diff --git a/tests/software/bowtie/align/main.nf b/tests/software/bowtie/align/main.nf
new file mode 100644
index 00000000..c31d5e2d
--- /dev/null
+++ b/tests/software/bowtie/align/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] )
+include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
+
+workflow test_bowtie_alignment_single_end {
+
+    def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_BUILD ( fasta )
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
+}
+
+workflow test_bowtie_alignment_paired_end {
+    
+    def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_BUILD ( fasta )
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
+}
diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml
new file mode 100644
index 00000000..0824644e
--- /dev/null
+++ b/tests/software/bowtie/align/test.yml
@@ -0,0 +1,47 @@
+- name: bowtie align single-end
+  command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
+  tags:
+    - bowtie
+    - bowtie_align
+    - bowtie_align_single_end
+  files:
+    - path: output/bowtie/bowtie/NC_010473.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/bowtie/NC_010473.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/bowtie/NC_010473.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/bowtie/NC_010473.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
+    - path: output/bowtie/test.out
+      md5sum: a81cb18024616415a6cec3108a36fccd
+    - path: output/bowtie/test.bam
+      md5sum: 9feed8a55d4b5e600dcc577768ef07fc
+
+- name: bowtie align paired-end
+  command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
+  tags:
+    - bowtie
+    - bowtie_align
+    - bowtie_align_paired_end
+  files:
+    - path: output/bowtie/bowtie/NC_010473.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/bowtie/NC_010473.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/bowtie/NC_010473.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/bowtie/NC_010473.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
+    - path: output/bowtie/test.out
+      md5sum: a23e9a2a76e949aeb3693bcfae41a615
+    - path: output/bowtie/test.bam
+      md5sum: cf6a6381aa504e8342638ff3b509721e
diff --git a/tests/software/bowtie/build/main.nf b/tests/software/bowtie/build/main.nf
new file mode 100644
index 00000000..4b43eb87
--- /dev/null
+++ b/tests/software/bowtie/build/main.nf
@@ -0,0 +1,10 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] )
+
+workflow test_bowtie_build {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_BUILD ( fasta )
+}
\ No newline at end of file
diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml
new file mode 100644
index 00000000..145836d6
--- /dev/null
+++ b/tests/software/bowtie/build/test.yml
@@ -0,0 +1,18 @@
+- name: bowtie build
+  command: nextflow run ./tests/software/bowtie -entry test_bowtie_build -c tests/config/nextflow.config
+  tags:
+    - bowtie
+    - bowtie_build
+  files:
+    - path: output/bowtie/bowtie/NC_010473.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/bowtie/NC_010473.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/bowtie/NC_010473.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/bowtie/NC_010473.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
\ No newline at end of file
diff --git a/tests/software/bowtie2/align/main.nf b/tests/software/bowtie2/align/main.nf
new file mode 100644
index 00000000..89e9f250
--- /dev/null
+++ b/tests/software/bowtie2/align/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] )
+include { BOWTIE2_ALIGN } from '../../../software/bowtie2/align/main.nf' addParams( options: [:] )
+
+workflow test_bowtie2_align_single_end {
+
+    def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE2_BUILD ( fasta )
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
+}
+
+workflow test_bowtie2_align_paired_end {
+    
+    def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE2_BUILD ( fasta )
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
+}
diff --git a/tests/software/bowtie2/align/test.yml b/tests/software/bowtie2/align/test.yml
new file mode 100644
index 00000000..2e9e3279
--- /dev/null
+++ b/tests/software/bowtie2/align/test.yml
@@ -0,0 +1,45 @@
+- name: bowtie2 align single-end
+  command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2_align_single_end
+  files:
+    - path: output/bowtie2/bowtie2/NC_010473.1.bt2
+      md5sum: 4db22d92e72111a5fbf609b3d9a43015
+    - path: output/bowtie2/bowtie2/NC_010473.2.bt2
+      md5sum: f4429ec74ee0064732c4bb26718a3eb1
+    - path: output/bowtie2/bowtie2/NC_010473.3.bt2
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie2/bowtie2/NC_010473.4.bt2
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
+      md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
+    - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
+      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
+    - path: output/bowtie2/test.bowtie2.log
+      md5sum: 90041c264231be535042adb93a279356
+    - path: output/bowtie2/test.bam
+      md5sum: 906102f401d8234b6473790988fb09cf
+
+- name: bowtie2 align paired-end
+  command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2_align_paired_end
+  files:
