From 043a7d1e3c6f408e3ef8f9134444eb525ce3c101 Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Tue, 13 Apr 2021 19:03:09 +0200
Subject: [PATCH] remove deprecated test tags (#440)

* remove deprecated test tags

* fix bowtie, gatk4/applybsqr

* fix gatk4 baserecalibrator

* fixed shovill

* fixed yara/mapper

* fixed kallistobustools/ref paths
---
 software/gatk4/applybqsr/main.nf               |  2 +-
 software/gatk4/baserecalibrator/main.nf        |  2 +-
 tests/software/adapterremoval/test.yml         |  3 ---
 tests/software/bowtie/align/main.nf            |  4 ++--
 tests/software/bowtie/align/test.yml           |  2 --
 tests/software/bowtie2/align/test.yml          |  2 --
 tests/software/bwa/mem/test.yml                |  2 --
 tests/software/bwamem2/mem/test.yml            |  2 --
 tests/software/cat/fastq/test.yml              |  2 --
 tests/software/cutadapt/test.yml               |  2 --
 tests/software/fastp/test.yml                  |  2 --
 tests/software/fastqc/test.yml                 |  2 --
 tests/software/gatk4/applybqsr/main.nf         |  2 ++
 tests/software/gatk4/applybqsr/test.yml        |  1 -
 tests/software/gatk4/baserecalibrator/main.nf  |  9 ++++++---
 tests/software/gatk4/baserecalibrator/test.yml |  2 --
 tests/software/gatk4/fastqtosam/test.yml       |  2 --
 tests/software/gatk4/mergevcfs/test.yml        |  1 -
 tests/software/gatk4/samtofastq/test.yml       |  2 --
 tests/software/hisat2/align/test.yml           |  2 --
 tests/software/kallistobustools/ref/main.nf    | 18 +++++++++---------
 tests/software/kallistobustools/ref/test.yml   |  3 ---
 tests/software/minimap2/align/main.nf          |  8 ++++----
 tests/software/minimap2/align/test.yml         |  2 --
 tests/software/picard/markduplicates/test.yml  |  1 -
 tests/software/preseq/lcextrap/test.yml        |  2 --
 tests/software/quast/test.yml                  |  2 --
 tests/software/salmon/quant/test.yml           |  2 --
 tests/software/seqkit/split2/test.yml          | 13 -------------
 tests/software/shovill/main.nf                 | 14 +++++++-------
 tests/software/shovill/test.yml                |  8 ++------
 tests/software/spades/test.yml                 | 12 +++++-------
 tests/software/star/align/test.yml             |  2 --
 tests/software/subread/featurecounts/test.yml  |  3 ---
 tests/software/tabix/tabix/test.yml            |  3 ---
 tests/software/tiddit/sv/test.yml              |  2 --
 tests/software/unicycler/main.nf               |  4 ++--
 tests/software/unicycler/test.yml              |  2 --
 tests/software/vcftools/test.yml               |  4 ----
 tests/software/yara/mapper/main.nf             | 18 ++++++++----------
 tests/software/yara/mapper/test.yml            |  2 --
 41 files changed, 49 insertions(+), 124 deletions(-)

diff --git a/software/gatk4/applybqsr/main.nf b/software/gatk4/applybqsr/main.nf
index dd98c012..abc6e270 100644
--- a/software/gatk4/applybqsr/main.nf
+++ b/software/gatk4/applybqsr/main.nf
@@ -19,7 +19,7 @@ process GATK4_APPLYBQSR {
     }
 
     input:
-    tuple val(meta), path(bam), path(bqsr_table)
+    tuple val(meta), path(bam), path(bai), path(bqsr_table)
     path fasta
     path fastaidx
     path dict
diff --git a/software/gatk4/baserecalibrator/main.nf b/software/gatk4/baserecalibrator/main.nf
index 6d9dd82e..31ffbd20 100644
--- a/software/gatk4/baserecalibrator/main.nf
+++ b/software/gatk4/baserecalibrator/main.nf
@@ -19,7 +19,7 @@ process GATK4_BASERECALIBRATOR {
     }
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai)
     path fasta
     path fastaidx
     path dict
diff --git a/tests/software/adapterremoval/test.yml b/tests/software/adapterremoval/test.yml
index 7666bc6d..4900a803 100644
--- a/tests/software/adapterremoval/test.yml
+++ b/tests/software/adapterremoval/test.yml
@@ -1,7 +1,6 @@
 - name: adapterremoval test_adapterremoval_single_end
   command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
   tags:
-    - adapterremoval_single_end
     - adapterremoval
   files:
     - path: output/adapterremoval/test.log
@@ -12,7 +11,6 @@
 - name: adapterremoval test_adapterremoval_paired_end
   command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
   tags:
-    - adapterremoval_paired_end
     - adapterremoval
   files:
     - path: output/adapterremoval/test.pair2.trimmed.fastq.gz
@@ -25,7 +23,6 @@
 - name: adapterremoval test_adapterremoval_paired_end_collapse
   command: nextflow run tests/software/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
   tags:
-    - adapterremoval_paired_end_collapse
     - adapterremoval
   files:
     - path: output/adapterremoval/test.log
diff --git a/tests/software/bowtie/align/main.nf b/tests/software/bowtie/align/main.nf
index a34de8b5..5c76f8e9 100644
--- a/tests/software/bowtie/align/main.nf
+++ b/tests/software/bowtie/align/main.nf
@@ -7,9 +7,9 @@ include { BOWTIE_ALIGN } from '../../../../software/bowtie/align/main.nf' addPar
 
