Explore Workflows

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

Graph Name Retrieved From View
workflow graph prep.cwl

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

Path: workflows/linc_target/prep.cwl

Branch/Commit ID: 1e91001f761abbddeb2c9f4528ed4cec41d113f3
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 9a657bc8c462542dc7f57fba9e04dc1669f966ba
workflow graph main.cwl

https://github.com/alpha-unito/streamflow-fl.git

Path: cwl/main.cwl

Branch/Commit ID: 21b6baeb5f4161a790f3b47413f55dddbc20797d
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 4aba7c6591c2f1ebd827a36d325a58738c429bea
workflow graph protein annotation

Proteins - predict, cluster, identify, annotate

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/protein-annotation.workflow.cwl

Branch/Commit ID: f906212e2c9a88280ae36545e5422f25752aa8f4
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: 4b73bfeb967ee9f57a0410276f7c39e784f0846f
workflow graph Trim Galore RNA-Seq pipeline paired-end strand specific

Modified 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 should be used only with the single-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 1 (after running STAR) 5. Generate BigWig file on the base of 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-dutp.cwl

Branch/Commit ID: 2caa50434966ebdf4b33e5ca689c2e4df32f9058
workflow graph conflict-wf.cwl#collision

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

Path: tests/conflict-wf.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2

Packed ID: collision
workflow graph workflow_input_sf_expr_array_v1_2.cwl

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

Path: testdata/workflow_input_sf_expr_array_v1_2.cwl

Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94