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:
Closes #282
:hammer_and_wrench: Changes Being Made
read_QC_trim_pe
andread_QC_trim_se
sub-workflows, and their associated parent workflows.fastq_scan
is the default module. To usefastqc
, the user must fill in"fastqc"
for the newread_QC_trim.read_qc
variable.Impacted Workflows/Tasks
:brain: Context and Rationale
FastQC was requested by a user.
:clipboard: Workflow/Task Steps
Instead of defaulting to
fastq_scan
, the user can optionally usefastqc
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
:With nothing in the
read_qc
variable:Scenarios for Reviewer to Test
fastqc
on and off.:microscope: Quality checks
Pull Request (PR) checklist: