Workflow: exome alignment and somatic variant detection for cle purpose
Fetched 2023-01-11 04:26:14 GMT
Verified with cwltool version 3.1.20221201130942
- 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 | String | ||
| tumor_name | String (Optional) | ||
| normal_name | String (Optional) | ||
| known_indels | File | ||
| somalier_vcf | File | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| tumor_sequence | https://w3id.org/cwl/view/git/742dbafb5fb103d8578f48a0576c14dd8dae3b2a/definitions/types/sequence_data.yml#sequence_data[] | ||
| disclaimer_text | String (Optional) | ||
| normal_sequence | https://w3id.org/cwl/view/git/742dbafb5fb103d8578f48a0576c14dd8dae3b2a/definitions/types/sequence_data.yml#sequence_data[] | ||
| varscan_p_value | Float (Optional) | ||
| target_intervals | File | target_intervals: interval_list file of targets used in the sequencing experiment |
target_intervals is an interval_list corresponding to the targets for the capture reagent. BED files with this information can be converted to interval_lists with Picard BedToIntervalList. In general for a WES exome reagent bait_intervals and target_intervals are the same. |
| summary_intervals | https://w3id.org/cwl/view/git/742dbafb5fb103d8578f48a0576c14dd8dae3b2a/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| disclaimer_version | String | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/742dbafb5fb103d8578f48a0576c14dd8dae3b2a/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) | ||
| filter_minimum_depth | Integer (Optional) | ||
| mutect_scatter_count | Integer | ||
| per_target_intervals | https://w3id.org/cwl/view/git/742dbafb5fb103d8578f48a0576c14dd8dae3b2a/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/742dbafb5fb103d8578f48a0576c14dd8dae3b2a/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| target_interval_padding | Integer | target_interval_padding |
The effective coverage of capture products generally extends out beyond the actual regions targeted. This parameter allows variants to be called in these wingspan regions, extending this many base pairs from each side of the target regions. |
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String | ||
| variants_to_table_genotype_fields | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| 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 | |
| pad_target_intervals |
../tools/interval_list_expand.cwl
(CommandLineTool)
|
expand interval list regions by a given number of basepairs | |
| tumor_alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc | |
| normal_alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc | |
| annotated_filter_vcf_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| add_disclaimer_to_final_tsv |
../tools/add_string_at_line.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a file | |
| add_disclaimer_version_to_final_tsv |
../tools/add_string_at_line.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a file | |
| add_disclaimer_to_final_filtered_vcf |
../tools/add_string_at_line_bgzipped.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a gzipped file | |
| add_disclaimer_version_to_final_filtered_vcf |
../tools/add_string_at_line_bgzipped.cwl
(CommandLineTool)
|
Insert an arbitrary string at a specific line of a gzipped file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| tumor_cram | File | ||
| normal_cram | File | ||
| vep_summary | File | ||
| tumor_flagstats | File | ||
| normal_flagstats | File | ||
| tumor_hs_metrics | File | ||
| docm_filtered_vcf | File | ||
| normal_hs_metrics | File | ||
| final_filtered_vcf | File | ||
| mutect_filtered_vcf | File | ||
| pindel_filtered_vcf | File | ||
| strelka_filtered_vcf | File | ||
| varscan_filtered_vcf | File | ||
| mutect_unfiltered_vcf | File | ||
| pindel_unfiltered_vcf | File | ||
| strelka_unfiltered_vcf | File | ||
| varscan_unfiltered_vcf | File | ||
| tumor_summary_hs_metrics | File[] | ||
| normal_summary_hs_metrics | File[] | ||
| tumor_insert_size_metrics | File | ||
| tumor_per_base_hs_metrics | File[] | ||
| tumor_verify_bam_id_depth | 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/742dbafb5fb103d8578f48a0576c14dd8dae3b2a/definitions/pipelines/somatic_exome_cle.cwl
