Explore Workflows

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

Graph Name Retrieved From View
workflow graph env-wf3.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl

Branch/Commit ID: 7c7615c44b80f8e76e659433f8c7875603ae0b25
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: 55b6ee46b0c9fb1c9949cd0888b388c6f11b73b1
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 708e141d99f6e5f30d9402d9f890562606a0d97e
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: ec2cf2da6c31ffedf827a0fb213b5204e172f510

Packed ID: main
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d
workflow graph step_valuefrom5_wf_v1_1.cwl

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

Path: testdata/step_valuefrom5_wf_v1_1.cwl

Branch/Commit ID: e78db9870cb744fe36674f43b3223c688e9989e1
workflow graph Task2

For CMRxRecon validation

https://github.com/CmrxRecon/CMRxRecon2024-snippets.git

Path: workflow-task2.cwl

Branch/Commit ID: 71bfacc9b005e0fd3359fcc8b466dd898a53940c
workflow graph rnaseq-pe-dutp.cwl

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

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

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: b4b7b2e7e508be5eac639f9e323d141daf714c0d
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: e238d1756f1db35571e84d72e1699e5d1540f10c
workflow graph scatter-valuefrom-wf5.cwl

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

Path: tests/scatter-valuefrom-wf5.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b