FastQC added as an optional module in all Illumina_PE and Illumina_SE workflows

[sage-wright]

Closes #282

:hammer_and_wrench: Changes Being Made

• FastQC is now included as part of the read_QC_trim_pe and read_QC_trim_se sub-workflows, and their associated parent workflows. fastq_scan is the default module. To use fastqc, the user must fill in "fastqc" for the new read_QC_trim.read_qc variable.

Impacted Workflows/Tasks

• TheiaCoV_Illumina_PE
• TheiaCoV_Illumina_SE
• TheiaProk_Illumina_PE
• TheiaProk_Illumina_SE
• TheiaMeta_Illumina_PE
• Freyja_FASTQ

  :brain: Context and Rationale

FastQC was requested by a user.

:clipboard: Workflow/Task Steps

Instead of defaulting to fastq_scan, the user can optionally use fastqc instead.

Inputs

One new input:

• read_qc_trim.read_qc: default to "fastq_scan", can be manually modified to "fastqc"

Outputs

Several new outputs:

For all _Illumina_PE workflows (and Freyja_FASTQ):

• fastqc_num_reads_raw1
• fastqc_num_reads_raw2
• fastqc_num_reads_raw_pairs
• fastqc_raw1_html
• fastqc_raw2_html
• fastqc_version
• fastqc_num_reads_clean1
• fastqc_num_reads_clean2
• fastqc_num_reads_clean_pairs
• fastqc_clean1_html
• fastqc_clean2_html

For all _Illumina_SE workflows:

• fastqc_num_reads_raw
• fastqc_num_reads_clean
• fastqc_version
• fastqc_raw_html
• fastqc_clean_html

Impacted Outputs

All original fastq_scan outputs will be blank if fastqc was chosen. These include the following:

• num_reads_raw1
• num_reads_raw2
• num_reads_raw_pairs
• fastq_scan_version
• num_reads_clean1
• num_reads_clean2
• num_reads_clean_pairs

:test_tube: Testing

Locally

Local tests of the fastqc tasks worked.

Terra

Using fastqc:

• [x] TheiaCoV_Illumina_PE: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/6fa346b4-be06-4420-8fe3-bf23d7598ecc
• [x] TheiaCoV_Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Wright_PHBG_Sandbox/job_history/60c747e5-e3ff-4e9c-a3bc-a0ca8714297c
• [x] TheiaProk_Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Wright_PHBG_Sandbox/job_history/ff840535-3e7f-46de-8c9a-5dbde9814747
• [x] TheiaProk_Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Wright_PHBG_Sandbox/job_history/60c747e5-e3ff-4e9c-a3bc-a0ca8714297c
• [x] TheiaMeta_Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Wright_PHBG_Sandbox/job_history/60c747e5-e3ff-4e9c-a3bc-a0ca8714297c
• [x] Freyja_FASTQ: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/c66348e3-7da7-42ce-be46-7ff590f4b4e6

With nothing in the read_qc variable:

• [x] TheiaCoV_Illumina_PE: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/94eb9d18-266a-47c6-8926-e3b9bc40fcae
• [x] TheiaCoV_Illumina_SE: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/2e5da617-ec12-49ba-b09d-fba81ab9dabe
• [x] TheiaMeta_Illumina_PE: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/8208d490-7e0d-4ff1-b1f9-5c5b0ce80b19
• [x] TheiaProk_Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Wright_PHBG_Sandbox/job_history/929e909d-ef60-45c2-a65d-afb047280dff
• [x] TheiaProk_Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Wright_PHBG_Sandbox/job_history/36756711-926c-43e9-a586-bd0717a7a0bb
• [x] Freyja_FASTQ: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/b525366c-dd69-438b-beea-0b2ab0fb3c95

Scenarios for Reviewer to Test

• All six workflows with fastqc on and off.

:microscope: Quality checks

Pull Request (PR) checklist:

• [x] Include a description of what is in this pull request in this message.
• [x] The workflow/task has been tested locally and on Terra
• [x] The CI/CD has been adjusted and tests are passing
• [x] Everything follows the style guide

[cimendes]

Testing with fastqc on the read_qc optional input :

• TheiaCoV_Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/5418ff72-f005-44f1-8f18-f016d1a414e0
• TheiaCoV_Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/a346e1b4-4b6d-4044-83d4-09328bdb3c95
• TheiaProk_Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/576913c7-b265-4f6c-ae68-7e5599fb131d ✅
• TheiaProk_Illumina_SE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/fef02568-a768-43bf-801e-6123b21006c2 ✅
• TheiaMeta_Illumina_PE: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/1d83b688-9edb-4121-8a2e-afcb67469925 (1 expected failure - negative control) ✅
• Freyja_FASTQ: Can't test 😭