Retaining all WT reads for variant counting and coverage calculation

[MaximilianStammnitz]

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• This comment contains a description of changes (with reason).
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[MaximilianStammnitz]

A min Phred score of Q40 during variant counting is the better default choice to reduce false counts at very high (10^6) sequencing depth.

This particular --min-q parameter (or --q for Fei's script) should be inherited from an open parameter in the nf-core pipeline config

[MaximilianStammnitz]

Also added the --fastq_qmax and --fastq_qmaxout flags in the read merging step, with their default values set to 41 (typical for Illumina NovaSeq). These should also be open parameters set in the nf-core pipeline config.

These parameters may be useful for tweaking when dealing with inputs from very high quality reads like AVITI's platforms.

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.