pipelines_chipseq_alignment_nonhuman.cwl
Travis CI User edited this page Feb 9, 2021
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Chipseq alignment for nonhuman 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[] | |
| trimming | ['../types/trimming_options.yml#trimming_options', 'null'] | |||
| 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 | |||
| minimum_mapping_quality | int? | |||
| minimum_base_quality | int? |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| bam | File | |||
| mark_duplicates_metrics | File | |||
| tag_directory | Directory | |||
| insert_size_metrics | File | |||
| insert_size_histogram | File | |||
| alignment_summary_metrics | File | |||
| wgs_metrics | File | |||
| gc_bias_metrics | File | |||
| gc_bias_metrics_chart | File | |||
| gc_bias_metrics_summary | File | |||
| flagstats | File | |||
| per_base_coverage_metrics | File[] | |||
| per_base_hs_metrics | File[] | |||
| per_target_coverage_metrics | File[] | |||
| summary_hs_metrics | File[] | |||
| per_target_hs_metrics | File[] | |||
| bamcoverage_bigwig | File |
| Name | CWL Run |
|---|---|
| alignment | subworkflows/sequence_to_bqsr_nonhuman.cwl |
| bam_to_sam | tools/bam_to_sam.cwl |
| homer_tag_directory | tools/homer_tag_directory.cwl |
| qc | subworkflows/qc_wgs_nonhuman.cwl |