Explore Workflows

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

Graph	Name	Retrieved From	View
	default-dir5.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/default-dir5.cwl Branch/Commit ID: 0e8110083bad6ea98fc487aa262953a6c5e010b5
	bam-filtering BAM filtering	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/subworkflows/bam_filtering.cwl Branch/Commit ID: d07f44fc5c253dc4044d86ea79ac6f9e03c01bfa
	metabarcode (gene amplicon) analysis for fastq files protein - qc, preprocess, annotation, index, abundance	https://github.com/MG-RAST/pipeline.git Path: CWL/Workflows/metabarcode-fastq.workflow.cwl Branch/Commit ID: 81feefc84ec0faecf1ade718001d5f07610e616e
	Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific https://chipster.csc.fi/manual/library-type-summary.html 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-smarter-dutp.cwl Branch/Commit ID: 8bf36bfad5624fbc8fc315e82783a44e9e5e4470
	bam_filtering BAM filtering	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/subworkflows/bam_filtering.cwl Branch/Commit ID: c3fd9c28e495c9bb7e3a8db53ed564b18d718b2a
	Creates FASTA file from BED coordinates This workflow creates FASTA file from BED coordinates	https://github.com/ncbi/cwl-ngs-workflows-cbb.git Path: workflows/File-formats/fasta-from-bed.cwl Branch/Commit ID: 527251ebb77750d02dcc9a370d978a153fc9328f
	default-dir5.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/default-dir5.cwl Branch/Commit ID: cd779a90a4336563dcf13795111f502372c6af83
	record-in-secondaryFiles-missing-wf.cwl	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/record-in-secondaryFiles-missing-wf.cwl Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3
	metabarcode (gene amplicon) analysis for fastq files protein - qc, preprocess, annotation, index, abundance	https://github.com/MG-RAST/pipeline.git Path: CWL/Workflows/metabarcode-fastq.workflow.cwl Branch/Commit ID: 4e4d2e674bde612f98f2b0370445f8b2a47587df
	protein_extract	https://github.com/ncbi/pgap.git Path: progs/protein_extract.cwl Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31