Update salmon quant arguments (#57)

* Make index an optional argument

* FIx argument type and add optional argument

src/salmon/salmon_quant/config.vsh.yaml

@@ -42,7 +42,7 @@ argument_groups:
         type: file
         description: |
           Salmon index.
-        required: true
+        required: false
         example: transcriptome_index
       - name: --unmated_reads
         alternatives: ["-r"]
@@ -320,12 +320,15 @@ argument_groups:
         example: 0.00001
       - name: --write_mappings
         alternatives: ["-z"]
-        type: file
-        direction: output
+        type: boolean_true
         description: |
           If this option is provided, then the selective-alignment results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead.
+      - name: --mapping_sam
+        type: file
+        description: Path to file that should output the selective-alignment results in SAM-compatible format. THis option must be provided while using --write_mappings
         required: false
-        example: mappings.sam 
+        direction: output
+        example: mappings.sam
       - name: --write_qualities
         type: boolean_true
         description: |

src/salmon/salmon_quant/script.sh

@@ -21,6 +21,7 @@ set -e
 [[ "$par_softclip_overhangs" == "false" ]] && unset par_softclip_overhangs
 [[ "$par_full_length_alignment" == "false" ]] && unset par_full_length_alignment
 [[ "$par_hard_filter" == "false" ]] && unset par_hard_filter
+[[ "$par_write_mappings" == "false" ]] && unset par_write_mappings
 [[ "$par_write_qualities" == "false" ]] && unset par_write_qualities
 [[ "$par_alternative_init_mode" == "false" ]] && unset par_alternative_init_mode
 [[ "$par_skip_quant" == "false" ]] && unset par_skip_quant
@@ -96,7 +97,7 @@ salmon quant \
     ${par_full_length_alignment:+--fullLengthAlignment} \
     ${par_hard_filter:+--hardFilter} \
     ${par_min_aln_prob:+--minAlnProb "${par_min_aln_prob}"} \
-    ${par_write_mappings:+-z "${par_write_mappings}"} \
+    ${par_write_mappings:+--write_mappings="${par_mappings_sam}"} \
     ${par_write_qualities:+--writeQualities} \
     ${par_hit_filter_policy:+--hitFilterPolicy "${par_hit_filter_policy}"} \
     ${par_alternative_init_mode:+--alternativeInitMode} \