Explore Workflows

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

Graph Name Retrieved From View
workflow graph step-valuefrom2-wf_v1_1.cwl

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

Path: testdata/step-valuefrom2-wf_v1_1.cwl

Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51
workflow graph rnaseq-se.cwl

RNA-Seq basic analysis workflow for single-read experiment.

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

Path: workflows/rnaseq-se.cwl

Branch/Commit ID: e284e3f6dff25037b209895c52f2abd37a1ce1bf
workflow graph io-union-input-default-wf.cwl

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

Path: tests/io-union-input-default-wf.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph env-wf2.cwl

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

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

Branch/Commit ID: fd6e054510e2bb65eed4069a3a88013d7ecbb99c
workflow graph download_gtf.cwl

https://github.com/yyoshiaki/VIRTUS.git

Path: workflow/download_gtf.cwl

Branch/Commit ID: d6a84da399d10d2386a5036a050fbb8d24b31caa
workflow graph RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific 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-dutp.cwl

Branch/Commit ID: 9b4dc225c537685b9c9a32d931d3892d20953dd7
workflow graph simple_two_step.cwl

https://github.com/ncbi/cwl-demos.git

Path: blast-pipelines/simple_two_step.cwl

Branch/Commit ID: 6e5f11a9e5a136deb39d4798da9c7cf28b912eae
workflow graph FASTQ to BQSR

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: d297528e53b6c1ecb69b1ab27b8e03323b4463ad
workflow graph Unaligned BAM to BQSR and VCF

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

Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl

Branch/Commit ID: dc2c019c1aa24cc01b451a0f048cf94a35f163c4