Workflow: exome alignment and somatic variant detection
Fetched 2025-02-16 14:17:35 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 | ||
| docm_vcf | File | ||
| omni_vcf | File | ||
| vep_pick | |||
| dbsnp_vcf | File | ||
| reference | File | ||
| cosmic_vcf | File (Optional) | ||
| tumor_name | String (Optional) | ||
| normal_name | String (Optional) | ||
| known_indels | File | ||
| somalier_vcf | File | ||
| interval_list | File | ||
| manta_non_wgs | Boolean (Optional) | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| known_variants | File (Optional) |
Previously discovered variants to be flagged in this pipelines's output vcf |
|
| tumor_sequence | https://w3id.org/cwl/view/git/22fce2dbdada0c4135b6f0677f78535cf980cb07/definitions/types/sequence_data.yml#sequence_data[] | ||
| normal_sequence | https://w3id.org/cwl/view/git/22fce2dbdada0c4135b6f0677f78535cf980cb07/definitions/types/sequence_data.yml#sequence_data[] | ||
| varscan_p_value | Float (Optional) | ||
| target_intervals | File | ||
| summary_intervals | https://w3id.org/cwl/view/git/22fce2dbdada0c4135b6f0677f78535cf980cb07/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| manta_call_regions | File (Optional) | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/22fce2dbdada0c4135b6f0677f78535cf980cb07/definitions/types/labelled_file.yml#labelled_file[] | ||
| pindel_insert_size | Integer | ||
| 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/22fce2dbdada0c4135b6f0677f78535cf980cb07/definitions/types/labelled_file.yml#labelled_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 |
|
| varscan_strand_filter | Integer (Optional) | ||
| vep_custom_annotations | https://w3id.org/cwl/view/git/22fce2dbdada0c4135b6f0677f78535cf980cb07/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| mutect_artifact_detection_mode | Boolean | ||
| picard_metric_accumulation_level | String | ||
| variants_to_table_genotype_fields | String[] | ||
| mutect_max_alt_alleles_in_normal_count | Integer (Optional) | ||
| mutect_max_alt_allele_in_normal_fraction | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| manta |
../tools/manta_somatic.cwl
(CommandLineTool)
|
Set up and execute manta | |
| cnvkit |
../tools/cnvkit_batch.cwl
(CommandLineTool)
|
||
| concordance |
../tools/concordance.cwl
(CommandLineTool)
|
Concordance checking between Tumor and Normal BAM | |
| detect_variants |
detect_variants.cwl
(Workflow)
|
Detect Variants workflow | |
| tumor_index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| normal_index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| tumor_bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| normal_bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| tumor_alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc | |
| normal_alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| cn_diagram | File (Optional) | ||
| tumor_cram | File | ||
| normal_cram | File | ||
| vep_summary | File | ||
| all_candidates | File | ||
| 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 | ||
| docm_filtered_vcf | File | ||
| normal_hs_metrics | File | ||
| final_filtered_vcf | File | ||
| reference_coverage | File (Optional) | ||
| mutect_filtered_vcf | File | ||
| pindel_filtered_vcf | File | ||
| tumor_only_variants | File (Optional) | ||
| intervals_antitarget | File (Optional) | ||
| strelka_filtered_vcf | File | ||
| varscan_filtered_vcf | File | ||
| mutect_unfiltered_vcf | File | ||
| pindel_unfiltered_vcf | File | ||
| tumor_target_coverage | File | ||
| normal_target_coverage | File | ||
| strelka_unfiltered_vcf | File | ||
| tumor_bin_level_ratios | File | ||
| tumor_segmented_ratios | File | ||
| varscan_unfiltered_vcf | File | ||
| tumor_summary_hs_metrics | File[] | ||
| normal_summary_hs_metrics | File[] | ||
| tumor_antitarget_coverage | File | ||
| tumor_insert_size_metrics | File | ||
| tumor_per_base_hs_metrics | File[] | ||
| tumor_verify_bam_id_depth | File | ||
| normal_antitarget_coverage | File | ||
| normal_insert_size_metrics | File | ||
| normal_per_base_hs_metrics | File[] | ||
| normal_verify_bam_id_depth | 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 | ||
| 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/22fce2dbdada0c4135b6f0677f78535cf980cb07/definitions/pipelines/somatic_exome.cwl
