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pipelines_bisulfite.cwl
Travis CI User edited this page Feb 9, 2021
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Bisulfite alignment and QC
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| reference_index | string | |||
| reference_sizes | File | |||
| instrument_data_bams | File[] | |||
| read_group_id | string[] | |||
| sample_name | string | |||
| trimming_adapters | File | |||
| trimming_adapter_trim_end | string | |||
| trimming_adapter_min_overlap | int | |||
| trimming_max_uncalled | int | |||
| trimming_min_readlength | int | |||
| QCannotation | File | |||
| assay_non_cpg_sites | Variable to determine if user wants to obtain obtain bed/bigwig files for non-CpG cytosines. Value - true or false | {'type': 'enum', 'symbols': ['true', 'false']} |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| cram | File | ['.crai', '^.crai'] | ||
| vcf | File | |||
| cpgs | File[] | |||
| cpg_bigwig | File[] | |||
| gathered_directory | Directory |
| Name | CWL Run |
|---|---|
| bam_to_trimmed_fastq_and_biscuit_alignments | subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl |
| merge | tools/merge_bams.cwl |
| pileup | tools/biscuit_pileup.cwl |
| bisulfite_qc | subworkflows/bisulfite_qc.cwl |
| vcf2bed | tools/bisulfite_vcf2bed.cwl |
| bedgraph_to_bigwig | tools/bedgraph_to_bigwig.cwl |
| bam_to_cram | tools/bam_to_cram.cwl |
| index_cram | tools/index_cram.cwl |