Experimental BD Rhapsody Support

Experimental BD Rhapsody Support based on COMBINE-lab/salmon#628 (comment)

Author: ACastanza

manifest

@@ -174,7 +174,7 @@ p3_value=
 p4_MODE=
 p4_TYPE=TEXT
 p4_default_value=dropseq
-p4_description=The chemistry used by the single-cell sequencing platform.<br>\nDrop-Seq, 10x Chromium v2, 10x Chromium v3, CITE-Seq, CEL-Seq, CEL-Seq2, and Quartz-Seq2 are currently supported.
+p4_description=The chemistry used by the single-cell sequencing platform.<br>\nDrop-Seq, 10x Chromium v2, 10x Chromium v3, CITE-Seq, CEL-Seq, CEL-Seq2, and Quartz-Seq2 are currently supported. BD Rhapsody support is experimental.
 p4_fileFormat=
 p4_flag=-c
 p4_name=Chemistry
@@ -183,7 +183,7 @@ p4_optional=
 p4_prefix=
 p4_prefix_when_specified=
 p4_type=java.lang.String
-p4_value=dropseq\=Drop-Seq;chromium\=10x Chromium v2;chromiumV3\=10x Chromium v3;citeseq\=CITE-Seq;celseq\=CEL-Seq;celseq2\=CEL-Seq2;quartzseq2\=Quartz-Seq2
+p4_value=dropseq\=Drop-Seq;chromium\=10x Chromium v2;chromiumV3\=10x Chromium v3;citeseq\=CITE-Seq;celseq\=CEL-Seq;celseq2\=CEL-Seq2;quartzseq2\=Quartz-Seq2;rhapsody\=BD Rhapsody (Experimental)
 p5_MODE=
 p5_TYPE=TEXT
 p5_default_value=ISR

salmon_alevin_quant.sh

@@ -255,6 +255,10 @@ params=()
 [[ $method == "celseq2" ]] && params+=(--celseq2)
 [[ $method == "quartzseq2" ]] && params+=(--quartzseq2)
 
+[[ $method == "rhapsody" ]] && params+=(--umi-geometry \'1[53-60]\')
+[[ $method == "rhapsody" ]] && params+=(--bc-geometry \'1[1-9,22-30,44-52]\')
+[[ $method == "rhapsody" ]] && params+=(--read-geometry \'2[1-end]\')
+
 [[ -e "$whitelist" ]] && params+=(--whitelist $whitelist)
 [[ -e "$mtrna" ]] && params+=(--mrna $mtrna)
 [[ -e "$rrna" ]] && params+=(--rrna $rrna)