use the default multiple separator

src/salmon/quant/config.vsh.yaml

@@ -41,7 +41,6 @@ argument_groups:
           List of files containing unmated reads of (e.g. single-end reads).
         required: false
         multiple: true
-        multiple_sep: " "
         example: sample.fq.gz
       - name: --mates1
         alternatives: ["-m1"]
@@ -50,7 +49,6 @@ argument_groups:
           File containing the #1 mates.
         required: false
         multiple: true
-        multiple_sep: " "
         example: sample_1.fq.gz
       - name: --mates2
         alternatives: ["-m2"]
@@ -59,7 +57,6 @@ argument_groups:
           File containing the #2 mates.
         required: false
         multiple: true
-        multiple_sep: " "
         example: sample_2.fq.gz
 
   - name: Alignment input options
@@ -75,7 +72,6 @@ argument_groups:
           Input alignment (BAM) file(s).
         required: false
         multiple: true
-        multiple_sep: " "
         example: sample.fq.gz
       - name: --eqclasses
         alternatives: ["-e"]

src/salmon/quant/script.sh

@@ -47,18 +47,18 @@ set -e
 [[ "$par_sample_unaligned" == "false" ]] && unset par_sample_unaligned
 [[ "$par_gencode" == "false" ]] && unset par_gencode
 
-IFS=" " read -ra unmated_reads <<< $par_unmated_reads
-IFS=" " read -ra mates1 <<< $par_mates1
-IFS=" " read -ra mates2 <<< $par_mates2
-IFS=" " read -ra alignment <<< $par_alignment
+IFS=";" read -ra unmated_reads <<< $par_unmated_reads
+IFS=";" read -ra mates1 <<< $par_mates1
+IFS=";" read -ra mates2 <<< $par_mates2
+IFS=";" read -ra alignment <<< $par_alignment
 
 salmon quant \
     ${par_lib_type:+-l "${par_lib_type}"} \
     ${par_index:+-i "${par_index}"} \
-    ${par_unmated_reads:+-r "${unmated_reads[*]}"} \
-    ${par_mates1:+-1 "${mates1[*]}"} \
-    ${par_mates2:+-2 "${mates2[*]}"} \
-    ${par_alignment:+-a "${alignment[*]}"} \
+    ${par_unmated_reads:+-r ${unmated_reads[*]}} \
+    ${par_mates1:+-1 ${mates1[*]}} \
+    ${par_mates2:+-2 ${mates2[*]}} \
+    ${par_alignment:+-a ${alignment[*]}} \
     ${par_discard_orphans:+--discardOrphans} \
     ${par_eqclasses:+-e "${par_eqclasses}"} \
     ${par_targets:+-t "${par_targets}"} \

src/salmon/quant/test.sh

@@ -39,8 +39,8 @@ echo "> Run salmon quant for paired-end reads with technical replicates"
 "$meta_executable" \
   --lib_type "A" \
   --index "$dir_in/salmon/transcriptome_index" \
-  --mates1 $dir_in/reads/a_1.fq.gz $dir_in/reads/b_1.fq.gz \
-  --mates2 $dir_in/reads/a_2.fq.gz $dir_in/reads/b_2.fq.gz \
+  --mates1 "$dir_in/reads/a_1.fq.gz;$dir_in/reads/b_1.fq.gz" \
+  --mates2 "$dir_in/reads/a_2.fq.gz;$dir_in/reads/b_2.fq.gz" \
   --output "quant_pe_rep_results" \
   --quant_results "quant_pe_rep.sf"