assembly.cwl Branch/Commit ID: d944d61ddc34a5b24ebac6e1701efd6f8fdf54ae
	Non-Coding Bacterial Genes	https://github.com/ncbi/pgap.git Path: bacterial_noncoding/wf_bacterial_noncoding.cwl Branch/Commit ID: 656113dcac0de7cef6cff6c688f61441ee05872a
	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: ef7f3345b352319ec22dffba26c79df033b141f9
	testTimeSIMLR.cwl	https://github.com/Gepiro/rCASC_StreamFlow.git Path: setting/testTimeSIMLR.cwl Branch/Commit ID: 578338a7fb45ce3d2a8da53e09baf46323711624
	Chipseq alignment for nonhuman with qc and creating homer tag directory	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/chipseq_alignment_nonhuman.cwl Branch/Commit ID: 87faba2fff8007ecc95160729b1c7cd0376e46f2
	cache_asnb_entries	https://github.com/ncbi/pgap.git Path: task_types/tt_cache_asnb_entries.cwl Branch/Commit ID: 7ebb8d2757914d16520b00571a281e2ad86a42cf
	steps.cwl	https://github.com/DimitraPanou/scRNAseq-cwl.git Path: steps.cwl Branch/Commit ID: a0809be8a2dda2c053536f7c6fc21193f1fe78f3
	apolloServer-createOrganism-workflow.cwl	https://github.com/NAL-i5K/Organism_Onboarding.git Path: apolloServer-createOrganism-workflow.cwl Branch/Commit ID: aa375dcaa5ccfbb4e2aa4433d10948c641b044eb
	Running cellranger count and lineage inference	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/single_cell_rnaseq.cwl Branch/Commit ID: fbeea265295ae596d5a3ba563e766be0c4fc26e8
	SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.	https://github.com/datirium/workflows.git Path: tools/soupx-subworkflow.cwl Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c