Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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exomeseq.cwl#exomeseq-02-variantdiscovery.cwl
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https://github.com/Duke-GCB/bespin-cwl.git
Path: packed/exomeseq.cwl Branch/Commit ID: ef08cb00bd55b4c712645d171dbc691e01ed6165 Packed ID: exomeseq-02-variantdiscovery.cwl |
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count-lines7-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/count-lines7-wf.cwl Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912 |
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igv-report_maf_workflow.cwl
Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/igv-report_maf_workflow.cwl Branch/Commit ID: ba3ff09328cc646d7254b2d2ee0fbe1abca3d4ad |
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kf_alignment_fq_input_wf.cwl
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https://github.com/cr-ste-justine/chujs-alignment-workflow.git
Path: workflows/kf_alignment_fq_input_wf.cwl Branch/Commit ID: 682ec407000059b7f397e5faaeff1317af1d9402 |
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example.cwl
Example CWL workflow that uses some advanced features |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/example.cwl Branch/Commit ID: ba3ff09328cc646d7254b2d2ee0fbe1abca3d4ad |
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count-lines8-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines8-wf.cwl Branch/Commit ID: cb81b22abc52838823da9945f04d06739ab32fda |
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count-lines1-wf-noET.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/count-lines1-wf-noET.cwl Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912 |
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consensus_bed.cwl
Workflow to merge a large number of maf files into a single consensus bed file |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/consensus_bed.cwl Branch/Commit ID: ba3ff09328cc646d7254b2d2ee0fbe1abca3d4ad |
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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: ba3ff09328cc646d7254b2d2ee0fbe1abca3d4ad |
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Single-cell Multiome ATAC and RNA-Seq Analyze
Single-cell Multiome ATAC and RNA-Seq Analyze Runs filtering, normalization, scaling, integration (optionally) and clustering for a single or aggregated single-cell Multiome ATAC and RNA-Seq datasets. |
https://github.com/Barski-lab/sc-seq-analysis.git
Path: workflows/sc-multiome-analyze-wf.cwl Branch/Commit ID: 9064af1cdd8e97bcdf4473e2a741e1ada1a7c4f3 |