Explore Workflows

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Graph Name Retrieved From View
workflow graph bacterial_orthology

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

Path: bacterial_orthology/wf_bacterial_orthology.cwl

Branch/Commit ID: 1e7aa9f0c34987ddafa35f9b1d2c77d99fafbdab
workflow graph Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass1.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
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: aedc0a14d4ba109ee65678a3201a52c5bb6ad473
workflow graph exome alignment with qc

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

Path: definitions/pipelines/alignment_exome.cwl

Branch/Commit ID: 9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e
workflow graph readme-assembly-workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_create_readme/readme-assembly-workflow.cwl

Branch/Commit ID: 0b58c250e8ab7c5efae29443f08ea74316127041
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 509938802c5e42bb8084c6a5a26ab6425c60e69a
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 33414c888997d558bdcb558ca33c3a728a3e6143
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph wf_get_peaks_scatter_se.cwl

The \"main\" workflow. Takes fastq files generated using the seCLIP protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991800/) and outputs candidate RBP binding regions (peaks). runs: wf_get_peaks_se.cwl through scatter across multiple samples.

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

Path: cwl/wf_get_peaks_scatter_se.cwl

Branch/Commit ID: b389f7fe3e76cb6e3f31c3a8e2e3b59bb400e74c