 workflow test_bowtie_align_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BOWTIE_BUILD ( fasta )
     BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml
index f6868b0f..86b390c6 100644
--- a/tests/software/bowtie/align/test.yml
+++ b/tests/software/bowtie/align/test.yml
@@ -3,7 +3,6 @@
   tags:
     - bowtie
     - bowtie/align
-    - bowtie_align_single_end
   files:
     - path: ./output/bowtie/test.bam
     - path: ./output/bowtie/test.out
@@ -26,7 +25,6 @@
   tags:
     - bowtie
     - bowtie/align
-    - bowtie_align_paired_end
   files:
     - path: ./output/bowtie/test.bam
     - path: ./output/bowtie/test.out
diff --git a/tests/software/bowtie2/align/test.yml b/tests/software/bowtie2/align/test.yml
index 27e54a66..c0e94b5d 100644
--- a/tests/software/bowtie2/align/test.yml
+++ b/tests/software/bowtie2/align/test.yml
@@ -3,7 +3,6 @@
   tags:
     - bowtie2
     - bowtie2/align
-    - bowtie2_align_single_end
   files:
     - path: ./output/bowtie2/test.bam
     - path: ./output/bowtie2/test.bowtie2.log
@@ -25,7 +24,6 @@
   tags:
     - bowtie2
     - bowtie2/align
-    - bowtie2_align_paired_end
   files:
     - path: ./output/bowtie2/test.bam
     - path: ./output/bowtie2/test.bowtie2.log
diff --git a/tests/software/bwa/mem/test.yml b/tests/software/bwa/mem/test.yml
index d5c23c16..1b36eea7 100644
--- a/tests/software/bwa/mem/test.yml
+++ b/tests/software/bwa/mem/test.yml
@@ -3,7 +3,6 @@
   tags:
     - bwa
     - bwa/mem
-    - bwa_mem_single_end
   files:
     - path: ./output/bwa/test.bam
       md5sum: 9165508bf914baee0e6347711aa7b23a
@@ -23,7 +22,6 @@
   tags:
     - bwa
     - bwa/mem
-    - bwa_mem_paired_end
   files:
     - path: ./output/bwa/test.bam
       md5sum: 670a53bddee62d6bd14ed7adaf103e7c
diff --git a/tests/software/bwamem2/mem/test.yml b/tests/software/bwamem2/mem/test.yml
index c015e221..00cb98fd 100644
--- a/tests/software/bwamem2/mem/test.yml
+++ b/tests/software/bwamem2/mem/test.yml
@@ -3,7 +3,6 @@
   tags:
     - bwamem2
     - bwamem2/mem
-    - bwamem2_mem_single_end
   files:
     - path: ./output/bwamem2/test.bam
       md5sum: 2133c011119ea11f06f0a9b1621ba05b
@@ -23,7 +22,6 @@
   tags:
     - bwamem2
     - bwamem2/mem
-    - bwamem2_mem_paired_end
   files:
     - path: ./output/bwamem2/test.bam
       md5sum: d8fadab5cef04faff1851a8162fc30b5
diff --git a/tests/software/cat/fastq/test.yml b/tests/software/cat/fastq/test.yml
index d309e542..56648fad 100644
--- a/tests/software/cat/fastq/test.yml
+++ b/tests/software/cat/fastq/test.yml
@@ -3,7 +3,6 @@
   tags:
     - cat
     - cat/fastq
-    - cat_fastqc_single_end
   files:
     - path: ./output/merged_fastq/test.merged.fastq.gz
       md5sum: 59f6dbe193741bb40f498f254aeb2e99
@@ -13,7 +12,6 @@
   tags:
     - cat
     - cat/fastq
-    - cat_fastqc_paired_end
   files:
     - path: ./output/merged_fastq/test_2.merged.fastq.gz
       md5sum: d2b1a836eef1058738ecab36c907c5ba
diff --git a/tests/software/cutadapt/test.yml b/tests/software/cutadapt/test.yml
index 9cadf0fb..f843fe2c 100644
--- a/tests/software/cutadapt/test.yml
+++ b/tests/software/cutadapt/test.yml
@@ -2,7 +2,6 @@
   command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_single_end -c tests/config/nextflow.config
   tags:
     - cutadapt
-    - cutadapt_single_end
   files:
