Explore Workflows

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

Graph Name Retrieved From View
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
workflow graph exomeseq-02-variantdiscovery.cwl

https://github.com/duke-gcb/bespin-cwl.git

Path: subworkflows/exomeseq-02-variantdiscovery.cwl

Branch/Commit ID: bbe24d8d7fde2e918583b96805909a2867b749d6
workflow graph count-lines4-wf.cwl

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

Path: v1.0/v1.0/count-lines4-wf.cwl

Branch/Commit ID: 17695244222b0301b37cb749fe4a8d89622cd1ad
workflow graph Trim Galore 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 **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow must be used with paired-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 2 (after running STAR) 5. Generate BigWig file using 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.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph umi molecular alignment fastq workflow

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

Path: definitions/pipelines/umi_molecular_alignment.cwl

Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c
workflow graph step_valuefrom5_wf_with_id_v1_2.cwl

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

Path: testdata/step_valuefrom5_wf_with_id_v1_2.cwl

Branch/Commit ID: 124a08ce3389eb49066c34a4163cbbed210a0355
workflow graph Seurat for comparative scRNA-seq analysis of across experimental conditions

Runs Seurat for comparative scRNA-seq analysis of across experimental conditions ================================================================================

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

Path: workflows/seurat-cluster.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph optional_src_mandatory_sink.cwl

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

Path: tests/wf/optional_src_mandatory_sink.cwl

Branch/Commit ID: f94719e862f86cc88600caf3628faba6c0d05042
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: f5a467a21b8f69aef5666fb7bbf35efd98c0cbea
workflow graph Filter ChIP/ATAC/cut&run/diffbind peaks for Tag Density Profile or Motif Enrichment analyses

Filters ChIP/ATAC/cut&run/diffbind peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC/cut&run/diffbind pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.

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

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

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3