Explore Workflows

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

Graph Name Retrieved From View
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: be9d12a3f8e1924183a1dc6a0bda6ada4195ca71
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: be9d12a3f8e1924183a1dc6a0bda6ada4195ca71
workflow graph scatter-valuefrom-wf3.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl

Branch/Commit ID: 65aedc5e7e1f3ccace7f9022f8a54b3f0d5c9a8c

Packed ID: main
workflow graph cache_test_workflow.cwl

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

Path: tests/wf/cache_test_workflow.cwl

Branch/Commit ID: cd1ba3df3745fba4b635f05c67ebeaf3b8a9f4ec
workflow graph rnaseq-se-dutp-mitochondrial.cwl

RNA-Seq strand specific mitochondrial workflow for single-read experiment based on BioWardrobe's basic analysis.

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

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

Branch/Commit ID: 3ceeb2e90f49579369b2e10485908516348381a9
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: dda9e6e06a656b7b3fa7504156474b962fe3953c
workflow graph Single-Cell Preprocessing Pipeline

Devel version of Single-Cell Preprocessing Pipeline ===================================================

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

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph WGS QC workflow mouse

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

Path: definitions/subworkflows/qc_wgs_mouse.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 3e7a3c1cc1ed5164ae0a51a96f20d7c480d1d70b
workflow graph PGAP Pipeline, simple user input, PGAPX-134

PGAP pipeline for external usage, powered via containers, simple user input: (FASTA + yaml only, no template)

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

Path: pgap.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8