     - path: ./output/cutadapt/test.cutadapt.log
     - path: ./output/cutadapt/test.trim.fastq.gz
@@ -11,7 +10,6 @@
   command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_paired_end -c tests/config/nextflow.config
   tags:
     - cutadapt
-    - cutadapt_paired_end
   files:
     - path: ./output/cutadapt/test.cutadapt.log
     - path: ./output/cutadapt/test_1.trim.fastq.gz
diff --git a/tests/software/fastp/test.yml b/tests/software/fastp/test.yml
index a2d14b19..f7f92ec8 100644
--- a/tests/software/fastp/test.yml
+++ b/tests/software/fastp/test.yml
@@ -1,7 +1,6 @@
 - name: fastp test_fastp_single_end
   command: nextflow run tests/software/fastp -entry test_fastp_single_end -c tests/config/nextflow.config
   tags:
-    - fastp_single_end
     - fastp
   files:
     - path: output/fastp/test.fastp.html
@@ -20,7 +19,6 @@
 - name: fastp test_fastp_paired_end
   command: nextflow run tests/software/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config
   tags:
-    - fastp_paired_end
     - fastp
   files:
     - path: output/fastp/test.fastp.html
diff --git a/tests/software/fastqc/test.yml b/tests/software/fastqc/test.yml
index 0fe0ebe0..0e0d0ee7 100644
--- a/tests/software/fastqc/test.yml
+++ b/tests/software/fastqc/test.yml
@@ -2,7 +2,6 @@
   command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
   tags:
     - fastqc
-    - fastqc_single_end
   files:
     - path: ./output/fastqc/test_fastqc.html
     - path: ./output/fastqc/test_fastqc.zip
@@ -11,7 +10,6 @@
   command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
   tags:
     - fastqc
-    - fastqc_paired_end
   files:
     - path: ./output/fastqc/test_1_fastqc.html
     - path: ./output/fastqc/test_2_fastqc.html
diff --git a/tests/software/gatk4/applybqsr/main.nf b/tests/software/gatk4/applybqsr/main.nf
index 2d3e532c..a33542b5 100644
--- a/tests/software/gatk4/applybqsr/main.nf
+++ b/tests/software/gatk4/applybqsr/main.nf
@@ -7,6 +7,7 @@ include { GATK4_APPLYBQSR } from '../../../../software/gatk4/applybqsr/main.nf'
 workflow test_gatk4_applybqsr {
     input = [ [ id:'test' ], // meta map
               file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
               file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
@@ -19,6 +20,7 @@ workflow test_gatk4_applybqsr {
 workflow test_gatk4_applybqsr_intervals {
     input = [ [ id:'test' ], // meta map
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
                 file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
               ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/software/gatk4/applybqsr/test.yml b/tests/software/gatk4/applybqsr/test.yml
index cbc9e3ed..c391a6ad 100644
--- a/tests/software/gatk4/applybqsr/test.yml
+++ b/tests/software/gatk4/applybqsr/test.yml
@@ -11,7 +11,6 @@
   command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
   tags:
     - gatk4
-    - gatk4/applybqsr/intervals
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.bam
diff --git a/tests/software/gatk4/baserecalibrator/main.nf b/tests/software/gatk4/baserecalibrator/main.nf
index 302ddb1f..72198c8a 100644
--- a/tests/software/gatk4/baserecalibrator/main.nf
+++ b/tests/software/gatk4/baserecalibrator/main.nf
@@ -6,7 +6,8 @@ include { GATK4_BASERECALIBRATOR } from '../../../../software/gatk4/baserecalibr
 
