Redefine processing from input BAM files

[emi80]

In the current implementation input BAM files are merged to the alignment files produced by the pipeline mapping step and then used for downstream processing. This approach can pose problems because:

• merging external BAMs is risky as there is no guarantee that the data has been processed in a consistent way
• sometime project data is kept for long-term storage in BAM format but we want fully reprocess the data with grape-nf (e.g. re-mapping with a different genome/annotation)

A possible better approach could be based on params.steps and act accordingly:

• if the mapping step is specified the BAM files should be re-processed
• if only downstream steps (e.g. quantification) are specified the BAM files are used as-is. An error should be reported If BAM files can be merged

Alternatives might be considered as well...