Explore Workflows

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

Graph Name Retrieved From View
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: f207d168f4e7eb4dd2279840d4062ba75d9c79c3
workflow graph tt_kmer_compare_wnode

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6
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: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca
workflow graph no-inputs-wf.cwl

Workflow without inputs.

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

Path: tests/no-inputs-wf.cwl

Branch/Commit ID: e515226f8ac0f7985cd94dae4a301150adae3050
workflow graph Filter Protein Alignments

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: 8af4e2aabf43d5e3c7162efae4ad4649df5601e2
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_mouse.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 6a55118f915e24d2ad008c93a02d9de5643f5511
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: f10de890d1d2271299931349fa8aea660acef4ee
workflow graph RNA-Seq pipeline paired-end 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 pair-end** 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 the pair-end 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-pe-dutp-mitochondrial.cwl

Branch/Commit ID: 730b40bc403263b724399a952c0f3e2d28f13519