Explore Workflows

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

Graph Name Retrieved From View
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6
workflow graph umi per-lane alignment subworkflow

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07
workflow graph preprocess_vcf.cwl

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

https://github.com/david4096/OxoG-Dockstore-Tools.git

Path: preprocess_vcf.cwl

Branch/Commit ID: 6366ed398da10019b6d81a789291af6d909f28f4
workflow graph Trim Galore RNA-Seq pipeline paired-end

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** 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-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. 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 files 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/trim-rnaseq-pe.cwl

Branch/Commit ID: a1f6ca50fcb0881781b3ba0306dd61ebf555eaba
workflow graph MACE ChIP-exo peak caller workflow for single-end samples

This workflow execute peak caller and QC from ChIP-exo for single-end samples using MACE

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/ChIP-exo/peak-caller-MACE-SE.cwl

Branch/Commit ID: e1c19e64f6fc210f65472ee227786d33c9b4909a
workflow graph Create tagAlign file

This workflow creates tagAlign file

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/create-tagAlign.cwl

Branch/Commit ID: e1c19e64f6fc210f65472ee227786d33c9b4909a
workflow graph tt_fscr_calls_pass1

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6
workflow graph Seed Search Compartments

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6
workflow graph testTimeSIMLR.cwl

https://github.com/Gepiro/rCASC_StreamFlow.git

Path: setting/testTimeSIMLR.cwl

Branch/Commit ID: 130d399d0fbbbd65042d103176be67d7952ba003
workflow graph module-3.cwl

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/module-3.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf