Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines1-wf.cwl

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

Path: tests/wf/count-lines1-wf.cwl

Branch/Commit ID: 83038feb2a6fc3bab952e1ecc2a11bfbc8c557b4
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

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

Path: definitions/pipelines/alignment_exome_nonhuman.cwl

Branch/Commit ID: 8c4e7372247a7f4ed9ed478ef8ea1d239bc88af0
workflow graph BD Rhapsody™ WTA Analysis Pipeline

The BD Rhapsody™ WTA Analysis Pipeline is used to create sequencing libraries from single cell transcriptomes without having to specify a targeted panel. After sequencing, the analysis pipeline takes the FASTQ files, a reference genome file and a transcriptome annotation file for gene alignment. The pipeline generates molecular counts per cell, read counts per cell, metrics, and an alignment file.

 https://github.com/longbow0/cwl.git

Path: v1.8/rhapsody_wta_1.8.cwl

Branch/Commit ID: b9ec66d82bc04934fbe9f9088ae7e802d72c4a4e

Packed ID: main
workflow graph Apply filters to VCF file

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/subworkflows/filter_vcf_mouse.cwl

Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 2229f26ec424f9ebeb3db7fec3bd3f84a38c7485
workflow graph wf_rescue_ratio_2inputs.cwl

Calculates the rescue ratio (see Gabe's protocols paper), given two eCLIP IP samples and 2 size-matched input samples. Also returns the reproducible peaks given these two samples. This is different from the 1input workflow in that each INPUT is first merged together and is used downstream instead of the 1input version, which remains unmodified. Merged inputs are NOT used in calculating true reproducible peaks.

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_rescue_ratio_2inputs.cwl

Branch/Commit ID: 18933d4d4b00e97a8a0d155abbebad1fdbc254aa
workflow graph wf_self_consistency_ratio.cwl

Computes the self-consistency ratio (see Gabe's protocols paper, or CHIP SEQ). Given two replicates, split each and perform IDR on each fragment. Returns the ratio of max(N1, N2)/min(N1, N2) where N1, N2 are the numbers of reproducible peaks found between each rep split pair.

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_self_consistency_ratio.cwl

Branch/Commit ID: 18933d4d4b00e97a8a0d155abbebad1fdbc254aa
workflow graph exome alignment and tumor-only variant detection

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/pipelines/tumor_only_exome.cwl

Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: 39ac49f5d080bbb6bfa97246f46a5b621254f622
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 39ac49f5d080bbb6bfa97246f46a5b621254f622