Enable aozan to run QC steps directly on fastq files generated by the sequencer (Miseq case)

[loraine-gueguen]

It could be useful that aozan can disable data demultiplexing and run QC tools directly on the fastqs produced by the sequencer.

In the Miseq results, the fastq files are all grouped together in an Alignment_1/<id>/Fastq directory (one fastq.gz file per sample).

In aozan report html file:

Sequencer Name: MiSeq M02439
Sequencer Family: MiSeq
Instrument S/N: M02439
Run Id: 240130_M02439_0060_000000000-KR2D8
Flow cell: 000000000-KR2D8
Run started: Tue 30 Jan 2024
Instrument run number: 60
Sequencer Application name: MiSeq Control Software
Sequencer Application version: 4.0.0.1769
Sequencer RTA version: 1.18.54.4

In sequencer RunParameters.xml:

  <ModuleName>GenerateFastQWorkflow</ModuleName>
  <ModuleVersion>3.0.1.49</ModuleVersion>

We can probably make a Miseq run available on our cluster if needed. Let us know when you need it.