Workflow: workflow_with_facets.cwl
Fetched 2024-11-21 13:14:10 GMT
Verified with cwltool version 3.1.20230201224320
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_sv.txt ├── data_fusions.txt ├── data_mutations_extended.txt ├── meta_clinical_patient.txt ├── meta_clinical_sample.txt ├── meta_CNA.txt ├── meta_sv.txt ├── meta_fusions.txt ├── meta_mutations_extended.txt ├── meta_study.txt ├── <project_id>_data_cna_hg19.seg └── <project_id>_meta_cna_hg19_seg.txt
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| pairs | https://w3id.org/cwl/view/git/59b69eed7ffefcffd81313ec8ffb84c0d716b933/cwl/types.yml#TNMafPileupPair[] |
list of tumor normal sample pairs |
|
| is_impact | Boolean |
whether or not the project is an IMPACT project; should be the value 'True' if so, otherwise any other value means 'False' |
|
| project_id | String |
unique identifier for the project |
|
| project_pi | String |
principle investigator for the project |
|
| request_pi | String |
principle investigator who requested the project |
|
| cancer_type | String |
the type of cancer used in the project |
|
| project_name | String |
a formal name for the project |
|
| targets_list | File | ||
| assay_coverage | String |
genome_coverage value; amount of the genome in bp covered by the assay |
|
| extra_cna_files | File[] (Optional) |
Extra CNA data files to be merged in with the portal CNA data |
|
| extra_pi_groups | String (Optional) |
a list of other groups to be associated with the project in cBioPortal |
|
| tumor_bam_files | File[] |
Array of tumor bam files. Must match the same order of sample pairs in 'pairs' input field |
|
| IMPACT_gene_list | File |
TSV file with gene labels and corresponding impact assays |
|
| extra_sample_ids | String[] (Optional) |
Extra sample ids that should be included in case list files |
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| normal_bam_files | File[] |
Array of normal bam files. Must match the same order of sample pairs in 'pairs' input field |
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| data_clinical_file | File | ||
| known_fusions_file | File | ||
| project_short_name | String |
a short name for the project in cBioPortal |
|
| project_description | String |
a description of the project |
|
| sample_summary_file | File (Optional) | ||
| analysis_sv_filename | String |
<project_id>.svs.maf |
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| argos_version_string | String |
the version label of Roslin / Argos used to run the project analysis |
|
| helix_filter_version | String |
the version label of this helix filter repo (git describe --all --long) |
|
| microsatellites_file | File |
Microsatellites list file to use with MSI Sensor |
|
| cbio_meta_sv_filename | String | ||
| cbio_sv_data_filename | String | ||
| cbio_cna_data_filename | String | ||
| cbio_meta_cna_filename | String | ||
| mutation_svs_maf_files | File[] |
*.svs.pass.vep.maf |
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| mutation_svs_txt_files | File[] |
*.svs.pass.vep.portal.txt |
|
| cancer_study_identifier | String |
a study identifier for the project to use in cBioPortal |
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| cbio_cases_all_filename | String | ||
| cbio_cases_cna_filename | String | ||
| cbio_meta_study_filename | String | ||
| cbio_fusion_data_filename | String | ||
| analysis_gene_cna_filename | String |
<project_id>.gene.cna.txt |
|
| cbio_cases_cnaseq_filename | String | ||
| cbio_meta_fusions_filename | String | ||
| cbio_segment_data_filename | String |
<project_id>_data_cna_hg19.seg |
|
| analysis_mutations_filename | String |
<project_id>.muts.maf |
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| cbio_cna_scna_data_filename | String | ||
| cbio_mutation_data_filename | String | ||
| cbio_cna_ascna_data_filename | String | ||
| cbio_meta_mutations_filename | String | ||
| analysis_segment_cna_filename | String |
<project_id>.seg.cna.txt |
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| cbio_cases_sequenced_filename | String | ||
| cbio_meta_cna_segments_filename | String |
<project_id>_meta_cna_hg19_seg.txt |
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| analysis_mutations_share_filename | String |
<project_id>.muts.share.maf |
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| cbio_clinical_sample_data_filename | String | ||
| cbio_clinical_sample_meta_filename | String | ||
| cbio_clinical_patient_data_filename | String | ||
| cbio_clinical_patient_meta_filename | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| run_msi |
msi_workflow.cwl
(Workflow)
|
Workflow to run the MSI analysis on a batch of samples |
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| merge_maf |
update_cBioPortal_data.cwl
(CommandLineTool)
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||
| run_facets |
facets-workflow.cwl
(Workflow)
|
Workflow for running Facets-suite on a set of tumor normal pairs
This workflow scatters over all the pairs in the input JSON to run all samples in parallel
Input JSON format -----------------
{ \"pairs\": [ { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal1.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.Normal1.maf\" }, \"pair_id\": \"Tumor1.Normal1\" }, { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal2.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.Normal2.maf\" }, \"pair_id\": \"Tumor2.Normal2\" } ] } |
|
| gather_msi_tsvs |
688c2b3cc756bc5b09c6eb48579960ca
(ExpressionTool)
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| gather_tmb_tsvs |
bb6b6286ac57c5c9d95b01c63c9122bb
(ExpressionTool)
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| make_facets_dir |
e2e76fd6ecbf6a25f9c50bf08d25452b
(Workflow)
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| run_tmb_workflow |
tmb_workflow.cwl
(Workflow)
|
Workflow to run the TMB analysis on a batch of samples and merge the results back into a single data clinical file |
|
| concat_facets_maf |
concat-tables.cwl
(CommandLineTool)
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| convert_msi_pairs |
convert_TNMafPileupPair_to_MSIInputPair.cwl
(ExpressionTool)
|
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| convert_tmb_pairs |
convert_TNMafPileupPair_to_TMBInputPair.cwl
(ExpressionTool)
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| gather_facets_files |
6e3869bac4b85376f5cdb860c9bae567
(ExpressionTool)
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| run_portal_workflow |
portal-workflow.cwl
(Workflow)
|
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| run_analysis_workflow |
analysis-workflow.cwl
(Workflow)
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Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| msi_dir | Directory | ||
| tmb_dir | Directory | ||
| facets_dir | Directory | ||
| portal_dir | Directory | ||
| analysis_dir | Directory |
https://w3id.org/cwl/view/git/59b69eed7ffefcffd81313ec8ffb84c0d716b933/cwl/workflow_with_facets.cwl