+    - path: output/bowtie2/bowtie2/NC_010473.1.bt2
+      md5sum: 4db22d92e72111a5fbf609b3d9a43015
+    - path: output/bowtie2/bowtie2/NC_010473.2.bt2
+      md5sum: f4429ec74ee0064732c4bb26718a3eb1
+    - path: output/bowtie2/bowtie2/NC_010473.3.bt2
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie2/bowtie2/NC_010473.4.bt2
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
+      md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
+    - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
+      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
+    - path: output/bowtie2/test.bowtie2.log
+      md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5
+    - path: output/bowtie2/test.bam
+      md5sum: 732a33cd9816b38ea9b919c25eeb78f8
diff --git a/tests/software/bowtie2/build/main.nf b/tests/software/bowtie2/build/main.nf
new file mode 100644
index 00000000..9742d3ce
--- /dev/null
+++ b/tests/software/bowtie2/build/main.nf
@@ -0,0 +1,10 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE2_BUILD } from '../../../software/bowtie2/build/main.nf' addParams( options: [:] )
+
+workflow test_bowtie2_build {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE2_BUILD ( fasta )
+}
\ No newline at end of file
diff --git a/tests/software/bowtie2/build/test.yml b/tests/software/bowtie2/build/test.yml
new file mode 100644
index 00000000..0c01844b
--- /dev/null
+++ b/tests/software/bowtie2/build/test.yml
@@ -0,0 +1,18 @@
+- name: bowtie2 build
+  command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config
+  tags:
+    - bowtie2
+    - bowtie2_build
+  files:
+    - path: output/bowtie2/bowtie2/NC_010473.1.bt2
+      md5sum: 4db22d92e72111a5fbf609b3d9a43015
+    - path: output/bowtie2/bowtie2/NC_010473.2.bt2
+      md5sum: f4429ec74ee0064732c4bb26718a3eb1
+    - path: output/bowtie2/bowtie2/NC_010473.3.bt2
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie2/bowtie2/NC_010473.4.bt2
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
+      md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
+    - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
+      md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
\ No newline at end of file
diff --git a/tests/software/bwa/index/main.nf b/tests/software/bwa/index/main.nf
new file mode 100644
index 00000000..93510a21
--- /dev/null
+++ b/tests/software/bwa/index/main.nf
@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] )
+
+workflow test_bwa_index {
+    BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
+}
\ No newline at end of file
diff --git a/tests/software/bwa/index/test.yml b/tests/software/bwa/index/test.yml
new file mode 100644
index 00000000..29d50d9b
--- /dev/null
+++ b/tests/software/bwa/index/test.yml
@@ -0,0 +1,14 @@
+- name: bwa index
+  command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_index
+  files:
+    - path: output/bwa/NC_010473.fa.amb
+      md5sum: 942a990ae872f1c0b8d72dda2db405d5
+    - path: output/bwa/NC_010473.fa.bwt
+      md5sum: 7301b52e2ecb893d429a49fa692447ae
+    - path: output/bwa/NC_010473.fa.pac
+      md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
+    - path: output/bwa/NC_010473.fa.sa
+      md5sum: a47dcc92e750e2f16fbd979b8ff9538e
\ No newline at end of file
diff --git a/tests/software/bwa/mem/main.nf b/tests/software/bwa/mem/main.nf
new file mode 100644
index 00000000..0324546d
--- /dev/null
+++ b/tests/software/bwa/mem/main.nf
@@ -0,0 +1,38 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWA_MEM } from '../../../software/bwa/mem/main.nf' addParams( options: [:] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_bwa_mem_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
+
+    BWA_MEM (
+        input,
+        file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
+        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_bwa_mem_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
+
+    BWA_MEM (
+        input,
+        file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
+        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    )
+}
diff --git a/tests/software/bwa/mem/test.yml b/tests/software/bwa/mem/test.yml
new file mode 100644
index 00000000..8c726066
--- /dev/null
+++ b/tests/software/bwa/mem/test.yml
@@ -0,0 +1,19 @@
+- name: bwa mem single-end
+  command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_mem
+    - bwa_mem_single_end
+  files:
+    - path: output/test_single_end/test.bam
+      md5sum: 3ee21210bac387e0335008146e4728bc
+
+- name: bwa mem paired-end
+  command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_mem
+    - bwa_mem_paired_end
+  files:
+    - path: output/test_paired_end/test.bam
+      md5sum: 510d8acc6448c07cdacce8e64ec0904c
diff --git a/tests/software/cutadapt/main.nf b/tests/software/cutadapt/main.nf
index fb3b5c52..bd632694 100644
--- a/tests/software/cutadapt/main.nf
+++ b/tests/software/cutadapt/main.nf
@@ -7,11 +7,11 @@ include { CUTADAPT } from '../../../software/cutadapt/main.nf'  addParams( optio
 /*
  * Test with single-end data
  */
-workflow test_cutadapt_se {
+workflow test_cutadapt_single_end {
+    
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
-
     CUTADAPT( input )
 }
 
