From 34ac993e081b32d2170ab790d0386b74122f9d36 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Sun, 4 Aug 2024 09:01:45 +1200
Subject: [PATCH] Updated test data paths batch 13 (#6087)

* Updated test data paths batch 13

* Updated snaphot

* Update modules/nf-core/deepbgc/pipeline/meta.yml

* Update modules/nf-core/propr/propr/meta.yml

* Update modules/nf-core/toulligqc/meta.yml

* Removed maintainers line

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 .../nf-core/bcftools/call/tests/main.nf.test  | 40 +++++++++----------
 .../nf-core/bcftools/query/tests/main.nf.test | 16 ++++----
 .../nf-core/bcftools/view/tests/main.nf.test  | 40 +++++++++----------
 modules/nf-core/deepbgc/pipeline/meta.yml     |  3 ++
 .../deepbgc/pipeline/tests/main.nf.test       |  2 +-
 .../merqury/merqury/tests/main.nf.test        | 14 +++----
 modules/nf-core/propr/grea/meta.yml           |  4 ++
 modules/nf-core/propr/grea/tests/main.nf.test | 10 ++---
 .../propr/grea/tests/main.nf.test.snap        |  6 +--
 modules/nf-core/propr/propr/meta.yml          |  4 ++
 .../nf-core/propr/propr/tests/main.nf.test    | 12 +++---
 .../nf-core/proteinortho/tests/main.nf.test   |  2 +-
 .../thermorawfileparser/tests/main.nf.test    |  4 +-
 modules/nf-core/toulligqc/meta.yml            | 14 ++-----
 modules/nf-core/toulligqc/tests/main.nf.test  | 10 ++---
 15 files changed, 92 insertions(+), 89 deletions(-)

diff --git a/modules/nf-core/bcftools/call/tests/main.nf.test b/modules/nf-core/bcftools/call/tests/main.nf.test
index fa766424d56..31c86efc046 100644
--- a/modules/nf-core/bcftools/call/tests/main.nf.test
+++ b/modules/nf-core/bcftools/call/tests/main.nf.test
@@ -19,8 +19,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -50,8 +50,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -84,8 +84,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -118,8 +118,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -152,11 +152,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true)
                 input[3] = []
                 """
             }
@@ -184,8 +184,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -216,8 +216,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -246,8 +246,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -276,8 +276,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test b/modules/nf-core/bcftools/query/tests/main.nf.test
index e9ea5a9d71b..39e67b35ad3 100644
--- a/modules/nf-core/bcftools/query/tests/main.nf.test
+++ b/modules/nf-core/bcftools/query/tests/main.nf.test
@@ -18,8 +18,8 @@ nextflow_process {
                 """
                 input[0] = [ 
                     [ id:'out' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -47,11 +47,11 @@ nextflow_process {
                 """
                 input[0] = [ 
                     [ id:'out' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true)
                 input[3] = []
                 """
             }
@@ -76,8 +76,8 @@ nextflow_process {
                 """
                 input[0] = [ 
                     [ id:'out' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test b/modules/nf-core/bcftools/view/tests/main.nf.test
index 14a7283d434..1e60c50d5a3 100644
--- a/modules/nf-core/bcftools/view/tests/main.nf.test
+++ b/modules/nf-core/bcftools/view/tests/main.nf.test
@@ -18,8 +18,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -49,8 +49,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -83,8 +83,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -117,8 +117,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -151,11 +151,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true)
                 input[3] = []
                 """
             }
@@ -183,8 +183,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -215,8 +215,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -245,8 +245,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -275,8 +275,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
diff --git a/modules/nf-core/deepbgc/pipeline/meta.yml b/modules/nf-core/deepbgc/pipeline/meta.yml
index 6c29cebc8df..5f939eaa4fd 100644
--- a/modules/nf-core/deepbgc/pipeline/meta.yml
+++ b/modules/nf-core/deepbgc/pipeline/meta.yml
@@ -27,6 +27,9 @@ input:
       type: file
       description: FASTA/GenBank/Pfam CSV file
       pattern: "*.{fasta,fa,fna,gbk,csv}"
+  - db:
+      type: directory
+      description: Database path
 output:
   - meta:
       type: map
diff --git a/modules/nf-core/deepbgc/pipeline/tests/main.nf.test b/modules/nf-core/deepbgc/pipeline/tests/main.nf.test
index 190b7e8f7ea..9dd24049e77 100644
--- a/modules/nf-core/deepbgc/pipeline/tests/main.nf.test
+++ b/modules/nf-core/deepbgc/pipeline/tests/main.nf.test
@@ -26,7 +26,7 @@ nextflow_process {
                 """
                 input[0] =  Channel.fromList([
                     tuple([ id:'test_gbk', single_end:false ], // meta map
-                            file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true))
+                            file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true))
                 ])
                 """
             }
diff --git a/modules/nf-core/merqury/merqury/tests/main.nf.test b/modules/nf-core/merqury/merqury/tests/main.nf.test
index 34c7b46c931..46a07c02a41 100644
--- a/modules/nf-core/merqury/merqury/tests/main.nf.test
+++ b/modules/nf-core/merqury/merqury/tests/main.nf.test
@@ -19,8 +19,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = 21
@@ -46,7 +46,7 @@ nextflow_process {
                 """
                 assembly = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[0] = MERYL_UNIONSUM.out.meryl_db.join( Channel.value( assembly ) )
                 """
@@ -91,7 +91,7 @@ nextflow_process {
                     input[0] = [
                         [ id:'test', single_end:false ], // meta map
                         [
-                            file(params.test_data['homo_sapiens']['illumina']['test2_1_fastq_gz'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz', checkIfExists: true)
                         ]
                     ]
                     input[1] = 21
@@ -106,7 +106,7 @@ nextflow_process {
                     input[0] = [
                         [ id:'test', single_end:false ], // meta map
                         [
-                            file(params.test_data['homo_sapiens']['illumina']['test2_2_fastq_gz'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)
                         ]
                     ]
                     input[1] = 21
@@ -120,7 +120,7 @@ nextflow_process {
                 """
                 ch_assembly = Channel.value([
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ])
 
