pipelines_alignment_exome_nonhuman.cwl

Documentation for alignment_exome_nonhuman.cwl

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Overview

exome alignment with qc, no bqsr, no verify_bam_id

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa']
sequence	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.	../types/sequence_data.yml#sequence_data[]
trimming			['../types/trimming_options.yml#trimming_options', 'null']
bait_intervals			File
final_name			string?
target_intervals			File
per_base_intervals			../types/labelled_file.yml#labelled_file[]
per_target_intervals			../types/labelled_file.yml#labelled_file[]
summary_intervals			../types/labelled_file.yml#labelled_file[]
picard_metric_accumulation_level			string
qc_minimum_mapping_quality			int?
qc_minimum_base_quality			int?

Outputs

Name	Label	Description	Type	Secondary Files
bam			File
mark_duplicates_metrics			File
insert_size_metrics			File
insert_size_histogram			File
alignment_summary_metrics			File
hs_metrics			File
per_target_coverage_metrics			File[]
per_target_hs_metrics			File[]
per_base_coverage_metrics			File[]
per_base_hs_metrics			File[]
summary_hs_metrics			File[]
flagstats			File

Steps

Name	CWL Run
alignment	subworkflows/sequence_to_bqsr_nonhuman.cwl
qc	subworkflows/qc_exome_no_verify_bam.cwl