@@ -19,12 +19,12 @@ workflow test_cutadapt_se {
  * Test with paired-end data
  */
 
-workflow test_cutadapt_pe {
+workflow test_cutadapt_paired_end {
+
     def input = []
     input = [ [ id:'test', single_end:false ], // meta map
               [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
                 file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
-
     CUTADAPT( input )
 }
 
diff --git a/tests/software/cutadapt/test.yml b/tests/software/cutadapt/test.yml
index c91a0713..9cadf0fb 100644
--- a/tests/software/cutadapt/test.yml
+++ b/tests/software/cutadapt/test.yml
@@ -1,17 +1,17 @@
-- name: Run cutadapt single-end test workflow
-  command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_se -c tests/config/nextflow.config
+- name: cutadapt single-end
+  command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_single_end -c tests/config/nextflow.config
   tags:
     - cutadapt
-    - cutadapt_se
+    - cutadapt_single_end
   files:
     - path: ./output/cutadapt/test.cutadapt.log
     - path: ./output/cutadapt/test.trim.fastq.gz
 
-- name: Run cutadapt paired-end test workflow
-  command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_pe -c tests/config/nextflow.config
+- name: cutadapt paired-end
+  command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_paired_end -c tests/config/nextflow.config
   tags:
     - cutadapt
-    - cutadapt_pe
+    - cutadapt_paired_end
   files:
     - path: ./output/cutadapt/test.cutadapt.log
     - path: ./output/cutadapt/test_1.trim.fastq.gz
diff --git a/tests/software/dsh/filterbed/main.nf b/tests/software/dsh/filterbed/main.nf
new file mode 100644
index 00000000..f4d63496
--- /dev/null
+++ b/tests/software/dsh/filterbed/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DSH_FILTERBED } from '../../../software/dsh/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] )
+
+workflow test_dsh_filterbed {
+
+    def input = []
+    input = [ [ id:'A' ], // meta map
+              [ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
+
+    DSH_FILTERBED ( input )
+}
\ No newline at end of file
diff --git a/tests/software/dsh/filterbed/test.yml b/tests/software/dsh/filterbed/test.yml
new file mode 100644
index 00000000..989da517
--- /dev/null
+++ b/tests/software/dsh/filterbed/test.yml
@@ -0,0 +1,8 @@
+- name: dsh filterbed
+  command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config
+  tags:
+    - dsh
+    - dsh_filterbed
+  files:
+    - path: output/dsh/A.filtered.bed.gz
+      md5sum: 91cee4392d6034793f99f6c53891d866
\ No newline at end of file
diff --git a/tests/software/dsh/splitbed/main.nf b/tests/software/dsh/splitbed/main.nf
new file mode 100644
index 00000000..ed8286b9
--- /dev/null
+++ b/tests/software/dsh/splitbed/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DSH_SPLITBED } from '../../../software/dsh/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] )
+
+workflow test_dsh_splitbed {
+
+    def input = []
+    input = [ [ id:'A' ], // meta map
+              [ file("${launchDir}/tests/data/bed/A.bed.gz", checkIfExists: true) ] ]
+
+    DSH_SPLITBED ( input )
+}
diff --git a/tests/software/dsh/splitbed/test.yml b/tests/software/dsh/splitbed/test.yml
new file mode 100644
index 00000000..268cd463
--- /dev/null
+++ b/tests/software/dsh/splitbed/test.yml
@@ -0,0 +1,10 @@
+- name: dsh splitbed
+  command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config
+  tags:
+    - dsh
+    - dsh_splitbed
+  files:
+    - path: output/dsh/A.0.bed.gz
+      md5sum: 619e51c435d0e7138ca41b660ed07e3a
+    - path: output/dsh/A.1.bed.gz
+      md5sum: 223bba025a0bb859de9a1bf385550a7e
diff --git a/tests/software/fastp/main.nf b/tests/software/fastp/main.nf
index 000fcdd8..f035bc9c 100644
--- a/tests/software/fastp/main.nf
+++ b/tests/software/fastp/main.nf
@@ -7,24 +7,23 @@ include { FASTP } from '../../../software/fastp/main.nf'  addParams( options: [:
 /*
  * Test with single-end data
  */
-workflow test_fastp_se {
+workflow test_fastp_single_end {
+    
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
-
-    FASTP( input )
+    FASTP ( input )
 }
 
 /*
  * Test with paired-end data
  */
+workflow test_fastp_paired_end {
 
-workflow test_fastp_pe {
     def input = []
     input = [ [ id:'test', single_end:false ], // meta map
               [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
                 file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
-
-    FASTP( input )
+    FASTP ( input )
 }
 
diff --git a/tests/software/fastp/test.yml b/tests/software/fastp/test.yml
index 5034c69a..b46c8dd7 100644
--- a/tests/software/fastp/test.yml
+++ b/tests/software/fastp/test.yml
@@ -1,8 +1,8 @@
-- name: fastp_se
-  command: nextflow run ./tests/software/fastp -entry test_fastp_se -c ./tests/config/nextflow.config
+- name: fastp single-end
+  command: nextflow run ./tests/software/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config
   tags:
     - fastp
-    - fastp_se
+    - fastp_single_end
   files:
     - path: ./output/fastp/test.fastp.json
       md5sum: b81d53bfa5c1553bed89f6475edcf437
@@ -11,11 +11,11 @@
     - path: ./output/fastp/test.fastp.log
     - path: ./output/fastp/test.fastp.html
 
-- name: fastp_pe
-  command: nextflow run ./tests/software/fastp -entry test_fastp_pe -c ./tests/config/nextflow.config
+- name: fastp paired-end
+  command: nextflow run ./tests/software/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config
   tags:
     - fastp
-    - fastp_pe
+    - fastp_paired_end
   files:
     - path: ./output/fastp/test.fastp.html
     - path: ./output/fastp/test.fastp.json
diff --git a/tests/software/fastqc/main.nf b/tests/software/fastqc/main.nf
index 27411a17..2ff1474a 100644
--- a/tests/software/fastqc/main.nf
+++ b/tests/software/fastqc/main.nf
@@ -2,35 +2,27 @@
 
 nextflow.enable.dsl = 2
 
-include { FASTQC as FASTQC_SE } from '../../../software/fastqc/main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
-include { FASTQC as FASTQC_PE } from '../../../software/fastqc/main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
+include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] )
 
 /*
  * Test with single-end data
  */
-workflow test_single_end {
+workflow test_fastqc_single_end {
 
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
-
-    FASTQC_SE ( input )
+    FASTQC ( input )
 }
 
 /*
  * Test with paired-end data
  */
-workflow test_paired_end {
+workflow test_fastqc_paired_end {
 
     def input = []
     input = [[id: 'test', single_end: false], // meta map
              [file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
               file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true)]]
-
-    FASTQC_PE(input)
-
-    emit:
-    html = FASTQC_PE.out.html
-    zip  = FASTQC_PE.out.zip
-
+    FASTQC (input)
 }
diff --git a/tests/software/fastqc/test.yml b/tests/software/fastqc/test.yml
index 2c0862dd..c883d599 100644
--- a/tests/software/fastqc/test.yml
+++ b/tests/software/fastqc/test.yml
@@ -1,15 +1,17 @@
-- name: Run fastqc single-end test workflow
-  command: nextflow run ./tests/software/fastqc/ -entry test_single_end -c tests/config/nextflow.config
+- name: fastqc single-end
+  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
   tags:
     - fastqc
+    - fastqc_single_end
   files:
     - path: output/test_single_end/test_fastqc.html
     - path: output/test_single_end/test_fastqc.zip
 
