Explore Workflows

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

Graph	Name	Retrieved From	View
	chipseq-header.cwl	https://github.com/datirium/workflows.git Path: metadata/chipseq-header.cwl Branch/Commit ID: c9e7f3de7f6ba38ee663bd3f9649e8d7dbac0c86
	Read quality control, trimming and contamination filter. Workflow for (paired) read quality control, trimming and contamination filtering. Will output a merged set of read pairs, when multiple datasets are used. Steps: - FastQC (read quality control) - fastp (read quality trimming) - bbduk used for rrna filtering - bbmap for contamination filter	https://git.wageningenur.nl/unlock/cwl.git Path: cwl/workflows/workflow_quality.cwl Branch/Commit ID: d6893a25b58b9b25fb76c5e060974b54d9eabc41
	rnaseq-header.cwl	https://github.com/datirium/workflows.git Path: metadata/rnaseq-header.cwl Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c
	spurious_annot	https://github.com/ncbi/pgap.git Path: spurious_annot/wf_spurious_annot_pass1.cwl Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
	bam to trimmed fastqs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl Branch/Commit ID: 457e101e3fb87e7fd792357afce00ed8ccbfbcdb
	assemble.cwl Assemble a set of reads using SKESA	https://github.com/ncbi/pgap.git Path: assemble.cwl Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
	Cell Ranger Count Gene Expression Cell Ranger Count Gene Expression =================================	https://github.com/datirium/workflows.git Path: workflows/single-cell-preprocess-cellranger.cwl Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c
	THOR - differential peak calling of ChIP-seq signals with replicates What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.	https://github.com/datirium/workflows.git Path: workflows/rgt-thor.cwl Branch/Commit ID: 09267e79fd867aa68a219c69e6db7d8e2e877be2
	workflow1.cwl	https://github.com/petehague/stoa.git Path: actions/workflow1.cwl Branch/Commit ID: ad2f292d7586aba6b1c4f229ab041404c4dc0413
	Instac stage-in Stage-in using Instac	https://github.com/EOEPCA/app-vegetation-index.git Path: instac.cwl Branch/Commit ID: f346f1024f124ebb9e193e3bd49559a3e5334f8b Packed ID: main