Explore Workflows

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

Graph Name Retrieved From View
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 42df0c0f9a4e5697abadd9cb52440691fafc8f5d
workflow graph Hello World

Outputs a message using echo

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

Path: tests/wf/hello-workflow.cwl

Branch/Commit ID: 31aa094dce60cbb176229d6b918bfd5ae09c0390
workflow graph checkm

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

Path: checkm/wf_checkm.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e
workflow graph Cell Ranger Aggregate (RNA, RNA+VDJ)

Cell Ranger Aggregate (RNA, RNA+VDJ) Combines outputs from multiple runs of either “Cell Ranger Count (RNA)” or “Cell Ranger Count (RNA+VDJ)” pipelines. The results of this workflow are primarily used in “Single-Cell RNA-Seq Filtering Analysis” and “Single-Cell Immune Profiling Analysis” pipelines.

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

Path: workflows/cellranger-aggr.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph Build Bowtie indices

Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome

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

Path: workflows/bowtie-index.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph spurious_annot pass2

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

Path: spurious_annot/wf_spurious_annot_pass2.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e
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: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
workflow graph directory.cwl

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

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

Path: tests/wf/directory.cwl

Branch/Commit ID: e2ec740fccc81ff7071dcd607c5c158fbc0dfb90
workflow graph rnaseq-se.cwl

Runs RNA-Seq BioWardrobe basic analysis with single-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/rnaseq-se.cwl

Branch/Commit ID: 144eee15187c1a1145ce1ee0239da69059fd2752
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2