 workflow test_gatk4_baserecalibrator {
     input     = [ [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
                   ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
@@ -19,7 +20,8 @@ workflow test_gatk4_baserecalibrator {
 
 workflow test_gatk4_baserecalibrator_intervals {
     input     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
                 ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
@@ -33,7 +35,8 @@ workflow test_gatk4_baserecalibrator_intervals {
 
 workflow test_gatk4_baserecalibrator_multiple_sites {
     input     = [ [ id:'test' ], // meta map
-                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
                 ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
diff --git a/tests/software/gatk4/baserecalibrator/test.yml b/tests/software/gatk4/baserecalibrator/test.yml
index a2ae8ebe..0185ec60 100644
--- a/tests/software/gatk4/baserecalibrator/test.yml
+++ b/tests/software/gatk4/baserecalibrator/test.yml
@@ -10,7 +10,6 @@
 - name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
   command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c tests/config/nextflow.config
   tags:
-    - gatk4/baserecalibrator/intervals
     - gatk4/baserecalibrator
     - gatk4
   files:
@@ -20,7 +19,6 @@
 - name: gatk4 baserecalibrator test_gatk4_baserecalibrator_multiple_sites
   command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c tests/config/nextflow.config
   tags:
-    - gatk4_baserecalibrator_multiple_sites
     - gatk4/baserecalibrator
     - gatk4
   files:
diff --git a/tests/software/gatk4/fastqtosam/test.yml b/tests/software/gatk4/fastqtosam/test.yml
index 6709d4c6..a3df1a6f 100644
--- a/tests/software/gatk4/fastqtosam/test.yml
+++ b/tests/software/gatk4/fastqtosam/test.yml
@@ -1,7 +1,6 @@
 - name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
   command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config
   tags:
-    - gatk4_fastqtosam_single_end
     - gatk4/fastqtosam
     - gatk4
   files:
@@ -11,7 +10,6 @@
 - name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
   command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config
   tags:
-    - gatk4_fastqtosam_paired_end
     - gatk4
     - gatk4/fastqtosam
   files:
diff --git a/tests/software/gatk4/mergevcfs/test.yml b/tests/software/gatk4/mergevcfs/test.yml
index 833cd36b..99e167b4 100644
--- a/tests/software/gatk4/mergevcfs/test.yml
+++ b/tests/software/gatk4/mergevcfs/test.yml
@@ -12,7 +12,6 @@
   tags:
     - gatk4/mergevcfs
     - gatk4
-    - gatk4/mergevcfs_refdict
   files:
     - path: output/gatk4/test.merged.vcf.gz
       md5sum: ff48f175e26db2d4b2957762f6d1c715
diff --git a/tests/software/gatk4/samtofastq/test.yml b/tests/software/gatk4/samtofastq/test.yml
index 52267191..d70da6dc 100644
--- a/tests/software/gatk4/samtofastq/test.yml
+++ b/tests/software/gatk4/samtofastq/test.yml
@@ -3,7 +3,6 @@
   tags:
     - gatk4
     - gatk4/samtofastq
-    - gatk4_samtofastq_single_end
   files:
     - path: output/gatk4/test.fastq.gz
       md5sum: 50ace41d4c24467f24f8b929540a7797
@@ -13,7 +12,6 @@
   tags:
     - gatk4
     - gatk4/samtofastq
-    - gatk4_samtofastq_paired_end
   files:
     - path: output/gatk4/test_1.fastq.gz
       md5sum: cfea607c9d75fd9ea9704780ad3a499c
diff --git a/tests/software/hisat2/align/test.yml b/tests/software/hisat2/align/test.yml
index ce303b23..e9a89de6 100644
--- a/tests/software/hisat2/align/test.yml
+++ b/tests/software/hisat2/align/test.yml
@@ -3,7 +3,6 @@
   tags:
     - hisat2
     - hisat2/align
-    - hisat2_align_single_end
   files:
     - path: output/hisat2/test.hisat2.summary.log
       md5sum: 7b8a9e61b7646da1089b041333c41a87
@@ -32,7 +31,6 @@
   tags:
     - hisat2
     - hisat2/align
-    - hisat2_align_paired_end
   files:
     - path: output/hisat2/test.hisat2.summary.log
       md5sum: 9839b31db795958cc4b70711a3414e9c
diff --git a/tests/software/kallistobustools/ref/main.nf b/tests/software/kallistobustools/ref/main.nf
index 8c430bb7..d9846691 100644
--- a/tests/software/kallistobustools/ref/main.nf
+++ b/tests/software/kallistobustools/ref/main.nf
@@ -6,27 +6,27 @@ include { KALLISTOBUSTOOLS_REF } from '../../../../software/kallistobustools/ref
 
 workflow test_kallistobustools_ref_standard {
 
-    fasta       = file("${launchDir}/tests/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
-    gtf         = file("${launchDir}/tests/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
+    fasta       = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
+    gtf         = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
     workflow    = "standard"
-    
+
     KALLISTOBUSTOOLS_REF(fasta, gtf, workflow)
 }
 
 workflow test_kallistobustools_ref_lamanno {
 
-    fasta       = file("${launchDir}/tests/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
-    gtf         = file("${launchDir}/tests/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
+    fasta       = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
+    gtf         = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
     workflow    = "standard"
-    
+
     KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
 }
 
