Allow cram output for parabricks/fq2bam module and remove fastq_align_parabricks

[famosab]

PR checklist

Closes #XXX

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[famosab]

I am wondering now: Do we even need a subworkflow if its just a wrapper around one module? 🤔 @maxulysse what do you think? Because for the sarek integration I think I need to chain this anyways with QC?

Edit: Subworkflows should combine tools that make up a logical unit in an analysis step. A subworkflow must contain at least two modules. -> I will remove the sbwf

[SPPearce]

I am wondering now: Do we even need a subworkflow if its just a wrapper around one module? 🤔 @maxulysse what do you think? Because for the sarek integration I think I need to chain this anyways with QC?

Edit: Subworkflows should combine tools that make up a logical unit in an analysis step. A subworkflow must contain at least two modules. -> I will remove the sbwf

But it had two modules, aligning and applying the BQSR?

[famosab]

I am wondering now: Do we even need a subworkflow if its just a wrapper around one module? 🤔 @maxulysse what do you think? Because for the sarek integration I think I need to chain this anyways with QC?
Edit: Subworkflows should combine tools that make up a logical unit in an analysis step. A subworkflow must contain at least two modules. -> I will remove the sbwf

But it had two modules, aligning and applying the BQSR?

Yes but I realized that fq2bam already does the BQSR and hence removed it and then its only fq2bam left in the subworkflow.

See:

[maxulysse]

In that particular, given that the subworkflow had no extra value, I think it was the good decision to remove it