diff --git a/README.md b/README.md
index 5e345ee2..44b4f41d 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@
 [![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)
 [![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
-> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!  
+> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!
 > PLEASE BE KIND TO OUR CODE REVIEWERS AND SUBMIT ONE PULL REQUEST PER MODULE :)
 
 A repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation.
@@ -42,7 +42,7 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
 
     ```console
     $ nf-core modules list
-    
+
                                           ,--./,-.
           ___     __   __   __   ___     /,-._.--~\
     |\ | |__  __ /  ` /  \ |__) |__         }  {
@@ -306,7 +306,7 @@ In order to test that each module added to `nf-core/modules` is actually working
 
 ### Running tests manually
 
-As outlined in the [nf-core modules create](#nf-core-modules-create) section we have made it quite trivial to create an initial yaml file (via the `nf-core modules create-test-yml` command) containing a listing of all of the module output files and their associated md5sums. However, md5sum checks may not be appropriate for all output files if for example they contain timestamps. This is why it is a good idea to re-run the tests locally with `pytest-workflow` before you create your pull request adding the module. If your files do indeed have timestamps or other issues that prevent you from using the md5sum check, then you can edit the `test.yml` file to instead check that the file contains some specific content or as a last resort, if it exists. The different test options are listed in the [pytest-workflow docs](https://pytest-workflow.readthedocs.io/en/stable/#test-options). 
+As outlined in the [nf-core modules create](#nf-core-modules-create) section we have made it quite trivial to create an initial yaml file (via the `nf-core modules create-test-yml` command) containing a listing of all of the module output files and their associated md5sums. However, md5sum checks may not be appropriate for all output files if for example they contain timestamps. This is why it is a good idea to re-run the tests locally with `pytest-workflow` before you create your pull request adding the module. If your files do indeed have timestamps or other issues that prevent you from using the md5sum check, then you can edit the `test.yml` file to instead check that the file contains some specific content or as a last resort, if it exists. The different test options are listed in the [pytest-workflow docs](https://pytest-workflow.readthedocs.io/en/stable/#test-options).
 
 Please follow the steps below to run the tests locally:
 
diff --git a/software/bowtie/build/main.nf b/software/bowtie/build/main.nf
index 4acb7e2c..5f4d695a 100644
--- a/software/bowtie/build/main.nf
+++ b/software/bowtie/build/main.nf
@@ -9,7 +9,7 @@ process BOWTIE_BUILD {
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
     conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/software/bowtie2/build/main.nf b/software/bowtie2/build/main.nf
index 56dca466..ca3527ee 100644
--- a/software/bowtie2/build/main.nf
+++ b/software/bowtie2/build/main.nf
@@ -9,7 +9,7 @@ process BOWTIE2_BUILD {
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
     conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/software/bwa/index/main.nf b/software/bwa/index/main.nf
index 69737dfb..0ae9f1ce 100644
--- a/software/bwa/index/main.nf
+++ b/software/bwa/index/main.nf
@@ -9,7 +9,7 @@ process BWA_INDEX {
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/software/bwamem2/index/main.nf b/software/bwamem2/index/main.nf
index 2de37358..b54d5897 100644
--- a/software/bwamem2/index/main.nf
+++ b/software/bwamem2/index/main.nf
@@ -9,7 +9,7 @@ process BWAMEM2_INDEX {
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::bwa-mem2=2.1" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/software/bwameth/index/main.nf b/software/bwameth/index/main.nf
index d51c579f..b2885aa4 100644