-- name: Run fastqc paired-end test workflow
-  command: nextflow run ./tests/software/fastqc/ -entry test_paired_end -c tests/config/nextflow.config
+- name: fastqc paired-end
+  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
   tags:
     - fastqc
+    - fastqc_paired_end
   files:
     - path: output/test_paired_end/test_1_fastqc.html
     - path: output/test_paired_end/test_2_fastqc.html
diff --git a/tests/software/gffread/test.yml b/tests/software/gffread/test.yml
index a05e609d..d8547daa 100644
--- a/tests/software/gffread/test.yml
+++ b/tests/software/gffread/test.yml
@@ -1,4 +1,4 @@
-- name: Run gffread  test workflow
+- name: gffread
   command: nextflow run ./tests/software/gffread/ -entry test_gffread -c tests/config/nextflow.config
   tags:
     - gffread
diff --git a/tests/software/multiqc/test.yml b/tests/software/multiqc/test.yml
index 21dc36df..68df353d 100644
--- a/tests/software/multiqc/test.yml
+++ b/tests/software/multiqc/test.yml
@@ -1,4 +1,4 @@
-- name: Run multiqc test workflow
+- name: multiqc
   command: nextflow run ./tests/software/multiqc/ -entry test_multiqc -c tests/config/nextflow.config
   tags:
     - multiqc
diff --git a/tests/software/picard/collectmultiplemetrics/main.nf b/tests/software/picard/collectmultiplemetrics/main.nf
new file mode 100644
index 00000000..423b10e1
--- /dev/null
+++ b/tests/software/picard/collectmultiplemetrics/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
+
+workflow test_picard_collectmultiplemetrics {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
+
+    PICARD_COLLECTMULTIPLEMETRICS (
+        input,
+        file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    )
+}
\ No newline at end of file
diff --git a/tests/software/picard/collectmultiplemetrics/test.yml b/tests/software/picard/collectmultiplemetrics/test.yml
new file mode 100644
index 00000000..0cda8949
--- /dev/null
+++ b/tests/software/picard/collectmultiplemetrics/test.yml
@@ -0,0 +1,16 @@
+- name: picard collectmultiplemetrics
+  command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_collectmultiplemetrics
+  files:
+    # These can't be md5'd consistently
+    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
\ No newline at end of file
diff --git a/tests/software/picard/markduplicates/main.nf b/tests/software/picard/markduplicates/main.nf
new file mode 100644
index 00000000..3b161b45
--- /dev/null
+++ b/tests/software/picard/markduplicates/main.nf
@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] )
+
+workflow test_picard_markduplicates_sorted_bam  {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+
+    PICARD_MARKDUPLICATES ( input )
+}
+
+workflow test_picard_markduplicates_unsorted_bam  {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
+
+    PICARD_MARKDUPLICATES ( input )
+}
diff --git a/tests/software/picard/markduplicates/test.yml b/tests/software/picard/markduplicates/test.yml
new file mode 100644
index 00000000..b9dfee34
--- /dev/null
+++ b/tests/software/picard/markduplicates/test.yml
@@ -0,0 +1,17 @@
+- name: picard markduplicates on sorted bam
+  command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_markduplicates
+  files:
+    - path: output/picard/test.MarkDuplicates.metrics.txt
+    - path: output/picard/test.bam
+      md5sum: 0ed0bfc94069380334ccd595f6d8207c
+
+- name: picard markduplicates on unsorted bam
+  command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_markduplicates
+    - should fail
+  exit_code: 1
diff --git a/tests/software/picard/mergesamfiles/main.nf b/tests/software/picard/mergesamfiles/main.nf
new file mode 100644
index 00000000..1835c8ba
--- /dev/null
+++ b/tests/software/picard/mergesamfiles/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
+
+workflow test_picard_mergesamfiles {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true), ] ]
+
+    PICARD_MERGESAMFILES ( input )
+}
diff --git a/tests/software/picard/mergesamfiles/test.yml b/tests/software/picard/mergesamfiles/test.yml
new file mode 100644
index 00000000..9273ff46
--- /dev/null
+++ b/tests/software/picard/mergesamfiles/test.yml
@@ -0,0 +1,8 @@
+- name: picard mergesamfiles
+  command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_mergesamfiles
+  files:
+    - path: output/picard/test.bam
+      md5sum: a9c8a28d1aac362df5973ba2d9923f86
\ No newline at end of file
diff --git a/tests/software/preseq/lcextrap/main.nf b/tests/software/preseq/lcextrap/main.nf
new file mode 100644
index 00000000..864e1230
--- /dev/null
+++ b/tests/software/preseq/lcextrap/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRESEQ_LCEXTRAP } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [:] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_preseq_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
+    PRESEQ_LCEXTRAP ( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_preseq_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
+
+    PRESEQ_LCEXTRAP ( input )
+}
+
diff --git a/tests/software/preseq/lcextrap/test.yml b/tests/software/preseq/lcextrap/test.yml
new file mode 100644
index 00000000..51a7b08c
--- /dev/null
+++ b/tests/software/preseq/lcextrap/test.yml
@@ -0,0 +1,21 @@
+- name: preseq lcextrap single-end
+  command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config
+  tags:
+    - preseq
+    - preseq_lcextrap
+    - preseq_lcextrap_single_end
+  files:
+    - path: output/test_preseq_single_end/test.ccurve.txt
+      md5sum: 76ae04c8eaf19c94e3210bb69da38498
+    - path: output/test_preseq_single_end/test.command.log
+
+- name: preseq lcextrap paired-end
+  command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config
+  tags:
+    - preseq
+    - preseq_lcextrap
+    - preseq_lcextrap_paired_end
+  files:
+    - path: output/test_preseq_paired_end/test.ccurve.txt
+      md5sum: 2836d2fabd2213f097fd7063db550276
+    - path: output/test_preseq_paired_end/test.command.log
diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml
index 17a7f056..43d909fd 100644
--- a/tests/software/quast/test.yml
+++ b/tests/software/quast/test.yml
@@ -1,4 +1,4 @@
-- name: quast_ref
+- name: quast with reference
   command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
   tags:
     - quast
@@ -87,7 +87,7 @@
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
 
