diff --git a/tests/modules/rsem/calculateexpression/test.yml b/tests/modules/rsem/calculateexpression/test.yml
index 9eb5effc..ac0866ea 100644
--- a/tests/modules/rsem/calculateexpression/test.yml
+++ b/tests/modules/rsem/calculateexpression/test.yml
@@ -1,8 +1,8 @@
 - name: rsem calculateexpression test_rsem_calculateexpression
   command: nextflow run tests/modules/rsem/calculateexpression -entry test_rsem_calculateexpression -c tests/config/nextflow.config
   tags:
-    - rsem/calculateexpression
     - rsem
+    - rsem/calculateexpression
   files:
     - path: output/index/rsem/Genome
       md5sum: a654229fbca6071dcb6b01ce7df704da
diff --git a/tests/modules/star/align/test.yml b/tests/modules/star/align/test.yml
index 79ab38f1..47731c5c 100644
--- a/tests/modules/star/align/test.yml
+++ b/tests/modules/star/align/test.yml
@@ -81,6 +81,7 @@
       md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
     - path: output/star/test.Aligned.out.bam
       md5sum: 38d08f0b944a2a1b981a250d675aa0d9
+    - path: output/star/test.Log.final.out
     - path: output/star/test.Log.out
     - path: output/star/test.Log.progress.out
     - path: output/star/test.SJ.out.tab
diff --git a/tests/modules/star/genomegenerate/test.yml b/tests/modules/star/genomegenerate/test.yml
index 1df59378..df8d5efc 100644
--- a/tests/modules/star/genomegenerate/test.yml
+++ b/tests/modules/star/genomegenerate/test.yml
@@ -1,8 +1,8 @@
 - name: star genomegenerate test_star_genomegenerate
   command: nextflow run tests/modules/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config
   tags:
-    - star/genomegenerate
     - star
+    - star/genomegenerate
   files:
     - path: output/star/star/Genome
       md5sum: a654229fbca6071dcb6b01ce7df704da
diff --git a/tests/modules/stringtie/merge/test.yml b/tests/modules/stringtie/merge/test.yml
index ea47ad48..e6436612 100644
--- a/tests/modules/stringtie/merge/test.yml
+++ b/tests/modules/stringtie/merge/test.yml
@@ -1,23 +1,49 @@
 - name: stringtie merge forward-strand
-  command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_forward_merge -c tests/config/nextflow.config
+  command: nextflow run tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c tests/config/nextflow.config
   tags:
     - stringtie
     - stringtie/merge
   files:
-    - path: ./output/stringtie/stringtie.merged.gtf
-      contains:
-      - 'stringtie'
-      - 'merge'
-      - 'chr22'
+    - path: output/stringtie/stringtie.merged.gtf
+      md5sum: 9fab7049ef2eafdea246fc787d1def40
+    - path: output/stringtie/test.ballgown/e2t.ctab
+      md5sum: 9ae42e056c955a88a883e5e917840d77
+    - path: output/stringtie/test.ballgown/e_data.ctab
+      md5sum: adbedee7b2f84c70362ad6dfa57442b7
+    - path: output/stringtie/test.ballgown/i2t.ctab
+      md5sum: 658131af118cfb416939044fdb5411de
+    - path: output/stringtie/test.ballgown/i_data.ctab
+      md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
+    - path: output/stringtie/test.ballgown/t_data.ctab
+      md5sum: 92a98902784e7406ffe054d2adbabc7c
+    - path: output/stringtie/test.coverage.gtf
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/stringtie/test.gene.abundance.txt
+      md5sum: 9708811bcefe0f6384293d6f419f3250
+    - path: output/stringtie/test.transcripts.gtf
+      md5sum: 0e42709bfe30c2c7f2574ba664f5fa9f
 
-- name: stringtie merge reverse-strand
-  command: nextflow run ./tests/modules/stringtie/merge/ -entry test_stringtie_reverse_merge -c tests/config/nextflow.config
+- name: stringtie merge test_stringtie_reverse_merge
+  command: nextflow run tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c tests/config/nextflow.config
   tags:
     - stringtie
     - stringtie/merge
   files:
-    - path: ./output/stringtie/stringtie.merged.gtf
-      contains:
-      - 'stringtie'
-      - 'merge'
-      - 'chr22'
+    - path: output/stringtie/stringtie.merged.gtf
+      md5sum: afc461bb3cbc368f268a7a45c1b54497
+    - path: output/stringtie/test.ballgown/e2t.ctab
+      md5sum: 9ae42e056c955a88a883e5e917840d77
+    - path: output/stringtie/test.ballgown/e_data.ctab
+      md5sum: fd8496d3957ade3b2c0853155f9a67da
+    - path: output/stringtie/test.ballgown/i2t.ctab
+      md5sum: 658131af118cfb416939044fdb5411de
+    - path: output/stringtie/test.ballgown/i_data.ctab
+      md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
+    - path: output/stringtie/test.ballgown/t_data.ctab
+      md5sum: 92a98902784e7406ffe054d2adbabc7c
+    - path: output/stringtie/test.coverage.gtf
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/stringtie/test.gene.abundance.txt
+      md5sum: 94b85145d60ab1b80a7f0f6cf08418b0
+    - path: output/stringtie/test.transcripts.gtf
+      md5sum: 3196e3d50fd461aae6408e0a70acae68