 workflow test_kallistobustools_ref_nucleus {
 
-    fasta       = file("${launchDir}/tests/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
-    gtf         = file("${launchDir}/tests/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
+    fasta       = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
+    gtf         = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
     workflow    = "standard"
-    
+
     KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
 }
diff --git a/tests/software/kallistobustools/ref/test.yml b/tests/software/kallistobustools/ref/test.yml
index aeeef936..18fc15e7 100644
--- a/tests/software/kallistobustools/ref/test.yml
+++ b/tests/software/kallistobustools/ref/test.yml
@@ -2,7 +2,6 @@
   command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_standard -c tests/config/nextflow.config
   tags:
     - kallistobustools
-    - kallistobustools_ref_standard
     - kallistobustools/ref
   files:
     - path: output/kallistobustools/cdna.fa
@@ -16,7 +15,6 @@
   command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c tests/config/nextflow.config
   tags:
     - kallistobustools
-    - kallistobustools_ref_lamanno
     - kallistobustools/ref
   files:
     - path: output/kallistobustools/cdna.fa
@@ -29,7 +27,6 @@
 - name: kallistobustools ref test_kallistobustools_ref_nucleus
   command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c tests/config/nextflow.config
   tags:
-    - kallistobustools_ref_nucleus
     - kallistobustools
     - kallistobustools/ref
   files:
diff --git a/tests/software/minimap2/align/main.nf b/tests/software/minimap2/align/main.nf
index 349332ae..aabb372e 100644
--- a/tests/software/minimap2/align/main.nf
+++ b/tests/software/minimap2/align/main.nf
@@ -6,9 +6,9 @@ include { MINIMAP2_ALIGN } from '../../../../software/minimap2/align/main.nf' ad
 
 workflow test_minimap2_align_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     MINIMAP2_ALIGN ( input, fasta )
 }
@@ -16,9 +16,9 @@ workflow test_minimap2_align_single_end {
 workflow test_minimap2_align_paired_end {
     input = [ [ id:'test', single_end:false ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] 
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     MINIMAP2_ALIGN ( input, fasta )
 }
diff --git a/tests/software/minimap2/align/test.yml b/tests/software/minimap2/align/test.yml
index b8ddde21..30b6bf90 100644
--- a/tests/software/minimap2/align/test.yml
+++ b/tests/software/minimap2/align/test.yml
@@ -3,7 +3,6 @@
   tags:
     - minimap2
     - minimap2/align
-    - minimap2_align_single_end
   files:
     - path: ./output/minimap2/test.paf
       md5sum: 5a9648fc67c30a2c83b0ef094171faa0
@@ -13,7 +12,6 @@
   tags:
     - minimap2
     - minimap2/align
-    - minimap2_align_paired_end
   files:
     - path: ./output/minimap2/test.paf
       md5sum: e7b952be872bdbef16bf99d512690df7
diff --git a/tests/software/picard/markduplicates/test.yml b/tests/software/picard/markduplicates/test.yml
index 0de69083..8516cb28 100644
--- a/tests/software/picard/markduplicates/test.yml
+++ b/tests/software/picard/markduplicates/test.yml
@@ -13,5 +13,4 @@
   tags:
     - picard
     - picard/markduplicates
-    - should fail
   exit_code: 1
diff --git a/tests/software/preseq/lcextrap/test.yml b/tests/software/preseq/lcextrap/test.yml
index e511dd40..0de3dfd7 100644
--- a/tests/software/preseq/lcextrap/test.yml
+++ b/tests/software/preseq/lcextrap/test.yml
@@ -3,7 +3,6 @@
   tags:
     - preseq
     - preseq/lcextrap
-    - preseq_lcextrap_single_end
   files:
     - path: output/preseq/test.ccurve.txt
       md5sum: 76ae04c8eaf19c94e3210bb69da38498
@@ -14,7 +13,6 @@
   tags:
     - preseq
     - preseq/lcextrap
-    - preseq_lcextrap_paired_end
   files:
     - path: output/preseq/test.ccurve.txt
       md5sum: 2836d2fabd2213f097fd7063db550276
diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml
index 283bf6da..86cc331c 100644
--- a/tests/software/quast/test.yml
+++ b/tests/software/quast/test.yml
@@ -2,7 +2,6 @@
   command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
   tags:
     - quast
-    - quast_reference
   files:
     - path: ./output/quast/report.tsv
     - path: ./output/quast/quast/transposed_report.txt
@@ -86,7 +85,6 @@
   command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config
   tags:
     - quast
-    - quast_no_reference
   files:
     - path: ./output/quast/report.tsv
       md5sum: 074e239aac0f298cf4cd2a28a9bb5690
diff --git a/tests/software/salmon/quant/test.yml b/tests/software/salmon/quant/test.yml
index 12fb94a1..f2465ee7 100644
--- a/tests/software/salmon/quant/test.yml
+++ b/tests/software/salmon/quant/test.yml
@@ -3,7 +3,6 @@
   tags:
     - salmon
     - salmon/quant
-    - salmon_quant_single_end
   files:
     - path: ./output/salmon/test/cmd_info.json
     - path: ./output/salmon/test/quant.sf
@@ -55,7 +54,6 @@
   tags:
     - salmon
     - salmon/quant
-    - salmon_quant_paired_end
   files:
     - path: ./output/salmon/test/cmd_info.json
     - path: ./output/salmon/test/quant.sf
diff --git a/tests/software/seqkit/split2/test.yml b/tests/software/seqkit/split2/test.yml
index ccdd01d2..a85da4f1 100644
--- a/tests/software/seqkit/split2/test.yml
+++ b/tests/software/seqkit/split2/test.yml
@@ -3,22 +3,17 @@
   tags:
     - seqkit
     - seqkit/split2
-    - seqkit_split2_single_end
-    - length
   files:
     - path: output/seqkit/test.split/test_1.part_001.fastq.gz
       md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
     - path: output/seqkit/test.split/test_1.part_002.fastq.gz
       md5sum: cf38c51506e45380fe25abdd1bd5ccc6
 