                 ch_input = MERYL_UNIONSUM.out.meryl_db
@@ -170,7 +170,7 @@ nextflow_process {
                 """
                 assembly = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[0] = MERYL_UNIONSUM.out.meryl_db.join( Channel.value( assembly ) )
                 """
diff --git a/modules/nf-core/propr/grea/meta.yml b/modules/nf-core/propr/grea/meta.yml
index de40abd3b15..d78d7c8b33f 100644
--- a/modules/nf-core/propr/grea/meta.yml
+++ b/modules/nf-core/propr/grea/meta.yml
@@ -47,6 +47,10 @@ output:
       type: file
       description: File containing GO terms and their enrichment values
       pattern: "*.{csv}"
+  - session_info:
+      type: file
+      description: R session log
+      pattern: "*.R_sessionInfo.log"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/propr/grea/tests/main.nf.test b/modules/nf-core/propr/grea/tests/main.nf.test
index afac1dec300..dd442b43459 100644
--- a/modules/nf-core/propr/grea/tests/main.nf.test
+++ b/modules/nf-core/propr/grea/tests/main.nf.test
@@ -1,17 +1,17 @@
 nextflow_process {
- 
+
     name "Test Process PROPR_GREA"
     script "../main.nf"
     process "PROPR_GREA"
-    
+
     tag "modules"
     tag "modules_nfcore"
     tag "propr"
     tag "propr/grea"
     tag "mygene"
     tag "propr/propr"
- 
-    test("grea chained to propr using default options") {  
+
+    test("grea chained to propr using default options") {
 
