Explore Workflows

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

Graph Name Retrieved From View
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: 664e99a23a3ed4ba36c08323ac597c4fbcd88df1
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 664e99a23a3ed4ba36c08323ac597c4fbcd88df1
workflow graph EMG pipeline v3.0 (paired end version)

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3-paired.cwl

Branch/Commit ID: cac44f2cf14110fde9951161c663c4525772f616
workflow graph cnv_exomedepth

CNV ExomeDepth calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/abstract_operations/subworkflows/cnv_exome_depth.cwl

Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: c18a7e5164cb6b19f06b3d1e869407c118a87f7e
workflow graph allele-alignreads-se-pe.cwl

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

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

Path: subworkflows/allele-alignreads-se-pe.cwl

Branch/Commit ID: 378f693ebfb3edf9f589007e366fec1195ec1464
workflow graph super-enhancer.cwl

Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl)

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

Path: workflows/super-enhancer.cwl

Branch/Commit ID: 12edfc2207507e53c6b5bb21e50decb5535a12f7
workflow graph cnv_manta

CNV Manta calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/abstract_operations/subworkflows/cnv_manta.cwl

Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c
workflow graph trim-rnaseq-pe.cwl

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

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

Path: workflows/trim-rnaseq-pe.cwl

Branch/Commit ID: 12edfc2207507e53c6b5bb21e50decb5535a12f7
workflow graph ROSE: rank ordering of super-enhancers

Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

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

Path: workflows/super-enhancer.cwl

Branch/Commit ID: 935a78f1aff757f977de4e3672aefead3b23606b