-
 - name: seqkit split2 single-end size
   command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
   tags:
     - seqkit
     - seqkit/split2
-    - seqkit_split2_single_end
-    - size
   files:
     - path: output/seqkit/test.split/test_1.part_001.fastq.gz
       md5sum: bf835e685d597fc1ab5e5ac7dd689619
@@ -30,8 +25,6 @@
   tags:
     - seqkit
     - seqkit/split2
-    - seqkit_split2_single_end
-    - part
   files:
     - path: output/seqkit/test.split/test_1.part_001.fastq.gz
       md5sum: fa25951435471238d5567fd2cae31f55
@@ -45,8 +38,6 @@
   tags:
     - seqkit
     - seqkit/split2
-    - seqkit_split2_paired_end
-    - length
   files:
     - path: output/seqkit/test.split/test_1.part_001.fastq.gz
       md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
@@ -62,8 +53,6 @@
   tags:
     - seqkit
     - seqkit/split2
-    - seqkit_split2_paired_end
-    - size
   files:
     - path: output/seqkit/test.split/test_1.part_001.fastq.gz
       md5sum: bf835e685d597fc1ab5e5ac7dd689619
@@ -79,8 +68,6 @@
   tags:
     - seqkit
     - seqkit/split2
-    - seqkit_split2_paired_end
-    - part
   files:
     - path: output/seqkit/test.split/test_1.part_001.fastq.gz
       md5sum: fa25951435471238d5567fd2cae31f55
diff --git a/tests/software/shovill/main.nf b/tests/software/shovill/main.nf
index d9c25094..2a1f65b8 100644
--- a/tests/software/shovill/main.nf
+++ b/tests/software/shovill/main.nf
@@ -10,7 +10,7 @@ include { SHOVILL as SHOVILL_VELVET  } from '../../../software/shovill/main.nf'
 workflow test_shovill {
     input = [ [ id:'test', single_end:false ], // meta map
               [ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true),
-                file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ] 
+                file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ]
             ]
 
     SHOVILL ( input )
@@ -18,8 +18,8 @@ workflow test_shovill {
 
 workflow test_shovill_megahit {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
 
     SHOVILL_MEGAHIT ( input )
@@ -27,8 +27,8 @@ workflow test_shovill_megahit {
 
 workflow test_shovill_skesa {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
 
     SHOVILL_SKESA ( input )
@@ -36,8 +36,8 @@ workflow test_shovill_skesa {
 
 workflow test_shovill_velvet {
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
 
