Workflow: Immunotherapy Workflow
Fetched 2023-01-10 10:36:37 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| mills | File | ||
| strand | |||
| refFlat | File | ||
| docm_vcf | File | ||
| expn_val | Float (Optional) | ||
| omni_vcf | File | ||
| rna_bams | File[] | ||
| tdna_cov | Integer (Optional) | ||
| tdna_vaf | Float (Optional) | ||
| trna_cov | Integer (Optional) | ||
| trna_vaf | Float (Optional) | ||
| vep_pick | |||
| dbsnp_vcf | File | ||
| reference | File | ||
| cosmic_vcf | File (Optional) | ||
| fasta_size | Integer (Optional) | ||
| normal_cov | Integer (Optional) | ||
| normal_vaf | Float (Optional) | ||
| tumor_name | String (Optional) | ||
| exclude_nas | Boolean (Optional) | ||
| netmhc_stab | Boolean (Optional) | ||
| normal_name | String (Optional) | ||
| sample_name | String | ||
| known_indels | File | ||
| somalier_vcf | File | ||
| gvcf_gq_bands | String[] | ||
| interval_list | File | ||
| manta_non_wgs | Boolean (Optional) | ||
| optitype_name | String (Optional) | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| clinical_calls | String[] (Optional) |
Clinical HLA typing results; element format: HLA-X*01:02[/HLA-X...] |
|
| kallisto_index | File | ||
| known_variants | File (Optional) |
Previously discovered variants to be flagged in this pipelines's output vcf |
|
| reference_dict | File | ||
| rna_readgroups | String[] | ||
| tumor_sequence | https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/sequence_data.yml#sequence_data[] | ||
| epitope_lengths | Integer[] (Optional) | ||
| net_chop_method | |||
| normal_sequence | https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/sequence_data.yml#sequence_data[] | ||
| pvacseq_threads | Integer (Optional) | ||
| reference_index | File | ||
| varscan_p_value | Float (Optional) | ||
| target_intervals | File | ||
| top_score_metric | |||
| binding_threshold | Integer (Optional) | ||
| read_group_fields | 909fb3285ac5d1d65659a63a56b57fad[] | ||
| summary_intervals | https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/labelled_file.yml#labelled_file[] | ||
| trimming_adapters | File | ||
| tumor_sample_name | String | ||
| manta_call_regions | File (Optional) | ||
| net_chop_threshold | Float (Optional) | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/labelled_file.yml#labelled_file[] | ||
| pindel_insert_size | Integer | ||
| minimum_fold_change | Float (Optional) | ||
| ribosomal_intervals | File (Optional) | ||
| vep_ensembl_species | String |
ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus |
|
| vep_ensembl_version | String |
ensembl version - Must be present in the cache directory. Example: 95 |
|
| vep_to_table_fields | String[] | ||
| annotate_coding_only | Boolean (Optional) | ||
| filter_docm_variants | Boolean (Optional) | ||
| manta_output_contigs | Boolean (Optional) | ||
| mutect_scatter_count | Integer | ||
| panel_of_normals_vcf | File (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/labelled_file.yml#labelled_file[] | ||
| reference_annotation | File | ||
| strelka_cpu_reserved | Integer (Optional) | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float (Optional) | ||
| vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
| prediction_algorithms | String[] | ||
| trimming_max_uncalled | Integer | ||
| varscan_strand_filter | Integer (Optional) | ||
| vep_custom_annotations | https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| peptide_sequence_length | Integer (Optional) | ||
| qc_minimum_base_quality | Integer (Optional) | ||
| trimming_min_readlength | Integer | ||
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| additional_report_columns | |||
| emit_reference_confidence | |||
| trimming_adapter_trim_end | String | ||
| downstream_sequence_length | String (Optional) | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| gene_transcript_lookup_table | File | ||
| phased_proximal_variants_vcf | File (Optional) | ||
| trimming_adapter_min_overlap | Integer | ||
| gatk_haplotypecaller_intervals | 5c248fb5f7454df07b8171e564a30e2f[] | ||
| mutect_artifact_detection_mode | Boolean | ||
| readcount_minimum_base_quality | Integer (Optional) | ||
| maximum_transcript_support_level | |||
| picard_metric_accumulation_level | String | ||
| readcount_minimum_mapping_quality | Integer (Optional) | ||
| variants_to_table_genotype_fields | String[] | ||
| allele_specific_binding_thresholds | Boolean (Optional) | ||
| mutect_max_alt_alleles_in_normal_count | Integer (Optional) | ||
| mutect_max_alt_allele_in_normal_fraction | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| rnaseq |
rnaseq.cwl
(Workflow)
|
RNA-Seq alignment and transcript/gene abundance workflow | |
| pvacseq |
../subworkflows/pvacseq.cwl
(Workflow)
|
Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs | |
| somatic |
