Workflow: exome alignment and somatic variant detection for cle purpose

Fetched 2023-01-13 12:48:19 GMT
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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_bams File[]
tumor_name String (Optional)
normal_bams File[]
normal_name String (Optional)
known_indels File
somalier_vcf File
interval_list File
synonyms_file File (Optional)
vep_cache_dir String
bait_intervals File
bqsr_intervals String[]
cle_vcf_filter Boolean
varscan_p_value Float (Optional)
target_intervals File
tumor_readgroups String[]
custom_gnomad_vcf File (Optional)
normal_readgroups String[]
summary_intervals https://w3id.org/cwl/view/git/4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c/definitions/types/labelled_file.yml#labelled_file[]
custom_clinvar_vcf File (Optional)
per_base_intervals https://w3id.org/cwl/view/git/4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c/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
panel_of_normals_vcf File (Optional)
per_target_intervals https://w3id.org/cwl/view/git/4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c/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
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
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/4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c/definitions/pipelines/cle_somatic_exome.cwl