This workflow runs postprocessing only.
| Input Name | Description | Type | Required | Default |
|---|---|---|---|---|
| pools | The names of the pools. | Array[String] | Yes | - |
| amplicon_info_files | The TSVs that contain amplicon information. | Array[File] | Yes | - |
| clusters | The clusters file. | File | Yes | - |
| just_concatenate | Whether non-overlaps should be concatenated. Optional. | Boolean | No | true |
| mask_tandem_repeats | Whether tandem repeats should be masked. Optional. | Boolean | No | true |
| mask_homopolymers | Whether homopolymers should be masked. Optional. | Boolean | No | true |
| amplicon_info_files | Amplicon info files. Used to be make concatenated amplicon info file. | Array[File] | No | - |
| targeted_reference_files | Targeted reference files. Will be used to create reference.fasta | Array[File] | No | - |
| refseq_fasta | Path to reference sequences (optional, auto-generated if not provided. If not provided genome must be provided) | File | No | - |
| genome | Path to genome file. (optional, but one of genome or refseq_fasta must be provided) | File | No | - |
| masked_fasta | The masked fasta file. Optional. | File | No | - |
| docker_image | Specifies a custom Docker image to use. Optional. | String | No | eppicenter/mad4hatter:develop |
| Output Name | Description | Type |
|---|---|---|
| amplicon_info | The processed amplicon info file | File |
| reference_fasta | The postprocessed reference FASTA file | File |
| alleledata | The final allele table after postprocessing | File |