somatic_exome.cwl
(Workflow)
|
somatic_exome: exome alignment and somatic variant detection |
somatic_exome is designed to perform processing of mutant/wildtype H.sapiens
exome sequencing data. It features BQSR corrected alignments, 4 caller variant
detection, and vep style annotations. Structural variants are detected via
manta and cnvkit. In addition QC metrics are run, including
somalier concordance metrics. |
| germline |
germline_exome_hla_typing.cwl
(Workflow)
|
exome alignment and germline variant detection, with optitype for HLA typing | |
| phase_vcf |
../subworkflows/phase_vcf.cwl
(Workflow)
|
phase VCF | |
| hla_consensus |
../tools/hla_consensus.cwl
(CommandLineTool)
|
Script to create consensus from optitype and clinical HLA typing | |
| extract_alleles |
../tools/extract_hla_alleles.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| gvcf | File[] | ||
| chart | File (Optional) | ||
| metrics | File | ||
| final_bam | File | ||
| final_tsv | File | ||
| flagstats | File | ||
| cn_diagram | File (Optional) | ||
| hs_metrics | File | ||
| phased_vcf | File | ||
| tumor_cram | File | ||
| normal_cram | File | ||
| optitype_tsv | File | ||
| allele_string | String[] | ||
| annotated_tsv | File | ||
| annotated_vcf | File | ||
| optitype_plot | File | ||
| all_candidates | File | ||
| gene_abundance | File | ||
| hla_call_files | Directory | ||
| cn_scatter_plot | File (Optional) | ||
| tumor_flagstats | File | ||
| diploid_variants | File (Optional) | ||
| intervals_target | File (Optional) | ||
| normal_flagstats | File | ||
| small_candidates | File | ||
| somatic_variants | File (Optional) | ||
| tumor_hs_metrics | File | ||
| consensus_alleles | String[] | ||
| docm_filtered_vcf | File | ||
| normal_hs_metrics | File | ||
| somatic_final_vcf | File | ||
| final_filtered_vcf | File | ||
| germline_final_vcf | File | ||
| mhc_i_all_epitopes | File (Optional) | ||
| reference_coverage | File (Optional) | ||
| summary_hs_metrics | File[] | ||
| insert_size_metrics | File | ||
| mhc_ii_all_epitopes | File (Optional) | ||
| mutect_filtered_vcf | File | ||
| per_base_hs_metrics | File[] | ||
| pindel_filtered_vcf | File | ||
| somatic_vep_summary | File | ||
| tumor_only_variants | File (Optional) | ||
| verify_bam_id_depth | File | ||
| germline_vep_summary | File | ||
| intervals_antitarget | File (Optional) | ||
| strelka_filtered_vcf | File | ||
| varscan_filtered_vcf | File | ||
| combined_all_epitopes | File (Optional) | ||
| germline_filtered_vcf | File | ||
| insert_size_histogram | File | ||
| mhc_i_ranked_epitopes | File (Optional) | ||
| mutect_unfiltered_vcf | File | ||
| per_target_hs_metrics | File[] | ||
| pindel_unfiltered_vcf | File | ||
| tumor_target_coverage | File | ||
| verify_bam_id_metrics | File | ||
| mhc_ii_ranked_epitopes | File (Optional) | ||
| normal_target_coverage | File | ||
| strelka_unfiltered_vcf | File | ||
| tumor_bin_level_ratios | File | ||
| tumor_segmented_ratios | File | ||
| varscan_unfiltered_vcf | File | ||
| mark_duplicates_metrics | File | ||
| mhc_i_filtered_epitopes | File (Optional) | ||
| transcript_abundance_h5 | File | ||
| combined_ranked_epitopes | File (Optional) | ||
| mhc_ii_filtered_epitopes | File (Optional) | ||
| stringtie_transcript_gtf | File | ||
| transcript_abundance_tsv | File | ||
| tumor_summary_hs_metrics | File[] | ||
| alignment_summary_metrics | File | ||
| normal_summary_hs_metrics | File[] | ||
| per_base_coverage_metrics | File[] | ||
| tumor_antitarget_coverage | File | ||
| tumor_insert_size_metrics | File | ||
| tumor_per_base_hs_metrics | File[] | ||
| tumor_verify_bam_id_depth | File | ||
| combined_filtered_epitopes | File (Optional) | ||
| normal_antitarget_coverage | File | ||
| normal_insert_size_metrics | File | ||
| normal_per_base_hs_metrics | File[] | ||
| normal_verify_bam_id_depth | File | ||
| per_target_coverage_metrics | File[] | ||
| tumor_per_target_hs_metrics | File[] | ||
| tumor_snv_bam_readcount_tsv | File | ||
| tumor_verify_bam_id_metrics | File | ||
| normal_per_target_hs_metrics | File[] | ||
| normal_snv_bam_readcount_tsv | File | ||
| normal_verify_bam_id_metrics | File | ||
| somalier_concordance_metrics | File | ||
| stringtie_gene_expression_tsv | File | ||
| tumor_indel_bam_readcount_tsv | File | ||
| tumor_mark_duplicates_metrics | File | ||
| normal_indel_bam_readcount_tsv | File | ||
| normal_mark_duplicates_metrics | File | ||
| somalier_concordance_statistics | File | ||
| tumor_alignment_summary_metrics | File | ||
| tumor_per_base_coverage_metrics | File[] | ||
| normal_alignment_summary_metrics | File | ||
| normal_per_base_coverage_metrics | File[] | ||
| tumor_per_target_coverage_metrics | File[] | ||
| normal_per_target_coverage_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/pipelines/immuno.cwl
