Workflow: exome alignment and somatic variant detection for cle purpose
- 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 | ||
interval_list | 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/844c10a4466ab39c02e5bfa7a210c195b8efa77a/definitions/types/sequence_data.yml#sequence_data[] | ||
disclaimer_text | String (Optional) | ||
normal_sequence | https://w3id.org/cwl/view/git/844c10a4466ab39c02e5bfa7a210c195b8efa77a/definitions/types/sequence_data.yml#sequence_data[] | ||
varscan_p_value | Float (Optional) | ||
target_intervals | File | ||
summary_intervals | https://w3id.org/cwl/view/git/844c10a4466ab39c02e5bfa7a210c195b8efa77a/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/844c10a4466ab39c02e5bfa7a210c195b8efa77a/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/844c10a4466ab39c02e5bfa7a210c195b8efa77a/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/844c10a4466ab39c02e5bfa7a210c195b8efa77a/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) | ||
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 | |
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/844c10a4466ab39c02e5bfa7a210c195b8efa77a/definitions/pipelines/somatic_exome_cle.cwl