-- name: quast_noref
+- name: quast without reference
   command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config
   tags:
     - quast
diff --git a/tests/software/salmon/index/main.nf b/tests/software/salmon/index/main.nf
new file mode 100644
index 00000000..24fb76e2
--- /dev/null
+++ b/tests/software/salmon/index/main.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
+
+workflow test_salmon_index {
+    def genome_fasta     = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
+    def transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
+}
\ No newline at end of file
diff --git a/tests/software/salmon/index/test.yml b/tests/software/salmon/index/test.yml
new file mode 100644
index 00000000..55bd848f
--- /dev/null
+++ b/tests/software/salmon/index/test.yml
@@ -0,0 +1,31 @@
+- name: salmon index
+  command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config
+  tags:
+    - salmon
+    - salmon_index
+  files:
+    - path: ./output/salmon/salmon/info.json
+      md5sum: 61ff4d3471134c280668355ddd39e99f
+    - path: ./output/salmon/salmon/mphf.bin
+      md5sum: 53669a47610e33e031faafd32703b714
+    - path: ./output/salmon/salmon/complete_ref_lens.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/ref_indexing.log
+    - path: ./output/salmon/salmon/versionInfo.json
+      md5sum: 204865f645102587c4953fccb256797c
+    - path: ./output/salmon/salmon/seq.bin
+    - path: ./output/salmon/salmon/pre_indexing.log
+    - path: ./output/salmon/salmon/rank.bin
+      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
+    - path: ./output/salmon/salmon/reflengths.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/ctable.bin
+    - path: ./output/salmon/salmon/ctg_offsets.bin
+      md5sum: 27a76542337df436436e66017f66dd25
+    - path: ./output/salmon/salmon/pos.bin
+    - path: ./output/salmon/salmon/duplicate_clusters.tsv
+      md5sum: 51b5292e3a874119c0e1aa566e95d70c
+    - path: ./output/salmon/salmon/refAccumLengths.bin
+      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
+    - path: ./output/salmon/salmon/refseq.bin
+      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
\ No newline at end of file
diff --git a/tests/software/salmon/quant/main.nf b/tests/software/salmon/quant/main.nf
new file mode 100644
index 00000000..12e2792b
--- /dev/null
+++ b/tests/software/salmon/quant/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams( options: [:] )
+include { SALMON_QUANT } from '../../../software/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
+
+workflow test_salmon_quant_single_end {
+
+    def genome_fasta     = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
+    def transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
+    def gtf   = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
+    def input = [ [ id:'test', single_end:true ], // meta map
+                  file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ]
+
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
+    SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false)
+    
+}
+
+workflow test_salmon_quant_paired_end {
+
+    def genome_fasta     = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
+    def transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
+    def gtf   = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
+    def input = [ [ id:'test', single_end:false ], // meta map
+                  [ file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true),
+                    file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ]
+
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
+    SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false)
+
+}
\ No newline at end of file
diff --git a/tests/software/salmon/quant/test.yml b/tests/software/salmon/quant/test.yml
new file mode 100644
index 00000000..961e1171
--- /dev/null
+++ b/tests/software/salmon/quant/test.yml
@@ -0,0 +1,107 @@
+- name: salmon quant single-end
+  command: nextflow run ./tests/software/salmon -entry test_salmon_quant_single_end -c tests/config/nextflow.config
+  tags:
+    - salmon
+    - salmon_quant
+    - salmon_quant_single_end
+  files:
+    - path: ./output/salmon/salmon/versionInfo.json
+      md5sum: 204865f645102587c4953fccb256797c
+    - path: ./output/salmon/salmon/ctg_offsets.bin
+      md5sum: 27a76542337df436436e66017f66dd25
+    - path: ./output/salmon/test/aux_info/meta_info.json
+    - path: ./output/salmon/salmon/duplicate_clusters.tsv
+      md5sum: 51b5292e3a874119c0e1aa566e95d70c
+    - path: ./output/salmon/salmon/pre_indexing.log
+    - path: ./output/salmon/salmon/rank.bin
+      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
+    - path: ./output/salmon/test/aux_info/observed_bias.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/test/aux_info/expected_bias.gz
+      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
+    - path: ./output/salmon/test/aux_info/fld.gz
+    - path: ./output/salmon/salmon/ctable.bin
+    - path: ./output/salmon/salmon/info.json
+      md5sum: 61ff4d3471134c280668355ddd39e99f
+    - path: ./output/salmon/test/quant.genes.sf
+      md5sum: 5b39785b4d8da533c08ee4a6c8bc1211
+    - path: ./output/salmon/salmon/refseq.bin
+      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
+    - path: ./output/salmon/salmon/complete_ref_lens.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/test/logs/salmon_quant.log
+    - path: ./output/salmon/test/libParams/flenDist.txt
+      md5sum: 2de170bdc9f6fd237d286429b292bb28
+    - path: ./output/salmon/salmon/ref_indexing.log
+    - path: ./output/salmon/salmon/refAccumLengths.bin
+      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
+    - path: ./output/salmon/salmon/seq.bin
+    - path: ./output/salmon/salmon/mphf.bin
+      md5sum: 53669a47610e33e031faafd32703b714
+    - path: ./output/salmon/test/aux_info/observed_bias_3p.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/test/lib_format_counts.json
+      md5sum: aca0a40187eb407b1b8fc85c01284583
+    - path: ./output/salmon/salmon/reflengths.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/pos.bin
+    - path: ./output/salmon/test/cmd_info.json
+      md5sum: d95f9bd2287a55fa44bbd9b9d4c4ff8a
+    - path: ./output/salmon/test/aux_info/ambig_info.tsv
+      md5sum: c3306d26186ffe018ad4f19d52256180
+    - path: ./output/salmon/test/quant.sf
+      md5sum: b08095ac70f89efc3146cdf488d0eb73
+
+- name: salmon quant paired end
+  command: nextflow run ./tests/software/salmon -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
+  tags:
+    - salmon
+    - salmon_quant
+    - salmon_quant_paired_end
+  files:
+    - path: ./output/salmon/salmon/pos.bin
+    - path: ./output/salmon/salmon/versionInfo.json
+      md5sum: 204865f645102587c4953fccb256797c
+    - path: ./output/salmon/salmon/complete_ref_lens.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/test/lib_format_counts.json
+      md5sum: a8b6e6bfbc28c6e790ddaec559fad9ea
+    - path: ./output/salmon/test/aux_info/expected_bias.gz
+      md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
+    - path: ./output/salmon/test/libParams/flenDist.txt
+      md5sum: f90c7256c9b18d4131f4d4ecb69d0f55
+    - path: ./output/salmon/salmon/ref_indexing.log
+    - path: ./output/salmon/test/aux_info/observed_bias_3p.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/salmon/ctable.bin
