Explore Workflows

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

Graph Name Retrieved From View
workflow graph strelka workflow

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

Path: definitions/subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: 86fbeb95ef85111f3b4c6bc2bba8f06cef64e157
workflow graph Align reference proteins plane complete workflow

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: aa64bf6a90e0780ab564de865dbb027df98c0a01
workflow graph count-lines6-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: a858bb4db58ef2df17b4856294ad7904643c5c6e
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: af468ae34c82dc88399aeedfd8f12f1e87052367
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: f5a467a21b8f69aef5666fb7bbf35efd98c0cbea
workflow graph any-type-compat.cwl

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

Path: cwltool/schemas/v1.0/v1.0/any-type-compat.cwl

Branch/Commit ID: cd779a90a4336563dcf13795111f502372c6af83
workflow graph Subworkflow to allow calling cnvkit with cram instead of bam files

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph RNA-Seq pipeline single-read stranded mitochondrial

Slightly changed 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. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-mitochondrial.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: cc7fb3e5c534036638921878527a610fd5e1c2ab
workflow graph count-lines12-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines12-wf.cwl

Branch/Commit ID: 49cd284a8fc7884de763573075d3e1d6a4c1ffdd