Explore Workflows

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

Graph	Name	Retrieved From	View
	cluster_blastp_wnode and gpx_qdump combined	https://github.com/ncbi/pgap.git Path: task_types/tt_cluster_and_qdump.cwl Branch/Commit ID: e3f18c61d1bbf65e40921dbd044369da4523ee3e
	Trim Galore RNA-Seq pipeline paired-end strand specific Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) RNA-Seq basic analysis for a pair-end experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file	https://github.com/datirium/workflows.git Path: workflows/trim-rnaseq-pe-dutp.cwl Branch/Commit ID: c5bae2ca862c764911b83d1f15ff6af4e2a0db28
	count-lines7-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff
	search.cwl#main	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/search.cwl Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf Packed ID: main
	Cellranger reanalyze - reruns secondary analysis performed on the feature-barcode matrix Devel version of Single-Cell Cell Ranger Reanalyze ================================================== Workflow calls \"cellranger aggr\" command to rerun secondary analysis performed on the feature-barcode matrix (dimensionality reduction, clustering and visualization) using different parameter settings. As an input we use filtered feature-barcode matrices in HDF5 format from cellranger count or aggr experiments. Note, we don't pass aggregation_metadata from the upstream cellranger aggr step. Need to address this issue when needed.	https://github.com/datirium/workflows.git Path: workflows/cellranger-reanalyze.cwl Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
	Calibration inputs to Simulation Model This workflow produces calibration inputs to simulation model: - atmospheric model - extinction hypercube - telescopes' cameras configurations - telescopes' PSFs - optical throughput	https://gitlab.cta-observatory.org/cta-computing/dpps/dpps-workflows.git Path: workflows/calibpipe/uc-cp-001.cwl Branch/Commit ID: eb6a98289850791cd1891c89e5209180c35c7858
	align_sort_sa	https://github.com/ncbi/pgap.git Path: task_types/tt_align_sort_sa.cwl Branch/Commit ID: 1e7aa9f0c34987ddafa35f9b1d2c77d99fafbdab
	Production Configuration This workflow prepares the configuration of the subsequent production steps.	https://gitlab.cta-observatory.org/cta-computing/dpps/dpps-workflows.git Path: workflows/wms/uc-wms-XXX.cwl Branch/Commit ID: eb6a98289850791cd1891c89e5209180c35c7858
	chipseq-gen-bigwig.cwl	https://github.com/datirium/workflows.git Path: subworkflows/chipseq-gen-bigwig.cwl Branch/Commit ID: 0ddfca10c41f83bb120c7633e0db9dba7441bca0
	directory.cwl Inspect provided directory and return filenames. Generate a new directory and return it (including content).	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/directory.cwl Branch/Commit ID: 8ef515037de411abd2f84b569ad4d4a4f7a2c7a0