Workflow: exome alignment with qc

Fetched 2023-01-09 22:39:35 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs final_name final_name alignment Raw sequence data to BQSR final_name->alignment final_name bqsr_known_sites bqsr_known_sites bqsr_known_sites->alignment bqsr_known_sites bait_intervals bait_intervals qc Exome QC workflow bait_intervals->qc bait_intervals omni_vcf omni_vcf omni_vcf->qc omni_vcf picard_metric_accumulation_level picard_metric_accumulation_level picard_metric_accumulation_level->qc picard_metric_accumulation_level trimming trimming trimming->alignment trimming per_target_intervals per_target_intervals per_target_intervals->qc per_target_intervals sequence sequence: sequencing data and readgroup information sequence->alignment unaligned target_intervals target_intervals target_intervals->qc target_intervals qc_minimum_base_quality qc_minimum_base_quality qc_minimum_base_quality->qc minimum_base_quality per_base_intervals per_base_intervals per_base_intervals->qc per_base_intervals qc_minimum_mapping_quality qc_minimum_mapping_quality qc_minimum_mapping_quality->qc minimum_mapping_quality bqsr_intervals bqsr_intervals bqsr_intervals->alignment bqsr_intervals summary_intervals summary_intervals summary_intervals->qc summary_intervals reference reference reference->qc reference reference->alignment reference insert_size_metrics insert_size_metrics flagstats flagstats hs_metrics hs_metrics per_base_coverage_metrics per_base_coverage_metrics mark_duplicates_metrics mark_duplicates_metrics insert_size_histogram insert_size_histogram summary_hs_metrics summary_hs_metrics bam bam per_target_coverage_metrics per_target_coverage_metrics alignment_summary_metrics alignment_summary_metrics per_base_hs_metrics per_base_hs_metrics verify_bam_id_metrics verify_bam_id_metrics verify_bam_id_depth verify_bam_id_depth per_target_hs_metrics per_target_hs_metrics qc->insert_size_metrics qc->flagstats qc->hs_metrics qc->per_base_coverage_metrics qc->insert_size_histogram qc->summary_hs_metrics qc->per_target_coverage_metrics qc->alignment_summary_metrics qc->per_base_hs_metrics qc->verify_bam_id_metrics qc->verify_bam_id_depth qc->per_target_hs_metrics alignment->mark_duplicates_metrics alignment->bam alignment->qc bam
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Inputs

ID Type Title Doc
omni_vcf File
sequence https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/sequence_data.yml#sequence_data[] sequence: sequencing data and readgroup information

sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.

trimming https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/trimming_options.yml#trimming_options (Optional)
reference File
final_name String (Optional)
bait_intervals File
bqsr_intervals String[] (Optional)
bqsr_known_sites File[]

One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.

target_intervals File
summary_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
per_target_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
qc_minimum_base_quality Integer (Optional)
qc_minimum_mapping_quality Integer (Optional)
picard_metric_accumulation_level String

Steps

ID Runs Label Doc
qc Exome QC workflow
alignment Raw sequence data to BQSR

Outputs

ID Type Label Doc
bam File
flagstats File
hs_metrics File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
verify_bam_id_depth File
insert_size_histogram File
per_target_hs_metrics File[]
verify_bam_id_metrics File
mark_duplicates_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
Permalink: https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/pipelines/alignment_exome.cwl