Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines5-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl

Branch/Commit ID: 5ae5798f1c0c8d2178986b77cfd74edff510877a
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: cc3e7f1ccfdc7101c22bf88792608504eea7d53a
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300
workflow graph HBA_target.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/HBA_target.cwl

Branch/Commit ID: a94862bb3d50860cd348a5d5d1aa76fa0cde332a
workflow graph HBA_calibrator.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/HBA_calibrator.cwl

Branch/Commit ID: a94862bb3d50860cd348a5d5d1aa76fa0cde332a
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: 6a55118f915e24d2ad008c93a02d9de5643f5511
workflow graph Dockstore.cwl

https://github.com/kathy-t/ghapps-single-workflow.git

Path: Dockstore.cwl

Branch/Commit ID: 996eb844118edb805f557ea1dcaf82677fc6f693
workflow graph RNA-Seq pipeline single-read

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **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.cwl

Branch/Commit ID: 4dcc405133f22c63478b6091fb5f591b6be8950f
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: f401b02285f30de1c12ac2859134099fe04be33f
workflow graph md5sum.cwl

https://github.com/dockstore-testing/dockstore-workflow-md5sum-unified.git

Path: md5sum/md5sum.cwl

Branch/Commit ID: 3a604c0e70b2dc62973917cc186dc6db5a6ce519