pipelines_alignment_umi_molecular.cwl
Travis CI User edited this page Feb 9, 2021
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umi molecular alignment fastq workflow
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| 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 for FASTQs. For BAMs, this pipeline assumes that the RG information is already in the header. | ../types/sequence_data.yml#sequence_data[] | |
| sample_name | string | |||
| read_structure | string[] | |||
| reference | ['string', 'File'] | ['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa'] | ||
| target_intervals | File? |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| aligned_cram | File | ['.crai', '^.crai'] | ||
| adapter_histogram | File[] | |||
| duplex_seq_metrics | File[] |
| Name | CWL Run |
|---|---|
| sequence_to_bam | tools/sequence_to_bam.cwl |
| alignment_workflow | subworkflows/molecular_alignment.cwl |
| bam_to_cram | tools/bam_to_cram.cwl |
| index_cram | tools/index_cram.cwl |