--- a/software/bwameth/index/main.nf
+++ b/software/bwameth/index/main.nf
@@ -9,7 +9,7 @@ process BWAMETH_INDEX {
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/software/hisat2/build/main.nf b/software/hisat2/build/main.nf
index b8642ef3..6d088c91 100644
--- a/software/hisat2/build/main.nf
+++ b/software/hisat2/build/main.nf
@@ -11,7 +11,7 @@ process HISAT2_BUILD {
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/software/rsem/preparereference/main.nf b/software/rsem/preparereference/main.nf
index 4f963f4d..633b3d90 100644
--- a/software/rsem/preparereference/main.nf
+++ b/software/rsem/preparereference/main.nf
@@ -9,7 +9,7 @@ process RSEM_PREPAREREFERENCE {
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/software/salmon/index/main.nf b/software/salmon/index/main.nf
index 763a4147..a0433c58 100644
--- a/software/salmon/index/main.nf
+++ b/software/salmon/index/main.nf
@@ -9,7 +9,7 @@ process SALMON_INDEX {
     label "process_medium"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
     conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/software/star/genomegenerate/main.nf b/software/star/genomegenerate/main.nf
index 7ca662d6..f1e3bba4 100644
--- a/software/star/genomegenerate/main.nf
+++ b/software/star/genomegenerate/main.nf
@@ -9,7 +9,7 @@ process STAR_GENOMEGENERATE {
     label 'process_high'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
     conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml
index 4ee5be10..503eda09 100644
--- a/tests/software/bowtie/align/test.yml
+++ b/tests/software/bowtie/align/test.yml
@@ -8,17 +8,17 @@
     - path: ./output/bowtie/test.bam
     - path: ./output/bowtie/test.out
       md5sum: 4b9140ceadb8a18ae9330885370f8a0b
-    - path: ./output/bowtie/bowtie/test_genome.3.ebwt
+    - path: ./output/index/bowtie/test_genome.3.ebwt
       md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie/bowtie/test_genome.2.ebwt
+    - path: ./output/index/bowtie/test_genome.2.ebwt
       md5sum: 02b44af9f94c62ecd3c583048e25d4cf
-    - path: ./output/bowtie/bowtie/test_genome.rev.2.ebwt
+    - path: ./output/index/bowtie/test_genome.rev.2.ebwt
       md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
-    - path: ./output/bowtie/bowtie/test_genome.4.ebwt
+    - path: ./output/index/bowtie/test_genome.4.ebwt
       md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie/bowtie/test_genome.rev.1.ebwt
+    - path: ./output/index/bowtie/test_genome.rev.1.ebwt
       md5sum: b37aaf11853e65a3b13561f27a912b06
-    - path: ./output/bowtie/bowtie/test_genome.1.ebwt
+    - path: ./output/index/bowtie/test_genome.1.ebwt
       md5sum: d9b76ecf9fd0413240173273b38d8199
 
 - name: bowtie align paired-end
@@ -30,15 +30,15 @@
   files:
     - path: ./output/bowtie/test.bam
     - path: ./output/bowtie/test.out
-    - path: ./output/bowtie/bowtie/test_genome.3.ebwt
+    - path: ./output/index/bowtie/test_genome.3.ebwt
       md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie/bowtie/test_genome.2.ebwt
+    - path: ./output/index/bowtie/test_genome.2.ebwt
       md5sum: 02b44af9f94c62ecd3c583048e25d4cf
-    - path: ./output/bowtie/bowtie/test_genome.rev.2.ebwt
+    - path: ./output/index/bowtie/test_genome.rev.2.ebwt
       md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
-    - path: ./output/bowtie/bowtie/test_genome.4.ebwt
+    - path: ./output/index/bowtie/test_genome.4.ebwt
       md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie/bowtie/test_genome.rev.1.ebwt
+    - path: ./output/index/bowtie/test_genome.rev.1.ebwt
       md5sum: b37aaf11853e65a3b13561f27a912b06
-    - path: ./output/bowtie/bowtie/test_genome.1.ebwt
+    - path: ./output/index/bowtie/test_genome.1.ebwt
       md5sum: d9b76ecf9fd0413240173273b38d8199
diff --git a/tests/software/bowtie/build_test/test.yml b/tests/software/bowtie/build_test/test.yml
index bdbd775d..67262eb8 100644
--- a/tests/software/bowtie/build_test/test.yml
+++ b/tests/software/bowtie/build_test/test.yml
@@ -4,15 +4,15 @@
     - bowtie
     - bowtie_build
   files:
