Allow skipping of salmon mapping in bulk

[jashapiro]

Similar to #41 and #81, we should continue our efforts to make expensive slow steps skippable by adding this functionality to the bulk workflow. Since we are unlikely to want to skip bulk but not single-cell or vice versa (an update to salmon would presumably affect both) we can consolidate the current --rad-skip option with this one to make a single --skip-mapping option.

Alternatively, we could rename the option --repeat-mapping, which has a nice little benefit that we can set it to false by default, and then nextflow will set the value to true when invoked without an argument. Which is to say we would not need to do something like nextflow run ... --rad-skip false as we do now, but rather just nextflow run ... --repeat-mapping, which is a bit cleaner.