Explore Workflows

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

Graph Name Retrieved From View
workflow graph Cell Ranger Aggregate

Cell Ranger Aggregate =====================

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

Path: workflows/cellranger-aggr.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be
workflow graph FastQC - a quality control tool for high throughput sequence data

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

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

Path: workflows/fastqc.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be
workflow graph workflow.cwl

https://github.com/reanahub/reana-demo-cms-h4l.git

Path: workflow/workflow.cwl

Branch/Commit ID: 05f6f04fc3eef5bef3bd1d6b147c81040003340b
workflow graph 03-map-se.cwl

ATAC-seq 03 mapping - reads: SE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/03-map-se.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134
workflow graph pipeline-pe-blacklist-removal.cwl

ATAC-seq pipeline - reads: PE - with blacklist removal

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 42df0c0f9a4e5697abadd9cb52440691fafc8f5d
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be
workflow graph chipseq-gen-bigwig.cwl

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

Path: subworkflows/chipseq-gen-bigwig.cwl

Branch/Commit ID: 3ceeb2e90f49579369b2e10485908516348381a9
workflow graph taxcheck.cwl

Perform taxonomic identification tasks on an input genome

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

Path: taxcheck.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
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: 8049a781ac4aae579fbd3036fa0bf654532f15be