Explore Workflows

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

Graph Name Retrieved From View
workflow graph workflow_input_sf_expr_array.cwl

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

Path: testdata/workflow_input_sf_expr_array.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0
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 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.cwl

Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e
workflow graph count-lines12-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines12-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph SetMirrorPanelAlignment

Derive mirror panel alignment parameters from measurements of the optical point-spread functions.

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

Path: workflows/SetMirrorPanelAlignment.cwl

Branch/Commit ID: bf4d4a44a543bcc04f4508ce020751c71550acf5
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e
workflow graph trim-rnaseq-se-dutp.cwl

Runs RNA-Seq dUTP BioWardrobe basic analysis with strand specific single-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: de847468843203ce92b6d19323c5fe77dc488e34
workflow graph WF6101.cwl

https://github.com/Marco-Salvi/dtc61.git

Path: WF6101.cwl

Branch/Commit ID: f435de822bbe32648738934700d340ba29dea215
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e