Explore Workflows

AltAnalyze ICGS ===============

https://github.com/datirium/workflows.git

Path: workflows/altanalyze-icgs.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5

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

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: 40097e1ed094c5b42b68f3db2ff2cbe78c182479

https://github.com/ebi-wp/webservice-cwl.git

Path: workflows/workflow-fetch-hmmscan.cwl

Branch/Commit ID: 5df6b762980b15b0f6389149311b82bdd6dff37d

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

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022

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

Path: task_types/tt_blastp_wnode_struct.cwl

Branch/Commit ID: 369afa7090a7480e6a0b144eff967a4a52b6fde2

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/genomel_cohort_gatk4.cwl

Branch/Commit ID: 7f01768479e6a77a5caf6b3382174aa038ba05fc

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: 7eb2b0a4d37018142233d770595ac2e00376dab4

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 369afa7090a7480e6a0b144eff967a4a52b6fde2

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_genomicsWorkspace/genomics-workspace-genome.cwl

Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945