+    - path: ./output/salmon/test/aux_info/meta_info.json
+    - path: ./output/salmon/test/aux_info/fld.gz
+    - path: ./output/salmon/salmon/refseq.bin
+      md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
+    - path: ./output/salmon/salmon/info.json
+      md5sum: 61ff4d3471134c280668355ddd39e99f
+    - path: ./output/salmon/salmon/seq.bin
+    - path: ./output/salmon/test/cmd_info.json
+      md5sum: 007676e4d79de0809a03e0ea045ed4a1
+    - path: ./output/salmon/test/aux_info/observed_bias.gz
+      md5sum: ef13c06a538e9c34ca9f84212c82f44e
+    - path: ./output/salmon/salmon/duplicate_clusters.tsv
+      md5sum: 51b5292e3a874119c0e1aa566e95d70c
+    - path: ./output/salmon/test/quant.genes.sf
+      md5sum: eb3e7b44801a0b3af07c25963927e20d
+    - path: ./output/salmon/salmon/rank.bin
+      md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
+    - path: ./output/salmon/salmon/mphf.bin
+      md5sum: 53669a47610e33e031faafd32703b714
+    - path: ./output/salmon/test/aux_info/ambig_info.tsv
+      md5sum: 950001575c24fb6bc2c7a6848043b126
+    - path: ./output/salmon/test/logs/salmon_quant.log
+    - path: ./output/salmon/salmon/pre_indexing.log
+    - path: ./output/salmon/salmon/refAccumLengths.bin
+      md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
+    - path: ./output/salmon/test/quant.sf
+      md5sum: addb78e233f248b8f62cae3e217bf689
+    - path: ./output/salmon/salmon/reflengths.bin
+      md5sum: f57562f1fca3ae7b133f895ae13c3d08
+    - path: ./output/salmon/salmon/ctg_offsets.bin
+      md5sum: 27a76542337df436436e66017f66dd25
diff --git a/tests/software/samtools/flagstat/main.nf b/tests/software/samtools/flagstat/main.nf
new file mode 100644
index 00000000..0d8a15b6
--- /dev/null
+++ b/tests/software/samtools/flagstat/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
+
+workflow test_samtools_flagstat {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
+    SAMTOOLS_FLAGSTAT ( input )
+}
\ No newline at end of file
diff --git a/tests/software/samtools/flagstat/test.yml b/tests/software/samtools/flagstat/test.yml
new file mode 100644
index 00000000..06f8ca9b
--- /dev/null
+++ b/tests/software/samtools/flagstat/test.yml
@@ -0,0 +1,8 @@
+- name: samtools flagstat
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_flagstat
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.flagstat
+      md5sum: 80590621c74f5ee43ada20d010a3837f
\ No newline at end of file
diff --git a/tests/software/samtools/idxstats/main.nf b/tests/software/samtools/idxstats/main.nf
new file mode 100644
index 00000000..aadb4465
--- /dev/null
+++ b/tests/software/samtools/idxstats/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
+
+workflow test_samtools_idxstats {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
+    SAMTOOLS_IDXSTATS ( input )
+}
\ No newline at end of file
diff --git a/tests/software/samtools/idxstats/test.yml b/tests/software/samtools/idxstats/test.yml
new file mode 100644
index 00000000..a1289a1b
--- /dev/null
+++ b/tests/software/samtools/idxstats/test.yml
@@ -0,0 +1,8 @@
+- name: samtools idxstats
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_idxstats
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.idxstats
+      md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
\ No newline at end of file
diff --git a/tests/software/samtools/index/main.nf b/tests/software/samtools/index/main.nf
new file mode 100644
index 00000000..181ae608
--- /dev/null
+++ b/tests/software/samtools/index/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] )
+
+workflow test_samtools_index {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+    SAMTOOLS_INDEX ( input )
+}
diff --git a/tests/software/samtools/index/test.yml b/tests/software/samtools/index/test.yml
new file mode 100644
index 00000000..52b5fd50
--- /dev/null
+++ b/tests/software/samtools/index/test.yml
@@ -0,0 +1,8 @@
+- name: samtools index
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_index
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.bai
+      md5sum: 67338c2995eae82c849830ca55aa7bd1
\ No newline at end of file
diff --git a/tests/software/samtools/mpileup/main.nf b/tests/software/samtools/mpileup/main.nf
new file mode 100644
index 00000000..e84fb944
--- /dev/null
+++ b/tests/software/samtools/mpileup/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_MPILEUP } from '../../../software/samtools/mpileup/main.nf' addParams( options: [:] )
+
+workflow test_samtools_mpileup {
+
+    def input = []
+    def fasta = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+    fasta = [  file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)  ]
+    SAMTOOLS_MPILEUP ( input, fasta )
+}
diff --git a/tests/software/samtools/mpileup/test.yml b/tests/software/samtools/mpileup/test.yml
new file mode 100644
index 00000000..b1998c99
--- /dev/null
+++ b/tests/software/samtools/mpileup/test.yml
@@ -0,0 +1,8 @@
+- name: samtools mpileup
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_mpileup
+  files:
+    - path: output/samtools/test.mpileup
+      md5sum: 95c2646fa7bd535207722008c581c81d
diff --git a/tests/software/samtools/sort/main.nf b/tests/software/samtools/sort/main.nf
new file mode 100644
index 00000000..53c2a088
--- /dev/null
+++ b/tests/software/samtools/sort/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
+
+workflow test_samtools_sort  {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+    SAMTOOLS_SORT ( input )
+}
\ No newline at end of file
diff --git a/tests/software/samtools/sort/test.yml b/tests/software/samtools/sort/test.yml
new file mode 100644
index 00000000..7055f8bc
--- /dev/null
+++ b/tests/software/samtools/sort/test.yml
@@ -0,0 +1,8 @@
+- name: samtools sort
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_sort
+  files:
+    - path: output/samtools/test.bam
+      md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
\ No newline at end of file
diff --git a/tests/software/samtools/stats/main.nf b/tests/software/samtools/stats/main.nf
new file mode 100644
index 00000000..f03fbd64
--- /dev/null
+++ b/tests/software/samtools/stats/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] )
+
+workflow test_samtools_stats {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
+    SAMTOOLS_STATS ( input )
+}
diff --git a/tests/software/samtools/stats/test.yml b/tests/software/samtools/stats/test.yml
new file mode 100644
index 00000000..9295b258
--- /dev/null
+++ b/tests/software/samtools/stats/test.yml
@@ -0,0 +1,8 @@
+- name: samtools stats
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_stats
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.stats
+      md5sum: 06c183864d6e47ab89b0650cae831a93
\ No newline at end of file
diff --git a/tests/software/samtools/view/main.nf b/tests/software/samtools/view/main.nf
new file mode 100644
index 00000000..13c1fdf4
--- /dev/null
+++ b/tests/software/samtools/view/main.nf
@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: [:] )
+
+workflow test_samtools_view {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+    SAMTOOLS_VIEW ( input )
+}
\ No newline at end of file
diff --git a/tests/software/samtools/view/test.yml b/tests/software/samtools/view/test.yml
new file mode 100644
index 00000000..9ffabea4
--- /dev/null
+++ b/tests/software/samtools/view/test.yml
@@ -0,0 +1,8 @@
+- name: samtools view
+  command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_view
