Provide BAI when running rseqc/tin (#1177)

* Provide BAI when running rseqc/tin

* Add md5sum

* Add proper md5sums

* md5sum not md5

* Add xls to meta.yml

modules/rseqc/tin/main.nf

@@ -8,11 +8,12 @@ process RSEQC_TIN {
         'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai)
     path  bed
 
     output:
     tuple val(meta), path("*.txt"), emit: txt
+    tuple val(meta), path("*.xls"), emit: xls
     path "versions.yml"           , emit: versions
 
     script:
@@ -22,8 +23,7 @@ process RSEQC_TIN {
     tin.py \\
         -i $bam \\
         -r $bed \\
-        $args \\
-        > ${prefix}.tin.txt
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/rseqc/tin/meta.yml

@@ -23,6 +23,10 @@ input:
       type: file
       description: Input BAM file
       pattern: "*.{bam}"
+  - bai:
+    type: file
+    description: Index for input BAM file
+    pattern: "*.{bai}"
   - bed:
       type: file
       description: BED file containing the reference gene model
@@ -30,8 +34,12 @@ input:
 output:
   - txt:
       type: file
-      description: tin.py results file
-      pattern: "*.tin.txt"
+      description: TXT file containing tin.py results summary
+      pattern: "*.txt"
+  - xls:
+      type: file
+      description: XLS file containing tin.py results
+      pattern: "*.xls"
   - versions:
       type: file
       description: File containing software versions

tests/modules/rseqc/tin/main.nf

@@ -8,7 +8,8 @@ workflow test_rseqc_tin {
 
     input = [
         [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
     ]
 
     bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)

tests/modules/rseqc/tin/test.yml

@@ -4,4 +4,7 @@
     - rseqc
     - rseqc/tin
   files:
-    - path: output/rseqc/test.tin.txt
+    - path: output/rseqc/test.paired_end.sorted.summary.txt
+      md5sum: 9d98447e178b89a89f6f5aba7a772fe6
+    - path: output/rseqc/test.paired_end.sorted.tin.xls
+      md5sum: 6b1b1b0dc1dc265342ba8c3f27fa60e6