     SHOVILL_VELVET ( input )
diff --git a/tests/software/shovill/test.yml b/tests/software/shovill/test.yml
index 9894b1d0..bc3ca318 100644
--- a/tests/software/shovill/test.yml
+++ b/tests/software/shovill/test.yml
@@ -2,7 +2,6 @@
   command: nextflow run ./tests/software/shovill -entry test_shovill -c tests/config/nextflow.config
   tags:
     - shovill
-    - shovill/spades
   files:
     - path: output/shovill/contigs.gfa
       md5sum: 277af5d8ae8a0d2432db59a316226828
@@ -17,7 +16,6 @@
   command: nextflow run ./tests/software/shovill -entry test_shovill_megahit -c tests/config/nextflow.config
   tags:
     - shovill
-    - shovill/megahit
   files:
     - path: output/shovill/shovill.corrections
       md5sum: d41d8cd98f00b204e9800998ecf8427e
@@ -26,17 +24,16 @@
     - path: output/shovill/contigs.fastg
     - path: output/shovill/megahit.fasta
     - path: output/shovill/shovill.log
-  
+
 - name: shovill with skesa
   command: nextflow run ./tests/software/shovill -entry test_shovill_skesa -c tests/config/nextflow.config
   tags:
     - shovill
-    - shovill/skesa
   files:
     - path: output/shovill/shovill.corrections
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/shovill/skesa.fasta
-      md5sum: c0c2d11b633310eb1437345cb599c33c
+      md5sum: 8157837dbe8315922f588dafa7af5ef8
     # MD5sum not reproducible (timestamp)
     - path: output/shovill/contigs.fa
     - path: output/shovill/shovill.log
@@ -45,7 +42,6 @@
   command: nextflow run ./tests/software/shovill -entry test_shovill_velvet -c tests/config/nextflow.config
   tags:
     - shovill
-    - shovill/velvet
   files:
     # MD5sum not reproducible (timestamp, contig order)
     - path: output/shovill/contigs.fa
diff --git a/tests/software/spades/test.yml b/tests/software/spades/test.yml
index 5b6c800a..e2bccf47 100644
--- a/tests/software/spades/test.yml
+++ b/tests/software/spades/test.yml
@@ -2,7 +2,6 @@
   command: nextflow run ./tests/software/spades -entry test_spades_single_end -c tests/config/nextflow.config
   tags:
     - spades
-    - spades_single_end
   files:
     - path: output/spades/test.assembly.gfa
       md5sum: b2616d2beba83ab7d361b54778d1e759
@@ -16,10 +15,9 @@
   command: nextflow run ./tests/software/spades -entry test_spades_paired_end -c tests/config/nextflow.config
   tags:
     - spades
-    - spades_paired_end
   files:
-      - path: output/spades/test.assembly.gfa
-        md5sum: faf76135ee390606b899c0197dc38e04
-      - path: output/spades/test.contigs.fa
-        md5sum: 6148e25b33890c80f176f90f2dd88989
-      - path: output/spades/test.spades.log
+    - path: output/spades/test.assembly.gfa
+      md5sum: faf76135ee390606b899c0197dc38e04
+    - path: output/spades/test.contigs.fa
+      md5sum: 6148e25b33890c80f176f90f2dd88989
+    - path: output/spades/test.spades.log
diff --git a/tests/software/star/align/test.yml b/tests/software/star/align/test.yml
index e4bbdb51..7cec005e 100644
--- a/tests/software/star/align/test.yml
+++ b/tests/software/star/align/test.yml
@@ -3,7 +3,6 @@
   tags:
     - star
     - star/align
-    - star_align_single_end
   files:
     - path: output/star/star/Genome
       md5sum: 323c992bac354f93073ce0fc43f222f8
@@ -41,7 +40,6 @@
   tags:
     - star
     - star/align
-    - star_align_paired_end
   files:
     - path: output/star/star/Genome
       md5sum: 323c992bac354f93073ce0fc43f222f8
diff --git a/tests/software/subread/featurecounts/test.yml b/tests/software/subread/featurecounts/test.yml
index 443ae2a6..efefcc10 100644
--- a/tests/software/subread/featurecounts/test.yml
+++ b/tests/software/subread/featurecounts/test.yml
@@ -3,7 +3,6 @@
   tags:
     - subread
     - subread/featurecounts
-    - subread_featurecounts_forward
   files:
     - path: output/subread/test.featureCounts.txt.summary
       md5sum: d78617192451a57f6ef249ddcaf13720
@@ -15,7 +14,6 @@
   tags:
     - subread
     - subread/featurecounts
-    - subread_featurecounts_reverse
   files:
     - path: output/subread/test.featureCounts.txt.summary
       md5sum: 4217004d0b55f870f77092364f59e44d
@@ -27,7 +25,6 @@
   tags:
     - subread
     - subread/featurecounts
-    - subread_featurecounts_unstranded
   files:
     - path: output/subread/test.featureCounts.txt.summary
       md5sum: ee585faeb1edfcd2188a5e486a0e98a9
diff --git a/tests/software/tabix/tabix/test.yml b/tests/software/tabix/tabix/test.yml
index 73724fb8..73c91168 100644
--- a/tests/software/tabix/tabix/test.yml
+++ b/tests/software/tabix/tabix/test.yml
@@ -3,7 +3,6 @@
   tags:
     - tabix
     - tabix/tabix
-    - bed
   files:
     - path: ./output/tabix/test.bed.gz.tbi
       md5sum: 115922d881d24879b15d20c3734495ac
@@ -12,7 +11,6 @@
   tags:
     - tabix
     - tabix/tabix
-    - gff
   files:
     - path: ./output/tabix/genome.gff3.gz.tbi
       md5sum: 4059fe4762568194cf293fc6df7b358b
@@ -21,7 +19,6 @@
   tags:
     - tabix
     - tabix/tabix
-    - vcf
   files:
     - path: output/tabix/test.vcf.gz.tbi
       md5sum: bbec39fd53cf2834909d52094980d094
diff --git a/tests/software/tiddit/sv/test.yml b/tests/software/tiddit/sv/test.yml
index 4cc0f910..dbe89475 100644
--- a/tests/software/tiddit/sv/test.yml
+++ b/tests/software/tiddit/sv/test.yml
@@ -3,7 +3,6 @@
   tags:
     - tiddit
     - tiddit/sv
-    - vcf
   files:
     - path: output/tiddit/test.ploidy.tab
       md5sum: 45e050b0e204f0a5a3a99627cc440eaa
@@ -17,7 +16,6 @@
   tags:
     - tiddit
     - tiddit/sv
-    - vcf
   files:
     - path: output/tiddit/test.ploidy.tab
       md5sum: 45e050b0e204f0a5a3a99627cc440eaa
diff --git a/tests/software/unicycler/main.nf b/tests/software/unicycler/main.nf
index 0587df1e..ff854c50 100644
--- a/tests/software/unicycler/main.nf
+++ b/tests/software/unicycler/main.nf
@@ -6,7 +6,7 @@ include { UNICYCLER } from '../../../software/unicycler/main.nf' addParams( opti
 
 workflow test_unicycler_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
             ]
 
