Explore Workflows

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

Graph Name Retrieved From View
workflow graph search.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/search.cwl

Branch/Commit ID: 1eb6bfe3c77aebaf69453a669d21ae7a5a78056f

Packed ID: main
workflow graph RNA-Seq pipeline paired-end strand specific

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe-dutp.cwl

Branch/Commit ID: 3fc68366adb179927af5528c27b153abaf94494d
workflow graph Nested workflow example

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

Path: tests/wf/nested.cwl

Branch/Commit ID: 0184e647cde1bc44279107d6df31b3ebb138769c
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: a2d6cd4c53bf3501f6bd79edebb7ca30bba8456f
workflow graph default_with_falsey_value.cwl

reproduces https://github.com/DataBiosphere/toil/issues/3141

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

Path: tests/default_with_falsey_value.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
workflow graph scatter-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl

Branch/Commit ID: 3ed10d0ea7ac57550433a89a92bdbe756bdb0e40
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 7b21dc40840852f3942c31b9c472346ea3f9a3ca
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 122aba2dafbb63241413c82b725b877c04523aaf