From 9d74c3b554f74d9e87c0fd4d7f18533dad1c9bdc Mon Sep 17 00:00:00 2001
From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com>
Date: Fri, 21 Jun 2024 22:28:44 +0200
Subject: [PATCH] Update salmon quant arguments (#57)

* Make index an optional argument

* FIx argument type and add optional argument
---
 src/salmon/salmon_quant/config.vsh.yaml | 11 +++++++----
 src/salmon/salmon_quant/script.sh       |  3 ++-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/salmon/salmon_quant/config.vsh.yaml b/src/salmon/salmon_quant/config.vsh.yaml
index 47d72665..b7e303f4 100644
--- a/src/salmon/salmon_quant/config.vsh.yaml
+++ b/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: |
diff --git a/src/salmon/salmon_quant/script.sh b/src/salmon/salmon_quant/script.sh
index ace79711..4c9f69d5 100644
--- a/src/salmon/salmon_quant/script.sh
+++ b/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} \