Explore Workflows

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

Graph Name Retrieved From View
workflow graph gathered exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle_gathered.cwl

Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f
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: 10ce6e113f749c7bd725e426445220c3bdc5ddf1
workflow graph Create Genomic Collection for Bacterial Pipeline

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

Path: genomic_source/wf_genomic_source.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f
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: 3247592a89deafaa0d9c5910a1cb1d000ef9b098
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f
workflow graph rnaseq-alignment-quantification

This workflow retrieve SRA fastqc data and execute QC, alignment and quantification from TPMCalculator

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

Path: workflows/RNA-Seq/rnaseq-alignment-quantification.cwl

Branch/Commit ID: 3247592a89deafaa0d9c5910a1cb1d000ef9b098
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f
workflow graph Unaligned to aligned BAM

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e