Explore Workflows
View already parsed workflows here or click here to add your own
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ldv_linc_target.cwl
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https://git.astron.nl/RD/LINC.git
Path: workflows/ldv_linc_target.cwl Branch/Commit ID: aa447a214b0be934805d1c751e4ce91f79b8922b |
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Bacterial Annotation, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_2nd_pass.cwl Branch/Commit ID: 192b813eed8c0d368e69057cb39415175dd15128 |
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count-lines12-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines12-wf.cwl Branch/Commit ID: a0f7d43bbc706af2a844be93fc19b2e4e4da626c |
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Chipseq alignment for mouse with qc and creating homer tag directory
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/chipseq_alignment_mouse.cwl Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb |
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count-lines12-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines12-wf.cwl Branch/Commit ID: 0db44e3c9805a070564f954222efff71cd791b70 |
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workflow.cwl
CWL workflow for generating Roslin / Argos post pipeline analysis files and cBioPortal data and metadata files Inputs ------ The following parameters are required: project_id project_pi request_pi project_short_name project_name project_description cancer_type cancer_study_identifier argos_version_string helix_filter_version is_impact extra_pi_groups The following filenames are required: analysis_mutations_filename analysis_gene_cna_filename analysis_sv_filename analysis_segment_cna_filename cbio_segment_data_filename cbio_meta_cna_segments_filename The following filenames have default values and are optional: cbio_mutation_data_filename cbio_cna_data_filename cbio_fusion_data_filename cbio_clinical_patient_data_filename cbio_clinical_sample_data_filename cbio_clinical_sample_meta_filename cbio_clinical_patient_meta_filename cbio_meta_study_filename cbio_meta_cna_filename cbio_meta_fusions_filename cbio_meta_mutations_filename cbio_cases_all_filename cbio_cases_cnaseq_filename cbio_cases_cna_filename cbio_cases_sequenced_filename Output ------ Workflow output should look like this: output ├── analysis │ ├── <project_id>.gene.cna.txt │ ├── <project_id>.muts.maf │ ├── <project_id>.seg.cna.txt │ └── <project_id>.svs.maf └── portal ├── case_list │ ├── cases_all.txt │ ├── cases_cnaseq.txt │ ├── cases_cna.txt │ └── cases_sequenced.txt ├── data_clinical_patient.txt ├── data_clinical_sample.txt ├── data_CNA.ascna.txt ├── data_CNA.scna.txt ├── data_CNA.txt ├── data_fusions.txt ├── data_mutations_extended.txt ├── meta_clinical_patient.txt ├── meta_clinical_sample.txt ├── meta_CNA.txt ├── meta_fusions.txt ├── meta_mutations_extended.txt ├── meta_study.txt ├── <project_id>_data_cna_hg19.seg └── <project_id>_meta_cna_hg19_seg.txt |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/workflow.cwl Branch/Commit ID: 2a88d5c2d139ff817b21b480ccf9c1cd7139b00c |
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concat.cwl
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https://github.com/mskcc/pluto-cwl.git
Path: cwl/concat.cwl Branch/Commit ID: 2a88d5c2d139ff817b21b480ccf9c1cd7139b00c |
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default-wf5.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/default-wf5.cwl Branch/Commit ID: 17268d1493d9e558113b2c35c0be6b3fb961b2a3 |
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Run genomic CMsearch (Rfam rRNA)
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https://github.com/ncbi/pgap.git
Path: bacterial_ncrna/wf_gcmsearch.cwl Branch/Commit ID: 192b813eed8c0d368e69057cb39415175dd15128 |
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facet_subtract.cwl
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https://git.astron.nl/RD/VLBI-cwl.git
Path: workflows/facet_subtract.cwl Branch/Commit ID: a58fba4c1343bed66a5b47ea6a197b0385dfd39a |
