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pipelines_chipseq.cwl
Travis CI User edited this page Feb 9, 2021
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Chipseq alignment with qc and creating homer tag directory
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? |
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 |
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 |