Improve output file names

modules/jacusa2.nf

@@ -8,12 +8,14 @@ process jacusa2 {
         tuple(path(genome), path(fastaindex))
 
     output:
-        path("*.txt")
+        path("*.site_edits_jacusa2.txt")
         path("*.filtered")
         // tuple(sample, path("filtered_output.txt", emit: tuple_sample_jacusa2_table))
 
     script:
+        base_name = bam.BaseName
+
         """
-        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 jacusa_out.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 D -f V -p ${task.cpus} -r ${base_name}.site_edits_jacusa2.txt -c 1 -s -R ${genome} ${bam}
         """
 }

modules/pluviometer.nf

@@ -9,10 +9,11 @@ process pluviometer {
         val(tool_format)
 
     output:
-        tuple(val(meta), path("feature_edits.tsv"), emit: tuple_sample_feature_edits)
+        tuple(val(meta), path("*.feature_edits.tsv"), emit: tuple_sample_feature_edits)
 
 
     script:
+        base_name = site_edits.BaseName
         """
         # cp ${workflow.projectDir}/bin/stats/*.py ./
         python ${workflow.projectDir}/bin/stats/pluviometer.py \
@@ -22,6 +23,6 @@ process pluviometer {
             --cov 1 \
             --edit_threshold ${params.edit_threshold} \
             --aggregation_mode ${params.aggregation_mode} \
-            --output feature_edits.tsv
+            --output ${base_name}.feature_edits.tsv
         """
 }

modules/reditools2.nf

@@ -1,6 +1,6 @@
 process reditools2 {
     label "reditools2"
-    publishDir("${params.outdir}/reditools", mode: "copy")
+    publishDir("${params.outdir}/reditools2", mode: "copy")
     tag "${meta.id}"
 
     input:
@@ -9,7 +9,7 @@ process reditools2 {
         val region
 
     output:
-        tuple(val(meta), path("edit_table.txt"), emit: tuple_sample_serial_table)
+        tuple(val(meta), path("*site_edits_reditools2.txt"), emit: tuple_sample_serial_table)
 
     script:
 
@@ -29,8 +29,9 @@ process reditools2 {
         // the reditools error message
         strand_orientation = meta.libtype
     }
+    base_name = bam.BaseName
 
     """
-    reditools.py -f ${bam} -r ${genome} -s ${strand_orientation} -o edit_table.txt
+    reditools.py -f ${bam} -r ${genome} -s ${strand_orientation} -o ${base_name}.site_edits_reditools2.txt
     """
 }

modules/sapin.nf

@@ -8,10 +8,11 @@ process sapin {
         path(reference)
 
     output:
-        path("restable.tsv")
+        path("*.site_edits_sapin.tsv")
 
     script:
+        base_name = bam.BaseName
         """
-        sapin -a ${bam} -f ${reference} > restable.tsv
+        sapin -a ${bam} -f ${reference} > ${base_name}.site_edits_sapin.tsv
         """
 }