Explore Workflows

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

Graph Name Retrieved From View
workflow graph Alignment without BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl

Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54
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