From e9c57083a0938c142e14ccf2b0275ed7724fe9a0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Fern=C3=A1ndez=20Navarro?=
 <jc.fernandez.navarro@gmail.com>
Date: Wed, 15 Sep 2021 20:55:08 +0200
Subject: [PATCH] Fix bug in gffread (#686)

* Fix bug in gffread that would cause it to fail if the input has .gtf as extension

* Update test.yml

* Update meta file

* Update main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/gffread/main.nf        |  6 +++++-
 modules/gffread/meta.yml       | 16 +++-------------
 tests/modules/gffread/main.nf  |  2 +-
 tests/modules/gffread/test.yml |  4 ++--
 4 files changed, 11 insertions(+), 17 deletions(-)

diff --git a/modules/gffread/main.nf b/modules/gffread/main.nf
index 6c5aecbc..6b0dd666 100644
--- a/modules/gffread/main.nf
+++ b/modules/gffread/main.nf
@@ -27,8 +27,12 @@ process GFFREAD {
 
     script:
     def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${gff.baseName}${options.suffix}" : "${gff.baseName}"
     """
-    gffread $gff $options.args -o ${gff.baseName}.gtf
+    gffread \\
+        $gff \\
+        $options.args \\
+        -o ${prefix}.gtf
     echo \$(gffread --version 2>&1) > ${software}.version.txt
     """
 }
diff --git a/modules/gffread/meta.yml b/modules/gffread/meta.yml
index 63d281f5..af2abb6e 100644
--- a/modules/gffread/meta.yml
+++ b/modules/gffread/meta.yml
@@ -14,26 +14,16 @@ tools:
       licence: ['MIT']
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - gff:
         type: file
-        description: A GFF file in either the GFF3 or GFF2 format.
-        patter: "*.gff"
+        description: A reference file in either the GFF3, GFF2 or GTF format.
+        pattern: "*.{gff, gtf}"
 
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - gtf:
       type: file
       description: GTF file resulting from the conversion of the GFF input file
-      pattern: "*.gtf"
+      pattern: "*.{gtf}"
   - version:
       type: file
       description: File containing software version
diff --git a/tests/modules/gffread/main.nf b/tests/modules/gffread/main.nf
index e7b5441a..87e95275 100644
--- a/tests/modules/gffread/main.nf
+++ b/tests/modules/gffread/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { GFFREAD } from '../../../modules/gffread/main.nf' addParams( options: [:] )
+include { GFFREAD } from '../../../modules/gffread/main.nf' addParams( options: [suffix: '.out'] )
 
 workflow test_gffread {
     input = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
diff --git a/tests/modules/gffread/test.yml b/tests/modules/gffread/test.yml
index 21a7bb6a..48096f1e 100644
--- a/tests/modules/gffread/test.yml
+++ b/tests/modules/gffread/test.yml
@@ -3,5 +3,5 @@
   tags:
     - gffread
   files:
-    - path: ./output/gffread/genome.gtf
-      md5sum: f184f856b7fe3e159d21b052b5dd3954
+    - path: ./output/gffread/genome.out.gtf
+      md5sum: fcbf5744ed806e47768bc456fa043263