Explore Workflows

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Graph Name Retrieved From View
workflow graph Single-Cell Preprocessing Cell Ranger Pipeline

Devel version of Single-Cell Preprocessing Cell Ranger Pipeline ===============================================================

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

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: 57437c1e9f881411b65f79acd64b7cf14df5b901
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: 57437c1e9f881411b65f79acd64b7cf14df5b901
workflow graph scatter-valuefrom-wf1.cwl

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

Path: tests/scatter-valuefrom-wf1.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph star_align_workflow.cwl

https://github.com/NCI-GDC/gdc-rnaseq-cwl.git

Path: workflows/subworkflows/rnaseq_processing/star_align_workflow.cwl

Branch/Commit ID: f0594206c230e53ad3ad9de14364fc6bce1d5cb7
workflow graph tt_fscr_calls_pass1

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: 49732e54e2fe2eafd2f82df3c482c73e642f6d64
workflow graph scatter-valuefrom-wf1.cwl

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

Path: tests/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
workflow graph delay-calibration.cwl

https://git.astron.nl/RD/VLBI-cwl.git

Path: workflows/delay-calibration.cwl

Branch/Commit ID: df8ae840c8223132825340b439393bc39ccfa2c5
workflow graph Deprecated. RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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) 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-se-dutp.cwl

Branch/Commit ID: aebf2355539fdf81fd9082616f8b21440d2691c6
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb
workflow graph stdout-wf_v1_1.cwl

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

Path: testdata/stdout-wf_v1_1.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c