Explore Workflows

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

Graph Name Retrieved From View
workflow graph Apply filters to VCF file

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/filter_vcf_mouse.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315
workflow graph RNA-Seq pipeline paired-end

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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/rnaseq-pe.cwl

Branch/Commit ID: bfa3843bcf36125ff258d6314f64b41336f06e6b
workflow graph blastp_wnode_naming

https://github.com/ncbi/pgap.git

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: f18c1dce463509170ee3bf2844d5a3637ff706f5
workflow graph scatter-valuefrom-wf6.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf6.cwl

Branch/Commit ID: a3d565bf8e630101d25d31804cfbceb0a0ba28de
workflow graph env-wf2.cwl

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/env-wf2.cwl

Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e
workflow graph format_rrnas_from_seq_entry

https://github.com/ncbi/pgap.git

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 803f6367d1b279a7b6dc1a4e8ae43f1bbec9f760
workflow graph assm_assm_blastn_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 61e3752f1f5e2ee498fa024c235226f8580be942
workflow graph WGS QC workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 1560e7817fdb71d58aca7f98aba68809d840ade1
workflow graph count-lines12-wf.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines12-wf.cwl

Branch/Commit ID: aaaece1c097c3f06afa21f7ecddcc85519e2bb2b
workflow graph scatter-valuefrom-wf2.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-valuefrom-wf2.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3