Explore Workflows

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

Graph Name Retrieved From View
workflow graph scatter-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf1.cwl

Branch/Commit ID: e8b3565a008d95859fc44227987a54e6a53a8c29
workflow graph schemadef_types_with_import-wf.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/schemadef_types_with_import-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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 file 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/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: 87f213456b3f966b773d396cce1fe5a272dad858
workflow graph step-valuefrom3-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl

Branch/Commit ID: 5ae5798f1c0c8d2178986b77cfd74edff510877a
workflow graph Single-Cell WNN Cluster Analysis

Single-Cell WNN Cluster Analysis Clusters cells by similarity on the basis of both gene expression and chromatin accessibility data from the outputs of the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” and “Single-Cell ATAC-Seq Dimensionality Reduction Analysis” pipelines run sequentially. The results of this workflow are used in the “Single-Cell Manual Cell Type Assignment”, “Single-Cell RNA-Seq Differential Expression Analysis”, “Single-Cell RNA-Seq Trajectory Analysis”, “Single-Cell Differential Abundance Analysis”, “Single-Cell ATAC-Seq Differential Accessibility Analysis”, and “Single-Cell ATAC-Seq Genome Coverage” pipelines.

 https://github.com/datirium/workflows.git

Path: workflows/sc-wnn-cluster.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6
workflow graph exome alignment and tumor-only variant detection

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

Path: definitions/pipelines/exome.cwl

Branch/Commit ID: ddb49a0951d9ad537269d7db3fe8f904495a8bf4
workflow graph Filter differentially expressed genes from DESeq for Tag Density Profile Analyses

Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.

https://github.com/datirium/workflows.git

Path: workflows/filter-deseq-for-heatmap.cwl

Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd
workflow graph Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

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

Path: definitions/pipelines/pvacseq.cwl

Branch/Commit ID: ddb49a0951d9ad537269d7db3fe8f904495a8bf4