+  files:
+    - path: output/samtools/test.bam
+      md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff
\ No newline at end of file
diff --git a/tests/software/seacr/callpeak/main.nf b/tests/software/seacr/callpeak/main.nf
new file mode 100644
index 00000000..9e4d9d9b
--- /dev/null
+++ b/tests/software/seacr/callpeak/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
+
+workflow test_seacr_callpeak {
+
+    def input = []
+    input = [[ id:'test_1'],
+              file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
+              file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ]
+
+    SEACR_CALLPEAK ( input )
+}
\ No newline at end of file
diff --git a/tests/software/seacr/callpeak/test.yml b/tests/software/seacr/callpeak/test.yml
new file mode 100644
index 00000000..6bdab27e
--- /dev/null
+++ b/tests/software/seacr/callpeak/test.yml
@@ -0,0 +1,8 @@
+- name: seacr callpeak
+  command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config
+  tags:
+    - seacr
+    - seacr_callpeak
+  files:
+    - path: output/seacr/test_1.stringent.bed
+      md5sum: 3ac70475669eb6a7b8ca89e19a08a28e
\ No newline at end of file
diff --git a/tests/software/star/align/main.nf b/tests/software/star/align/main.nf
new file mode 100644
index 00000000..1089c012
--- /dev/null
+++ b/tests/software/star/align/main.nf
@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
+include { STAR_ALIGN          } from '../../../software/star/align/main.nf'          addParams( options: [args: '--readFilesCommand zcat'] )
+
+workflow test_star_alignment_single_end {
+    
+    def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
+    def gtf   = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
+    STAR_GENOMEGENERATE ( fasta, gtf )
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
+    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
+}
+
+workflow test_star_alignment_paired_end {
+    
+    def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
+    def gtf   = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
+    STAR_GENOMEGENERATE ( fasta, gtf )
+
+    input = [ [ id:'test', single_end:false ], // meta map
+               [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                 file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+    STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
+}
diff --git a/tests/software/star/align/test.yml b/tests/software/star/align/test.yml
new file mode 100644
index 00000000..00d25140
--- /dev/null
+++ b/tests/software/star/align/test.yml
@@ -0,0 +1,75 @@
+- name: star align single-end
+  command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config
+  tags:
+    - star
+    - star_align
+    - star_align_single_end
+  files:
+    - path: output/star/star/Genome
+      md5sum: 323c992bac354f93073ce0fc43f222f8
+    - path: output/star/star/SA
+      md5sum: 3e70e4fc6d031e1915bb510727f2c559
+    - path: output/star/star/SAindex
+      md5sum: a94198b95a245d4f64af2a7133b6ec7b
+    - path: output/star/star/chrLength.txt
+      md5sum: f2bea3725fe1c01420c57fb73bdeb31a
+    - path: output/star/star/chrNameLength.txt
+      md5sum: c7ceb0a8827b2ea91c386933bee48742
+    - path: output/star/star/chrStart.txt
+      md5sum: faf5c55020c99eceeef3e34188ac0d2f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
+    - path: output/star/star/exonInfo.tab
+      md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
+    - path: output/star/star/genomeParameters.txt
+      md5sum: ed47b8b034cae2fefcdb39321aea47cd
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 8fbe69abbbef4f89da3854873984dbac
+    - path: output/star/test.Aligned.out.bam
+      md5sum: d7f59c1728482e76a18e3f6eb9c66c25
+    - path: output/star/test.SJ.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+
+- name: star align paired-end
+  command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config
+  tags:
+    - star
+    - star_align
+    - star_align_paired_end
+  files:
+    - path: output/star/star/Genome
+      md5sum: 323c992bac354f93073ce0fc43f222f8
+    - path: output/star/star/SA
+      md5sum: 3e70e4fc6d031e1915bb510727f2c559
+    - path: output/star/star/SAindex
+      md5sum: a94198b95a245d4f64af2a7133b6ec7b
+    - path: output/star/star/chrLength.txt
+      md5sum: f2bea3725fe1c01420c57fb73bdeb31a
+    - path: output/star/star/chrNameLength.txt
+      md5sum: c7ceb0a8827b2ea91c386933bee48742
+    - path: output/star/star/chrStart.txt
+      md5sum: faf5c55020c99eceeef3e34188ac0d2f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
+    - path: output/star/star/exonInfo.tab
+      md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
+    - path: output/star/star/genomeParameters.txt
+      md5sum: ed47b8b034cae2fefcdb39321aea47cd
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 8fbe69abbbef4f89da3854873984dbac
+    - path: output/star/test.Aligned.out.bam
+      md5sum: 5c52bcaa15e86914ad6b895638235166
+    - path: output/star/test.SJ.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
diff --git a/tests/software/star/genomegenerate/main.nf b/tests/software/star/genomegenerate/main.nf
new file mode 100644
index 00000000..c511ccd6
--- /dev/null
+++ b/tests/software/star/genomegenerate/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
+
+workflow test_star_genomegenerate {
+
+    def fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
+    def gtf   = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
+    STAR_GENOMEGENERATE ( fasta, gtf )
+}
\ No newline at end of file
diff --git a/tests/software/star/genomegenerate/test.yml b/tests/software/star/genomegenerate/test.yml
new file mode 100644
index 00000000..e9533766
--- /dev/null
+++ b/tests/software/star/genomegenerate/test.yml
@@ -0,0 +1,32 @@
+- name: star genomegenerate
+  command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config
+  tags:
+    - star
+    - star_genomegenerate
+  files:
+    - path: output/star/star/Genome
+      md5sum: 323c992bac354f93073ce0fc43f222f8
+    - path: output/star/star/SA
+      md5sum: 3e70e4fc6d031e1915bb510727f2c559
+    - path: output/star/star/SAindex
+      md5sum: a94198b95a245d4f64af2a7133b6ec7b
+    - path: output/star/star/chrLength.txt
+      md5sum: f2bea3725fe1c01420c57fb73bdeb31a
+    - path: output/star/star/chrNameLength.txt
+      md5sum: c7ceb0a8827b2ea91c386933bee48742
+    - path: output/star/star/chrStart.txt
+      md5sum: faf5c55020c99eceeef3e34188ac0d2f
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
+    - path: output/star/star/exonInfo.tab
+      md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
+    - path: output/star/star/genomeParameters.txt
+      md5sum: ed47b8b034cae2fefcdb39321aea47cd
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 8fbe69abbbef4f89da3854873984dbac
\ No newline at end of file
diff --git a/tests/software/stringtie/test.yml b/tests/software/stringtie/test.yml
index 5bbf002b..f180d0c4 100644
--- a/tests/software/stringtie/test.yml
+++ b/tests/software/stringtie/test.yml
@@ -1,4 +1,4 @@
-- name: Run stringtie forward strand test workflow
+- name: stringtie forward-strand
   command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config
   tags:
     - stringtie
@@ -20,7 +20,7 @@
     - path: output/test_stringtie_forward/test.ballgown/t_data.ctab
       md5sum: 0106f70121a8b520d98b8739aed92915
 
