[FastP & FastQC] output FastP and FastQC reports & output name changes

[sage-wright]

This PR closes #336.

🗑️ This dev branch should be deleted after merging to main.

:brain: Aim, Context and Functionality

• Requested to output the HTML reports for FastP and FastQC. These are now output in all applicable workflows.
• All fastq_scan outputs are now prefaced by fastq_scan_ in order to differentiate them from FastQC outputs.
• clean_read_screen and raw_read_screen are now read_screen_clean and read_screen_raw to make them easier to compare

:hammer_and_wrench: Impacted Workflows/Tasks & Changes Being Made

This will affect the behavior of the workflow(s) even if users don’t change any workflow inputs relative to the last version : No

Running this workflow on different occasions could result in different results, e.g. due to use of a live database, "latest" docker image, or stochastic data processing : No

• Only output changes were made in this PR

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

No data processing changes

➡️ Inputs

• Exposed the default rasusa downsampling coverage to be user-modifiable instead of hard-code as 150
  • Float downsampling_coverage = 150 in wf_read_QC_trim_ont.wdl

⬅️ Outputs

Old	New	Where
num_reads_raw1	fastq_scan_num_reads_raw1	Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
num_reads_raw2	fastq_scan_num_reads_raw2	Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
num_reads_raw	fastq_scan_num_reads_raw1	TheiaCoV_Illumina_SE
num_reads_raw_pairs	fastq_scan_num_reads_raw_pairs	Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
num_reads_clean1	fastq_scan_num_reads_clean1	Freyja_FASTQ, TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
num_reads_clean2	fastq_scan_num_reads_clean2	Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
num_reads_clean	fastq_scan_num_reads_clean1	TheiaCoV_Illumina_SE
num_reads_clean_pairs	fastq_scan_num_reads_clean_pairs	Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_PE
raw_read_screen	read_screen_raw	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
clean_read_screen	read_screen_clean	TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaCoV_ONT, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_ONT
--	Int? fastqc_num_reads_raw1	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
--	Int? fastqc_num_reads_raw2	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
Int? fastqc_num_reads_raw	Int? fastqc_num_reads_raw1	TheiaCoV_Illumina_SE
--	String? fastqc_num_reads_raw_pairs	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
--	Int? fastqc_num_reads_clean1	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
--	Int? fastqc_num_reads_clean2	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
Int? fastqc_num_reads_clean	Int? fastqc_num_reads_clean1	TheiaCoV_Illumina_SE
--	String? fastqc_num_reads_clean_pairs	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
--	File? fastqc_raw1_html	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
--	File? fastqc_raw2_html	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
File? fastqc_raw_html	File? fastqc_raw1_html	read_QC_trim_SE, TheiaCoV_Illumina_SE
--	File? fastqc_clean1_html	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
--	File? fastqc_clean2_html	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
File? fastqc_clean_html	File? fastqc_clean1_html	read_QC_trim_SE, TheiaCoV_Illumina_SE
--	String? fastqc_version	TheiaCoV_Illumina_PE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE
--	String? fastqc_docker	Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
--	String? trimmomatic_docker	read_QC_trim_SE, Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaProk_Illumina_PE, TheiaProk_Illumina_SE
--	String? fastp_version	Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE
--	File? fastp_html_report	read_QC_trim_SE, read_QC_trim_PE, Freyja_FASTQ, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, TheiaEuk_Illumina_PE, TheiaMeta_Illumina_PE, TheiaProk_Illumina_SE, TheiaProk_Illumina_SE
Int? fastq_scan_raw_number_reads	Int? fastq_scan_raw1	read_QC_trim_SE (mimics read_QC_trim_PE now)
Int? fastq_scan_clean_number_reads	Int? fastq_scan_clean1	read_QC_trim_SE (mimics read_QC_trim_PE now)
Int? fastqc_raw_number_reads	Int? fastqc_raw1	read_QC_trim_SE (mimics read_QC_trim_PE now)
Int? fastqc_clean_number_reads	Int? fastqc_clean1	read_QC_trim_SE (mimics read_QC_trim_PE now)

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Terra Testing

• [x] Freyja_FASTQ with "fastqc" for read_qc here
• [x] TheiaCoV_Illumina_PE with fastp for read processing here
• [x] TheiaCoV_Illumina_SE with all default params here
• [x] TheiaProk_ONT with all default params here

Suggested Scenarios for Reviewer to Test

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

• [x] The workflow/task has been tested locally and results, including file contents, are as anticipated
• [ ] The workflow/task has been tested on Terra and results, including file contents, are as anticipated
• [x] The CI/CD has been adjusted and tests are passing (to be completed by Theiagen developer)
• [x] Code changes follow the style guide

🎯 Reviewer Checklist

• [x] All impacted workflows/tasks have been tested on Terra with a different dataset than used for development
• [x] All reviewer-suggested scenarios have been tested and any additional
• [x] All changed results have been confirmed to be accurate
• [x] All workflows/tasks impacted by change/s have been tested using a standard validation dataset to ensure no unintended change of functionality
• [x] All code adheres to the style guide
• [x] MD5 sums have been updated
• [x] The PR author has addressed all comments

🗂️ Associated Documentation (to be completed by Theiagen developer)

• [ ] Relevant documentation on the Public Health Resources "PHB Main" has been updated
• [ ] Workflow diagrams have been updated to reflect changes

[cimendes]

Inputs:

• downsampling_coverage present in both TheiaCoV_ONT and TheiaProk_ONT
  • 
  • 

[cimendes]

Freyja_FASTQ

• Expected output params present in the workflow
  • 

TheiaCoV_ClearLabs

• Expected output params present in the workflow
  • 

TheiaCoV_Illumina_PE

• Expected output params present in the workflow
  • 
  • 
  • 

TheiaCoV_Illumina_SE

• Expected output params present in the workflow
  • 
  • 

[cimendes]

TheiaEuk_Illumina_PE

• Expected output params present in the workflow
  • 
  • 

TheiaMeta_Illumina_PE

• Expected output params present in the workflow
  • 
  • A side note: The clean reads are saved as read1_clean and read2_clean

[cimendes]

TheiaProk_Illumina_PE

• Expected output params present in the workflow
  • 
  • 

TheiaProk_Illumina_SE

• Expected output params present in the workflow
  • 
  • 
  • 

[cimendes]

All inputs and outputs have been verified as present in all the affected workflows. As a bonus, the trimmomatic_docker was also exposed in all the workflows.

Code changes look good! 🌟 Approving!