-    - path: ./output/bowtie/bowtie/test_genome.3.ebwt
+    - path: ./output/index/bowtie/test_genome.3.ebwt
       md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie/bowtie/test_genome.2.ebwt
+    - path: ./output/index/bowtie/test_genome.2.ebwt
       md5sum: 02b44af9f94c62ecd3c583048e25d4cf
-    - path: ./output/bowtie/bowtie/test_genome.rev.2.ebwt
+    - path: ./output/index/bowtie/test_genome.rev.2.ebwt
       md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
-    - path: ./output/bowtie/bowtie/test_genome.4.ebwt
+    - path: ./output/index/bowtie/test_genome.4.ebwt
       md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie/bowtie/test_genome.rev.1.ebwt
+    - path: ./output/index/bowtie/test_genome.rev.1.ebwt
       md5sum: b37aaf11853e65a3b13561f27a912b06
-    - path: ./output/bowtie/bowtie/test_genome.1.ebwt
+    - path: ./output/index/bowtie/test_genome.1.ebwt
       md5sum: d9b76ecf9fd0413240173273b38d8199
diff --git a/tests/software/bowtie2/align/test.yml b/tests/software/bowtie2/align/test.yml
index db895f45..8e246d88 100644
--- a/tests/software/bowtie2/align/test.yml
+++ b/tests/software/bowtie2/align/test.yml
@@ -7,17 +7,17 @@
   files:
     - path: ./output/bowtie2/test.bam
     - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/bowtie2/test_genome.3.bt2
+    - path: ./output/index/bowtie2/test_genome.3.bt2
       md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie2/bowtie2/test_genome.2.bt2
+    - path: ./output/index/bowtie2/test_genome.2.bt2
       md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: ./output/bowtie2/bowtie2/test_genome.1.bt2
+    - path: ./output/index/bowtie2/test_genome.1.bt2
       md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
-    - path: ./output/bowtie2/bowtie2/test_genome.4.bt2
+    - path: ./output/index/bowtie2/test_genome.4.bt2
       md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie2/bowtie2/test_genome.rev.1.bt2
+    - path: ./output/index/bowtie2/test_genome.rev.1.bt2
       md5sum: 52be6950579598a990570fbcf5372184
-    - path: ./output/bowtie2/bowtie2/test_genome.rev.2.bt2
+    - path: ./output/index/bowtie2/test_genome.rev.2.bt2
       md5sum: e3b4ef343dea4dd571642010a7d09597
 
 - name: bowtie2 align paired-end
@@ -29,15 +29,15 @@
   files:
     - path: ./output/bowtie2/test.bam
     - path: ./output/bowtie2/test.bowtie2.log
-    - path: ./output/bowtie2/bowtie2/test_genome.3.bt2
+    - path: ./output/index/bowtie2/test_genome.3.bt2
       md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie2/bowtie2/test_genome.2.bt2
+    - path: ./output/index/bowtie2/test_genome.2.bt2
       md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: ./output/bowtie2/bowtie2/test_genome.1.bt2
+    - path: ./output/index/bowtie2/test_genome.1.bt2
       md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
-    - path: ./output/bowtie2/bowtie2/test_genome.4.bt2
+    - path: ./output/index/bowtie2/test_genome.4.bt2
       md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie2/bowtie2/test_genome.rev.1.bt2
+    - path: ./output/index/bowtie2/test_genome.rev.1.bt2
       md5sum: 52be6950579598a990570fbcf5372184
-    - path: ./output/bowtie2/bowtie2/test_genome.rev.2.bt2
+    - path: ./output/index/bowtie2/test_genome.rev.2.bt2
       md5sum: e3b4ef343dea4dd571642010a7d09597
diff --git a/tests/software/bowtie2/build_test/test.yml b/tests/software/bowtie2/build_test/test.yml
index 136e7ba8..2c5bc1f9 100644
--- a/tests/software/bowtie2/build_test/test.yml
+++ b/tests/software/bowtie2/build_test/test.yml
@@ -4,15 +4,15 @@
     - bowtie2
     - bowtie2_build
   files:
-    - path: ./output/bowtie2/bowtie2/test_genome.3.bt2
+    - path: ./output/index/bowtie2/test_genome.3.bt2
       md5sum: 4ed93abba181d8dfab2e303e33114777
-    - path: ./output/bowtie2/bowtie2/test_genome.2.bt2
+    - path: ./output/index/bowtie2/test_genome.2.bt2
       md5sum: 47b153cd1319abc88dda532462651fcf
-    - path: ./output/bowtie2/bowtie2/test_genome.1.bt2
+    - path: ./output/index/bowtie2/test_genome.1.bt2
