- 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 | ||
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 | ||
tumor_sequence | https://w3id.org/cwl/view/git/a23f42ef49c10a588fd35a3afaad5de03e253533/definitions/types/sequence_data.yml#sequence_data[] | ||
normal_sequence | https://w3id.org/cwl/view/git/a23f42ef49c10a588fd35a3afaad5de03e253533/definitions/types/sequence_data.yml#sequence_data[] | ||
varscan_p_value | Float (Optional) | ||
target_intervals | File | ||
custom_gnomad_vcf | File (Optional) | ||
summary_intervals | https://w3id.org/cwl/view/git/a23f42ef49c10a588fd35a3afaad5de03e253533/definitions/types/labelled_file.yml#labelled_file[] | ||
custom_clinvar_vcf | File (Optional) | ||
manta_call_regions | File (Optional) | ||
per_base_intervals | https://w3id.org/cwl/view/git/a23f42ef49c10a588fd35a3afaad5de03e253533/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/a23f42ef49c10a588fd35a3afaad5de03e253533/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) | ||
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 |
exome_alignment.cwl
(Workflow)
|
exome alignment with qc | |
normal_alignment_and_qc |
exome_alignment.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/a23f42ef49c10a588fd35a3afaad5de03e253533/definitions/pipelines/somatic_exome.cwl