Explore Workflows

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

Graph	Name	Retrieved From	View
	cram_to_bam workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cram_to_bam_and_index.cwl Branch/Commit ID: ddd748516b25256a461ea9277303406fa2759b00
	ani_top_n	https://github.com/ncbi/pgap.git Path: task_types/tt_ani_top_n.cwl Branch/Commit ID: add6b7724698694e0e72d972e2e85e1ae4e67902
	kmer_top_n_extract	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_top_n_extract.cwl Branch/Commit ID: dc6014dc7c1f160ec4ae3d5a57388a6dceaacbc5
	STAR-RNA-Seq alignment and transcript/gene abundance workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/rnaseq_star_fusion.cwl Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
	cnv_exomedepth CNV ExomeDepth calling	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/cwl/abstract_operations/subworkflows/cnv_exome_depth.cwl Branch/Commit ID: aaecc710f76be9285288a975cc786e354bc9bedf
	bam to trimmed fastqs and biscuit alignments	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl Branch/Commit ID: ec5355f335852e51c6938809c16ea1d230a3f983
	bacterial_orthology_cond	https://github.com/ncbi/pgap.git Path: bacterial_orthology/wf_bacterial_orthology_conditional.cwl Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
	workflow_with_facets.cwl CWL workflow for generating Roslin / Argos post pipeline analysis files and cBioPortal data and metadata files This workflow includes Facets and Facets Suite usages 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 pairs 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 ├── facets │ ├── <tumor_id>.<normal_id> (passed) │ │ └── <facets_files> │ └── <tumor_id>.<normal_id> (failed) │ └── <log_files> └── 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_with_facets.cwl Branch/Commit ID: 45604eaeea15030c7302941c761464ce392abf74
	Spectral_counting_workflow.cwl	https://github.com/adamscharlotte/CWL-workflow.git Path: Spectral_counting_workflow.cwl Branch/Commit ID: f165c14d6d2e20a5133fc42251ae565fcbe520f6
	Vcf concordance evaluation workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/vcf_eval_concordance.cwl Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d