       md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
-    - path: ./output/bowtie2/bowtie2/test_genome.4.bt2
+    - path: ./output/index/bowtie2/test_genome.4.bt2
       md5sum: c25be5f8b0378abf7a58c8a880b87626
-    - path: ./output/bowtie2/bowtie2/test_genome.rev.1.bt2
+    - path: ./output/index/bowtie2/test_genome.rev.1.bt2
       md5sum: 52be6950579598a990570fbcf5372184
-    - path: ./output/bowtie2/bowtie2/test_genome.rev.2.bt2
+    - path: ./output/index/bowtie2/test_genome.rev.2.bt2
       md5sum: e3b4ef343dea4dd571642010a7d09597
diff --git a/tests/software/bwa/index/test.yml b/tests/software/bwa/index/test.yml
index a2b074bf..f9d16f13 100644
--- a/tests/software/bwa/index/test.yml
+++ b/tests/software/bwa/index/test.yml
@@ -4,13 +4,13 @@
     - bwa
     - bwa_index
   files:
-    - path: ./output/bwa/bwa/test_genome.bwt
+    - path: ./output/index/bwa/test_genome.bwt
       md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/test_genome.amb
+    - path: ./output/index/bwa/test_genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/test_genome.sa
+    - path: ./output/index/bwa/test_genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-    - path: ./output/bwa/bwa/test_genome.pac
+    - path: ./output/index/bwa/test_genome.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/test_genome.ann
+    - path: ./output/index/bwa/test_genome.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567
diff --git a/tests/software/bwamem2/index/test.yml b/tests/software/bwamem2/index/test.yml
index c5de40a8..27a0f533 100644
--- a/tests/software/bwamem2/index/test.yml
+++ b/tests/software/bwamem2/index/test.yml
@@ -4,13 +4,13 @@
     - bwamem2
     - bwamem2_index
   files:
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.amb
+    - path: ./output/index/bwamem2/test_genome.fasta.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.pac
+    - path: ./output/index/bwamem2/test_genome.fasta.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.0123
+    - path: ./output/index/bwamem2/test_genome.fasta.0123
       md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.bwt.2bit.64
+    - path: ./output/index/bwamem2/test_genome.fasta.bwt.2bit.64
       md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.ann
+    - path: ./output/index/bwamem2/test_genome.fasta.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567
diff --git a/tests/software/bwameth/index/test.yml b/tests/software/bwameth/index/test.yml
index 3375a8b1..662b79b8 100644
--- a/tests/software/bwameth/index/test.yml
+++ b/tests/software/bwameth/index/test.yml
@@ -4,15 +4,15 @@
     - bwameth
     - bwameth_index
   files:
-    - path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t
+    - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t
       md5sum: 98039984526a41d04d6bd92fcc040c62
-    - path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.pac
+    - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.pac
       md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653
-    - path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.amb
+    - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.amb
       md5sum: 249a4195069071ce47cd0bae68abe376
-    - path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.ann
+    - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.ann
       md5sum: 46524d4359dcdfb203a235ab3b930dbb
-    - path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.bwt
+    - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.bwt
       md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b
-    - path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.sa
+    - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.sa
       md5sum: d25f6486f5134f57ed5b258f6fbb8673
diff --git a/tests/software/salmon/index/test.yml b/tests/software/salmon/index/test.yml
index 56746ca9..efd3dac1 100644
--- a/tests/software/salmon/index/test.yml
+++ b/tests/software/salmon/index/test.yml
@@ -4,28 +4,28 @@
     - salmon
     - salmon_index
   files:
-    - path: ./output/salmon/salmon/ref_indexing.log