         tag "default"
         config "./grea_test.config"
@@ -49,7 +49,7 @@ nextflow_process {
                 """
             }
         }
- 
+
         then {
             assertAll(
                 { assert process.success },
diff --git a/modules/nf-core/propr/grea/tests/main.nf.test.snap b/modules/nf-core/propr/grea/tests/main.nf.test.snap
index a915603dd71..2db674fc5ae 100644
--- a/modules/nf-core/propr/grea/tests/main.nf.test.snap
+++ b/modules/nf-core/propr/grea/tests/main.nf.test.snap
@@ -18,14 +18,14 @@
                     {
                         "id": "test_adj"
                     },
-                    "test_adj.go.tsv:md5,914d8b750ba303a297efb7331ec238b7"
+                    "test_adj.go.tsv:md5,904e1fe3eed0f2dded8e5b64321a0269"
                 ]
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-04-29T10:45:07.508934"
+        "timestamp": "2024-08-03T16:06:25.669444"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/propr/propr/meta.yml b/modules/nf-core/propr/propr/meta.yml
index c2c9a11d85f..206565168cc 100644
--- a/modules/nf-core/propr/propr/meta.yml
+++ b/modules/nf-core/propr/propr/meta.yml
@@ -67,6 +67,10 @@ output:
       type: file
       description: dump of R SessionInfo
       pattern: "*.R_sessionInfo.log"
+  - warnings:
+      type: file
+      description: Warnings
+      pattern: "*.warnings.log"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/propr/propr/tests/main.nf.test b/modules/nf-core/propr/propr/tests/main.nf.test
index e262d2cfbfc..1f2e67fe5ef 100644
--- a/modules/nf-core/propr/propr/tests/main.nf.test
+++ b/modules/nf-core/propr/propr/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    //file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true)
+                    //file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                     file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv")
                 ]
                 """
@@ -44,7 +44,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 """
             }
@@ -69,7 +69,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 """
             }
@@ -95,7 +95,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 """
             }
@@ -120,7 +120,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 """
             }
@@ -145,7 +145,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/proteinortho/tests/main.nf.test b/modules/nf-core/proteinortho/tests/main.nf.test
index 28bb372ee51..2ac0a906379 100644
--- a/modules/nf-core/proteinortho/tests/main.nf.test
+++ b/modules/nf-core/proteinortho/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             }
             process {
                 """
-                file_a = file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
+                file_a = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
                 file_a.copyTo("${workDir}/prot1.fasta")
                 file_a.copyTo("${workDir}/prot2.fasta")
                 file_a = file("${workDir}/prot1.fasta", checkIfExists:true)
diff --git a/modules/nf-core/thermorawfileparser/tests/main.nf.test b/modules/nf-core/thermorawfileparser/tests/main.nf.test
index 85cfed35522..90f8aa1b046 100644
--- a/modules/nf-core/thermorawfileparser/tests/main.nf.test
+++ b/modules/nf-core/thermorawfileparser/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test'], // meta map
-                    file(params.test_data['proteomics']['msspectra']['hla2_file'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'proteomics/msspectra/PXD012083_e005640_II.raw', checkIfExists: true)
                     ]
                 """
             }
@@ -41,7 +41,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test'], // meta map
-                    file(params.test_data['proteomics']['msspectra']['hla2_file'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'proteomics/msspectra/PXD012083_e005640_II.raw', checkIfExists: true)
                     ]
                 """
             }
diff --git a/modules/nf-core/toulligqc/meta.yml b/modules/nf-core/toulligqc/meta.yml
index 682a8ef3281..61c69794c29 100644
--- a/modules/nf-core/toulligqc/meta.yml
+++ b/modules/nf-core/toulligqc/meta.yml
@@ -20,18 +20,10 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - seq_summary:
+  - ontfile:
       type: file
-      description: Basecaller sequencing summary source
-      pattern: "*.txt"
-  - fastq:
-      type: file
-      description: FASTQ file (necessary if no sequencing summary file)
-      pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
-  - bam:
-      type: file
-      description: BAM file (necessary if no sequencing summary file)
-      pattern: "*.bam"
+      description: Input ONT file
+      pattern: "*.{fastq,fastq.gz,fq,fq.gz,txt,txt.gz,bam}"
 
 output:
   - meta:
diff --git a/modules/nf-core/toulligqc/tests/main.nf.test b/modules/nf-core/toulligqc/tests/main.nf.test
index c88b30f02bc..5bbad941f75 100644
--- a/modules/nf-core/toulligqc/tests/main.nf.test
+++ b/modules/nf-core/toulligqc/tests/main.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test2_sequencing_summary'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test2.sequencing_summary.txt', checkIfExists: true),
                     ]
                 """
             }
@@ -38,7 +38,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test2_sequencing_summary'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test2.sequencing_summary.txt', checkIfExists: true),
                     ]
                 """
             }
@@ -61,7 +61,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true),
                     ]
                 """
             }
@@ -84,7 +84,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test_sorted_bam'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/bam/test.sorted.bam', checkIfExists: true)
                     ]
                 """
             }
@@ -109,7 +109,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test_sorted_bam'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/bam/test.sorted.bam', checkIfExists: true)
                     ]
                 """
             }