DSL2: Ensure modules config consistency: all modules have an ext.prefix and publishDir attribute, and follow conventions.

[TCLamnidis]

Best for publishDir to be explicitly on/off, and all modules (even when not publishing) need an ext.prefix, now that we don't have meta.id anymore.
Also ensure that all module configurations follow the code conventions (attribute order etc)

Results from quick check on 26/04/2024:

• HOST_REMOVAL : has no ext.prefix
• SAMTOOLS_INDEX_BAM_INPUT : has neither
• SAMTOOLS_VIEW_GENOME: no ext.prefix
• SAMTOOLS_INDEX_DAMAGE_RESCALED: no ext.prefix
• SAMTOOLS_INDEX_DAMAGE_FILTERED: no ext.prefix
• SAMTOOLS_INDEX_DAMAGE_TRIMMED: no ext.prefix
• ANGSD_DOCOUNTS: wrong attribute order
• MTNUCRATIO : no ext.prefix
• QUALIMAP_BAMQC_WITHBED|QUALIMAP_BAMQC_NOBED: no ext.prefix
• SAMTOOLS_DEPTH_SEXDETERRMINE: wrong attribute order