-    - path: ./output/salmon/salmon/refseq.bin
+    - path: ./output/index/salmon/ref_indexing.log
+    - path: ./output/index/salmon/refseq.bin
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
-    - path: ./output/salmon/salmon/versionInfo.json
+    - path: ./output/index/salmon/versionInfo.json
       md5sum: 204865f645102587c4953fccb256797c
-    - path: ./output/salmon/salmon/complete_ref_lens.bin
+    - path: ./output/index/salmon/complete_ref_lens.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/mphf.bin
+    - path: ./output/index/salmon/mphf.bin
       md5sum: 53669a47610e33e031faafd32703b714
-    - path: ./output/salmon/salmon/pre_indexing.log
-    - path: ./output/salmon/salmon/ctable.bin
-    - path: ./output/salmon/salmon/duplicate_clusters.tsv
+    - path: ./output/index/salmon/pre_indexing.log
+    - path: ./output/index/salmon/ctable.bin
+    - path: ./output/index/salmon/duplicate_clusters.tsv
       md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: ./output/salmon/salmon/reflengths.bin
+    - path: ./output/index/salmon/reflengths.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/info.json
+    - path: ./output/index/salmon/info.json
       md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: ./output/salmon/salmon/refAccumLengths.bin
+    - path: ./output/index/salmon/refAccumLengths.bin
       md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: ./output/salmon/salmon/ctg_offsets.bin
+    - path: ./output/index/salmon/ctg_offsets.bin
       md5sum: 27a76542337df436436e66017f66dd25
-    - path: ./output/salmon/salmon/rank.bin
+    - path: ./output/index/salmon/rank.bin
       md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: ./output/salmon/salmon/pos.bin
-    - path: ./output/salmon/salmon/seq.bin
+    - path: ./output/index/salmon/pos.bin
+    - path: ./output/index/salmon/seq.bin
diff --git a/tests/software/star/genomegenerate/test.yml b/tests/software/star/genomegenerate/test.yml
index 1f238cb9..ac7464e2 100644
--- a/tests/software/star/genomegenerate/test.yml
+++ b/tests/software/star/genomegenerate/test.yml
@@ -4,29 +4,28 @@
     - star
     - star_genomegenerate
   files:
-    - path: output/star/star/Genome
+    - path: ./output/index/star/Genome
       md5sum: 323c992bac354f93073ce0fc43f222f8
-    - path: output/star/star/SA
+    - path: ./output/index/star/SA
       md5sum: 3e70e4fc6d031e1915bb510727f2c559
-    - path: output/star/star/SAindex
+    - path: ./output/index/star/SAindex
       md5sum: a94198b95a245d4f64af2a7133b6ec7b
-    - path: output/star/star/chrLength.txt
+    - path: ./output/index/star/chrLength.txt
       md5sum: f2bea3725fe1c01420c57fb73bdeb31a
-    - path: output/star/star/chrNameLength.txt
+    - path: ./output/index/star/chrNameLength.txt
       md5sum: c7ceb0a8827b2ea91c386933bee48742
-    - path: output/star/star/chrStart.txt
+    - path: ./output/index/star/chrStart.txt
       md5sum: faf5c55020c99eceeef3e34188ac0d2f
-    - path: output/star/star/exonGeTrInfo.tab
+    - path: ./output/index/star/exonGeTrInfo.tab
       md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
-    - path: output/star/star/exonInfo.tab
+    - path: ./output/index/star/exonInfo.tab
       md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
-    - path: output/star/star/genomeParameters.txt
-      md5sum: 05e1041cbfb7f81686e17bc80b3ddcea
-    - path: output/star/star/sjdbInfo.txt
+    - path: ./output/index/star/sjdbInfo.txt
       md5sum: 1082ab459363b3f2f7aabcef0979c1ed
-    - path: output/star/star/sjdbList.fromGTF.out.tab
+    - path: ./output/index/star/sjdbList.fromGTF.out.tab
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/star/star/sjdbList.out.tab
+    - path: ./output/index/star/sjdbList.out.tab
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/star/star/transcriptInfo.tab
-      md5sum: 8fbe69abbbef4f89da3854873984dbac
\ No newline at end of file
+    - path: ./output/index/star/transcriptInfo.tab
+      md5sum: 8fbe69abbbef4f89da3854873984dbac
+    - path: ./output/index/star/genomeParameters.txt