-- name: Run stringtie reverse strand test workflow
+- name: stringtie reverse-strand
   command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config
   tags:
     - stringtie
diff --git a/tests/software/trimgalore/main.nf b/tests/software/trimgalore/main.nf
index 0f03ee70..168805e8 100644
--- a/tests/software/trimgalore/main.nf
+++ b/tests/software/trimgalore/main.nf
@@ -2,8 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { TRIMGALORE as TRIMGALORE_SE } from '../../../software/trimgalore/main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
-include { TRIMGALORE as TRIMGALORE_PE } from '../../../software/trimgalore/main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
+include { TRIMGALORE } from '../../../software/trimgalore/main.nf' addParams( options: [:] )
 
 /*
  * Test with single-end data
@@ -13,19 +12,9 @@ workflow test_trimgalore_single_end {
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
-
-    TRIMGALORE_SE ( input )
+    TRIMGALORE ( input )
 }
 
-// workflow test_trimgalore_single_end {
-
-//     def input = []
-//     input = [ [ id:'test', single_end:false ], // meta map
-//               [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
-
-//     TRIMGALORE_SE ( input )
-// }
-
 /*
  * Test with paired-end data
  */
@@ -36,5 +25,5 @@ workflow test_trimgalore_paired_end {
               [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
                 file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
 
-    TRIMGALORE_PE ( input )
+    TRIMGALORE ( input )
 }
diff --git a/tests/software/trimgalore/test.yml b/tests/software/trimgalore/test.yml
index 34d880db..a37ffdb6 100644
--- a/tests/software/trimgalore/test.yml
+++ b/tests/software/trimgalore/test.yml
@@ -1,4 +1,4 @@
-- name: Run trimgalore single-end test workflow
+- name: trimgalore single-end
   command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_single_end -c tests/config/nextflow.config
   tags:
     - trimgalore
@@ -8,7 +8,7 @@
     - path: output/test_single_end/test.fastq.gz_trimming_report.txt
     - path: output/test_single_end/test_trimmed.fq.gz
 
-- name: Run trimgalore paired-end test workflow
+- name: trimgalore paired-end
   command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_paired_end -c tests/config/nextflow.config
   tags:
     - trimgalore
diff --git a/tests/software/ucsc/bedgraphtobigwig/main.nf b/tests/software/ucsc/bedgraphtobigwig/main.nf
new file mode 100644
index 00000000..deb13910
--- /dev/null
+++ b/tests/software/ucsc/bedgraphtobigwig/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_BEDGRAPHTOBIGWIG  } from '../../../software/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] )
+
+workflow test_ucsc_bedgraphtobigwig {
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ] ]
+              
+    UCSC_BEDGRAPHTOBIGWIG (
+        input,
+        file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/chrom.sizes', checkIfExists: true)
+    )
+}
diff --git a/tests/software/ucsc/bedgraphtobigwig/test.yml b/tests/software/ucsc/bedgraphtobigwig/test.yml
new file mode 100644
index 00000000..d6052e6f
--- /dev/null
+++ b/tests/software/ucsc/bedgraphtobigwig/test.yml
@@ -0,0 +1,7 @@
+- name: ucsc bedgraphtobigwig
+  command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
+  tags:
+    - ucsc_bedgraphtobigwig
+  files:
+    - path: output/ucsc/test.bigWig
+      md5sum: 5346de25b01ecbff91b63178b3bfbeec