Merge pull request #26 from Juke34/jacusa

jacusa2: pass library type and print all sites (including unedited)

Author: eascarrunz

modules/jacusa2.nf

@@ -8,14 +8,38 @@ process jacusa2 {
         tuple(path(genome), path(fastaindex))
 
     output:
-        path("*.site_edits_jacusa2.txt")
+        tuple(val(meta), path("*.site_edits_jacusa2.txt"), emit: tuple_sample_jacusa2_table)
         path("*.filtered")
-        // tuple(sample, path("filtered_output.txt", emit: tuple_sample_jacusa2_table))
 
     script:
         base_name = bam.BaseName
-        
+        // Set the strand orientation parameter from the library type parameter
+        // Terms explained in https://salmon.readthedocs.io/en/latest/library_type.html
+        if (meta.libtype in ["ISR", "SR"]) {
+            // First-strand oriented
+            jacusa_strand_param = "FR_SECONDSTRAND"
+        } else if (meta.libtype in ["ISF", "SF"]) {
+            // Second-strand oriented
+            jacusa_strand_param = "RF_FIRSTSTRAND"
+        } else if (meta.libtype in ["IU", "U"]) {
+            // Unstranded
+            jacusa_strand_param = "UNSTRANDED"
+        } else {
+            // Unsupported: Pass the library type string so that it's reported in
+            // the Jacusa2 error message
+            jacusa_strand_param = meta.libtype
+        }
         """
-        java -Xmx${task.memory.toMega()}M -jar /usr/local/bin/JACUSA_v2.0.4.jar call-1 -a D -f V -p ${task.cpus} -r ${base_name}.site_edits_jacusa2.txt -c 1 -s -R ${genome} ${bam}
+        java -Xmx${task.memory.toMega()}M -jar /usr/local/bin/JACUSA_v2.0.4.jar \
+            call-1 \
+            -A \
+            -f V \
+            -p ${task.cpus} \
+            -r ${base_name}.site_edits_jacusa2.txt \
+            -c 1 \
+            -s \
+            -R ${genome} \
+            -P ${jacusa_strand_param} \
+            ${bam}                                      
         """
 }