Workflow: mutect2_calling.cwl
Fetched 2025-01-16 03:21:41 GMT
Verified with cwltool version 3.1.20230201224320
GATK4.1.2 Mutect2 workflow
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer | ||
| pedigree | File (Optional) | ||
| intervals | File | ||
| java_heap | String | ||
| kmer_size | Integer (Optional) | ||
| reference | File | ||
| tumor_bam | File | ||
| bam_output | Boolean | ||
| has_normal | Integer[] | ||
| normal_bam | File (Optional) | ||
| normal_lod | Float (Optional) | ||
| showHidden | Boolean (Optional) | ||
| f1r2_min_bq | Integer (Optional) | ||
| f1r2_tar_gz | Boolean | ||
| min_pruning | Integer (Optional) | ||
| force_active | Boolean (Optional) | ||
| pcr_snv_qual | Integer (Optional) | ||
| gvcf_lod_band | Float (Optional) | ||
| output_prefix | String | ||
| callable_depth | Integer (Optional) | ||
| f1r2_max_depth | Integer (Optional) | ||
| f1r2_median_mq | Integer (Optional) | ||
| pcr_indel_qual | Integer (Optional) | ||
| smith_waterman | String (Optional) | ||
| bam_writer_type | String (Optional) | ||
| chunk_java_heap | String | ||
| pcr_indel_model | String (Optional) | ||
| max_mnp_distance | Integer (Optional) | ||
| panel_of_normals | File (Optional) | ||
| germline_resource | File (Optional) | ||
| initial_tumor_lod | Float (Optional) | ||
| max_population_af | Float (Optional) | ||
| mitochondria_mode | Boolean (Optional) | ||
| tumor_lod_to_emit | Float (Optional) | ||
| genotype_pon_sites | Boolean (Optional) | ||
| downsampling_stride | Integer (Optional) | ||
| emit_ref_confidence | String (Optional) | ||
| num_pruning_samples | Integer (Optional) | ||
| ignore_itr_artifacts | Boolean (Optional) | ||
| interval_merging_rule | String (Optional) | ||
| max_unpruned_variants | Integer (Optional) | ||
| pruning_lod_threshold | Float (Optional) | ||
| sites_only_vcf_output | Boolean (Optional) | ||
| enable_all_annotations | Boolean (Optional) | ||
| min_base_quality_score | Integer (Optional) | ||
| assembly_region_padding | Integer (Optional) | ||
| genotype_germline_sites | Boolean (Optional) | ||
| minimum_allele_fraction | Float (Optional) | ||
| native_pair_hmm_threads | Integer (Optional) | ||
| pair_hmm_implementation | String (Optional) | ||
| disable_adaptive_pruning | Boolean (Optional) | ||
| dont_trim_active_regions | Boolean (Optional) | ||
| max_assembly_region_size | Integer (Optional) | ||
| min_assembly_region_size | Integer (Optional) | ||
| disable_bam_index_caching | Boolean (Optional) | ||
| genotype_filtered_alleles | Boolean (Optional) | ||
| min_dangling_branch_length | Integer (Optional) | ||
| dont_use_soft_clipped_bases | Boolean (Optional) | ||
| active_probability_threshold | Float (Optional) | ||
| base_quality_score_threshold | Integer (Optional) | ||
| af_of_alleles_not_in_resource | Float (Optional) | ||
| allow_non_unique_kmers_in_ref | Boolean (Optional) | ||
| max_prob_propagation_distance | Integer (Optional) | ||
| max_reads_per_alignment_start | Integer (Optional) | ||
| recover_all_dangling_branches | Boolean (Optional) | ||
| disable_tool_default_annotations | Boolean (Optional) | ||
| max_num_haplotypes_in_population | Integer (Optional) | ||
| pair_hmm_gap_continuation_penalty | Integer (Optional) | ||
| adaptive_pruning_initial_error_rate | Float (Optional) | ||
| dont_increase_kmer_sizes_for_cycles | Boolean (Optional) | ||
| native_pair_hmm_use_double_precision | Boolean (Optional) | ||
| disable_sequence_dictionary_validation | Boolean (Optional) | ||
| max_suspicious_reads_per_alignment_start | Integer (Optional) | ||
| phred_scaled_global_read_mismapping_rate | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| merge_vcfs |
../tools/filter_mutect2/merge_vcf.cwl
(CommandLineTool)
|
||
| mutect2_calling |
../tools/filter_mutect2/gatk4_multithread_mutect2.cwl
(CommandLineTool)
|
||
| merge_mutect2_stats |
../tools/filter_mutect2/merge_mutect_stats.cwl
(CommandLineTool)
|
||
| get_normal_sample_name |
../tools/filter_mutect2/get_sample_name.cwl
(CommandLineTool)
|
||
| learn_read_orientation_model |
../tools/filter_mutect2/learn_read_orientation_model.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| mutect2_vcf | File | ||
| mutect2_stats | File | ||
| mutect2_artifacts_priors | File | ||
| mutect2_reassembly_bamouts | File[] (Optional) |
Permalink:
https://w3id.org/cwl/view/git/0debfe681fc16cfee943d799dcebc7fe4bb82495/subworkflows/mutect2_calling.cwl
