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pipelines_chipseq.cwl

Travis CI User edited this page Feb 9, 2021 · 21 revisions

Documentation for chipseq.cwl

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Overview

Chipseq alignment with qc and creating homer tag directory

Inputs

Name Label Description Type Secondary Files
reference ['string', 'File'] ['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa']
final_name string?
chipseq_sequence chipseq_sequence: sequencing data and readgroup information chipseq_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[]
omni_vcf File ['.tbi']
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
bqsr_known_sites One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. File[] ['.tbi']
bqsr_intervals string[]
minimum_mapping_quality int?
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
gc_bias_metrics File
gc_bias_metrics_chart File
gc_bias_metrics_summary File
wgs_metrics File
flagstats File
verify_bam_id_metrics File
verify_bam_id_depth File
per_base_coverage_metrics File[]
per_base_hs_metrics File[]
per_target_coverage_metrics File[]
per_target_hs_metrics File[]
summary_hs_metrics File[]
tag_directory Directory

Steps

Name CWL Run
alignment subworkflows/sequence_to_bqsr.cwl
bam_to_sam tools/bam_to_sam.cwl
homer_tag_directory tools/homer_tag_directory.cwl
qc subworkflows/qc_wgs.cwl
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