Mad4HatterQcOnly

This workflow runs quality control only on the selected samples.

Inputs:

| 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 | - | | forward_fastqs | List of forward fastqs. Must be in correct order. | Array[File] | Yes | - | | reverse_fastqs | List of reverse fastqs. Must be in correct order. | Array[File] | Yes | - | | cutadapt_minlen | The minimum length used for cutadapt. Optional. | Int | No | 100 | | gtrim | If true, --nextseq-trim will be used to trim trailing G in cutadapt. | Bool | No | false | | quality_score | The quality score threshold to apply in cutadapt. | Int | No | 20 | | allowed_errors | The number of errors allowed to be encountered in cutadapt. Optional. | Int | No | 0 | | docker_image | Specifies a custom Docker image to use. Optional. | String | No | eppicenter/mad4hatter:develop |

Outputs:

| Output Name | Description | Type | |-------------------------|----------------------------------------------------|------| | amplicon_info | The processed amplicon info file | File | | amplicon_coverage | The sample coverage file (from QC) | File | | sample_coverage | The amplicon coverage file (from QC) | File |