This is a request from me, but everyone will benefit from this add.
I frequently look at the fastq-scan output JSON files when reviewing raw & cleaned read lengths and quality scores, and always have to dig into the execution directories for samples individually and it's very annoying to have to click around so much to review these QC metrics.
Can we please output the fastq-scan JSON files as part of:
read_qc_trim_pe subworkflow
read_qc_trim_se subworkflow
TheiaCoV_illumina_pe workflow
theiacov_illumina_se workflow
TheiaProk_illumina_pe workflow
TheiaProk_Illumina_se workflow
theiameta_illumina_pe workflow
any other workflows I have missed?
We output the HTML files from fastqc (not the default FASTQ-scanning tool), why not do something similar for fastq-scan? Is there a reason we do not output this file?
:books: Context
:chart_with_upwards_trend: Desired Behavior
output these JSON files by default, like we do with fastqc html output files
:cool:
:pushpin: Explain the Request
This is a request from me, but everyone will benefit from this add.
I frequently look at the
fastq-scanoutput JSON files when reviewing raw & cleaned read lengths and quality scores, and always have to dig into the execution directories for samples individually and it's very annoying to have to click around so much to review these QC metrics.Can we please output the
fastq-scanJSON files as part of:We output the HTML files from fastqc (not the default FASTQ-scanning tool), why not do something similar for fastq-scan? Is there a reason we do not output this file?
:books: Context
:chart_with_upwards_trend: Desired Behavior
output these JSON files by default, like we do with fastqc html output files
:information_source: Additional Information