Remove sample specific options and use them as rule specific.

Closes #158 (closed). The features softclip, passmode, multimappers of STAR are relocated to the rule config and given a default value. The documentation is updated and these options are removed from the immutable lists in the corresponding rules.

tests/input_files/rule_config.yaml

@@ -122,12 +122,24 @@ map_genome_star:
     --outFilterMultimapScoreRange: '0'
     # keep only those reads that contain junctions that passed filtering into SJ.out.tab. (default 'Normal', ZARP recommends 'BySJout', as this reduces the number of ”spurious” junctions )
     --outFilterType: 'BySJout'
+    # type of read ends alignment: force end-to-end read alignment, do not soft-clip
+    --alignEndsType: 'EndToEnd'
+    #  extract junctions, insert them into the genome index and re-map reads in a 2nd mapping pass
+    --twopassMode: Basic
+    # alignments (all of them) will be output only if the read maps to no more loci than 10
+    --outFilterMultimapNmax: '10'
 
 pe_map_genome_star:
     # the score range below the maximum score for multimapping alignments (default 1, ZARP recommends 0)
     --outFilterMultimapScoreRange: '0'
     # keep only those reads that contain junctions that passed filtering into SJ.out.tab. (default 'Normal', ZARP recommends 'BySJout', as this reduces the number of ”spurious” junctions )
     --outFilterType: 'BySJout'
+    # type of read ends alignment: force end-to-end read alignment, do not soft-clip
+    --alignEndsType: 'EndToEnd'
+    #  extract junctions, insert them into the genome index and re-map reads in a 2nd mapping pass
+    --twopassMode: Basic
+    # alignments (all of them) will be output only if the read maps to no more loci than 10
+    --outFilterMultimapNmax: '10'
 
 quantification_salmon:
     # correct for sequence specific biases](https://salmon.readthedocs.io/en/latest/salmon.html#seqbias