     UNICYCLER ( input )
@@ -15,7 +15,7 @@ workflow test_unicycler_single_end {
 workflow test_unicycler_paired_end {
     input = [ [ id:'test', single_end:false ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] 
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
 
     UNICYCLER ( input )
diff --git a/tests/software/unicycler/test.yml b/tests/software/unicycler/test.yml
index 5e6dd790..df7eb0de 100644
--- a/tests/software/unicycler/test.yml
+++ b/tests/software/unicycler/test.yml
@@ -2,7 +2,6 @@
   command: nextflow run ./tests/software/unicycler -entry test_unicycler_single_end -c tests/config/nextflow.config
   tags:
     - unicycler
-    - unicycler_single_end
   files:
     - path: output/unicycler/test.scaffolds.fa
     - path: output/unicycler/test.assembly.gfa
@@ -14,7 +13,6 @@
   command: nextflow run ./tests/software/unicycler -entry test_unicycler_paired_end -c tests/config/nextflow.config
   tags:
     - unicycler
-    - unicycler_paired_end
   files:
     - path: output/unicycler/test.scaffolds.fa
     - path: output/unicycler/test.assembly.gfa
diff --git a/tests/software/vcftools/test.yml b/tests/software/vcftools/test.yml
index b7a7f784..24955f2f 100644
--- a/tests/software/vcftools/test.yml
+++ b/tests/software/vcftools/test.yml
@@ -2,7 +2,6 @@
   command: nextflow run tests/software/vcftools -entry test_vcftools_vcf_base -c tests/config/nextflow.config
   tags:
     - vcftools
-    - vcftools_vcf_base
   files:
     - path: output/vcftools/test.frq
       md5sum: 7f126655f17268fd1a338734f62868e9
@@ -10,7 +9,6 @@
 - name: vcftools test_vcftools_vcfgz_base
   command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_base -c tests/config/nextflow.config
   tags:
-    - vcftools_vcfgz_base
     - vcftools
   files:
     - path: output/vcftools/test.frq
@@ -20,7 +18,6 @@
   command: nextflow run tests/software/vcftools -entry test_vcftools_vcf_optional -c tests/config/nextflow.config
   tags:
     - vcftools
-    - vcftools_vcf_optional
   files:
     - path: output/vcftools/test.frq
       md5sum: 7f126655f17268fd1a338734f62868e9
@@ -29,7 +26,6 @@
   command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_optional -c tests/config/nextflow.config
   tags:
     - vcftools
-    - vcftools_vcfgz_optional
   files:
     - path: output/vcftools/test.frq
       md5sum: 7f126655f17268fd1a338734f62868e9
diff --git a/tests/software/yara/mapper/main.nf b/tests/software/yara/mapper/main.nf
index 41ad173c..d2b3d922 100644
--- a/tests/software/yara/mapper/main.nf
+++ b/tests/software/yara/mapper/main.nf
@@ -8,25 +8,23 @@ include { YARA_MAPPER } from '../../../../software/yara/mapper/main.nf' addParam
 
 workflow test_yara_single_end {
 
-    def fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
-    YARA_INDEX ( fasta )
-
-    def input = []
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     input = [ [ id:'test', single_end:true ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
 
+
+    YARA_INDEX ( fasta )
     YARA_MAPPER ( input, YARA_INDEX.out.index )
 }
 
 workflow test_yara_paired_end {
 
-    def fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
-    YARA_INDEX ( fasta )
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] ]
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
 
+    YARA_INDEX ( fasta )
     YARA_MAPPER ( input, YARA_INDEX.out.index )
 }
diff --git a/tests/software/yara/mapper/test.yml b/tests/software/yara/mapper/test.yml
index 311824e6..59cac33b 100644
--- a/tests/software/yara/mapper/test.yml
+++ b/tests/software/yara/mapper/test.yml
@@ -1,7 +1,6 @@
 - name: yara mapper test_yara_single_end
   command: nextflow run tests/software/yara/mapper -entry test_yara_single_end -c tests/config/nextflow.config
   tags:
-    - yara_single_end
     - yara/mapper
     - yara
   files:
@@ -37,7 +36,6 @@
   command: nextflow run tests/software/yara/mapper -entry test_yara_paired_end -c tests/config/nextflow.config
   tags:
     - yara/mapper
-    - yara_paired_end
     - yara
   files:
     - path: output/yara/test_2.mapped.bam