Explore Workflows

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

Graph Name Retrieved From View
workflow graph default-dir5.cwl

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

Path: tests/wf/default-dir5.cwl

Branch/Commit ID: 7bfe73a708dbf31d037303bb5a8fed1a79984b0f
workflow graph directory.cwl

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

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

Path: tests/wf/directory.cwl

Branch/Commit ID: 691dea280b40ac177b4a38b33375139ca0ce7e81
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph FastQC - a quality control tool for high throughput sequence data

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

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

Path: workflows/fastqc.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 9144d08fa7f4e852498761481dceab477167fa65
workflow graph rnaseq-pe.cwl

Runs RNA-Seq BioWardrobe basic analysis with pair-end data file.

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

Path: workflows/rnaseq-pe.cwl

Branch/Commit ID: 852fa49a70fe0965de6892fa0832f30b710f0e75
workflow graph rnaseq-se.cwl

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

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

Path: workflows/rnaseq-se.cwl

Branch/Commit ID: 852fa49a70fe0965de6892fa0832f30b710f0e75
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: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph Pairwise genomic regions intersection

Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments

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

Path: workflows/peak-intersect.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895