Merge pull request #85 from karlaarz/dev

stringtie subworkflow and gffcompare. Went through extensive testing by @ctuni

Author: Emeerdink

conf/modules.config

@@ -22,6 +22,14 @@ process {
         ext.args = '--quiet'
     }
 
+    withName: 'GFFCOMPARE' {
+        publishDir = [
+            path: { "${params.outdir}/gffcompare/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

modules.json

@@ -45,6 +45,11 @@
                         "git_sha": "6d7806c166ec5e19f9681b8f86e2c68bc86b34ca",
                         "installed_by": ["fastq_subsample_fq_salmon"]
                     },
+                    "gffcompare": {
+                        "branch": "master",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"]
+                    },
                     "gffread": {
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",