diff --git a/CHANGELOG.md b/CHANGELOG.md
index c11a0218a98..62419ae673a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -164,6 +164,7 @@
 
 * `convert/from_10xh5_to_h5mu`: add .uns slot to mdata root when metrics file is provided (PR #887).
 
+* Use `params.resources_test` in test workflows in order to point to an alternative location (e.g. a cache).
 * Fix ingestion components not working when optional arguments are unset (PR #894).
 
 ## DOCUMENTATION
diff --git a/_viash.yaml b/_viash.yaml
index ca7657ff537..d9050e54922 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,7 +1,5 @@
 viash_version: 0.9.0
 
-version: dev
-
 source: src
 target: target
 
diff --git a/src/compression/tar_extract/config.vsh.yaml b/src/compression/tar_extract/config.vsh.yaml
index 77743fb00ab..ed29f8617bc 100644
--- a/src/compression/tar_extract/config.vsh.yaml
+++ b/src/compression/tar_extract/config.vsh.yaml
@@ -1,7 +1,7 @@
 name: tar_extract
 namespace: compression
 description: Extract files from a tar archive
-arguments:                     
+arguments:
   - name: "--input"
     alternatives: ["-i"]
     type: file
@@ -44,4 +44,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [ singlecpu, lowmem ]
\ No newline at end of file
+      label: [ singlecpu, lowmem ]
diff --git a/src/workflows/gdo/gdo_singlesample/integration_test.sh b/src/workflows/gdo/gdo_singlesample/integration_test.sh
index fc19615d9ec..6a2ab79fae5 100755
--- a/src/workflows/gdo/gdo_singlesample/integration_test.sh
+++ b/src/workflows/gdo/gdo_singlesample/integration_test.sh
@@ -1,22 +1,16 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q gdo_singlesample
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/gdo/gdo_singlesample/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
diff --git a/src/workflows/gdo/gdo_singlesample/test.nf b/src/workflows/gdo/gdo_singlesample/test.nf
index 0006e726526..430d6d4bd68 100644
--- a/src/workflows/gdo/gdo_singlesample/test.nf
+++ b/src/workflows/gdo/gdo_singlesample/test.nf
@@ -2,9 +2,11 @@ nextflow.enable.dsl=2
 
 include { gdo_singlesample } from params.rootDir + "/target/nextflow/workflows/gdo/gdo_singlesample/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -33,4 +35,4 @@ workflow test_wf {
       assert (output_list.collect({it[1].output.getFileName().toString()}) as Set).equals(["simple_execution_test.final.h5mu"] as Set)
 
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/ingestion/bd_rhapsody/integration_test.sh b/src/workflows/ingestion/bd_rhapsody/integration_test.sh
index f2888f3fd9d..f69a5235db0 100755
--- a/src/workflows/ingestion/bd_rhapsody/integration_test.sh
+++ b/src/workflows/ingestion/bd_rhapsody/integration_test.sh
@@ -1,22 +1,16 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/bd_rhapsody/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
+  -c src/workflows/utils/integration_tests.config 
 
diff --git a/src/workflows/ingestion/bd_rhapsody/test.nf b/src/workflows/ingestion/bd_rhapsody/test.nf
index e0d369d488f..92c262b194b 100644
--- a/src/workflows/ingestion/bd_rhapsody/test.nf
+++ b/src/workflows/ingestion/bd_rhapsody/test.nf
@@ -3,15 +3,17 @@ nextflow.enable.dsl=2
 include { bd_rhapsody } from params.rootDir + "/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf"
 include { bd_rhapsody_test } from params.rootDir + "/target/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList(
     [
       [
         id: "foo",
-        reads: file("$resources_test/bdrhap_5kjrt/raw/12*.fastq.gz"),
+        reads: file("${params.resources_test}/bdrhap_5kjrt/raw/12*.fastq.gz"),
         reference_archive: resources_test.resolve("reference_gencodev41_chr1/reference_bd_rhapsody.tar.gz"),
         abseq_reference: resources_test.resolve("bdrhap_5kjrt/raw/BDAbSeq_ImmuneDiscoveryPanel.fasta"),
         cell_calling_data: "mRNA",
@@ -44,4 +46,4 @@ workflow test_wf {
 
     // | view { output -> output[1]}
     // | check_format(args: {""}) // todo: check whether output h5mu has the right slots defined
-}
\ No newline at end of file
+}
diff --git a/src/workflows/ingestion/cellranger_mapping/integration_test.sh b/src/workflows/ingestion/cellranger_mapping/integration_test.sh
index 72d6160f82b..c2744e1c69e 100755
--- a/src/workflows/ingestion/cellranger_mapping/integration_test.sh
+++ b/src/workflows/ingestion/cellranger_mapping/integration_test.sh
@@ -1,22 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-viash ns build -q ingestion/cellranger_mapping --setup cb --platform nextflow
-
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/cellranger_mapping/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
\ No newline at end of file
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/ingestion/cellranger_mapping/test.nf b/src/workflows/ingestion/cellranger_mapping/test.nf
index 422541297db..3ab5f95fc22 100644
--- a/src/workflows/ingestion/cellranger_mapping/test.nf
+++ b/src/workflows/ingestion/cellranger_mapping/test.nf
@@ -3,9 +3,11 @@ nextflow.enable.dsl=2
 include { cellranger_mapping } from params.rootDir + "/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf"
 include { cellranger_mapping_test } from params.rootDir + "/target/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [  
@@ -33,4 +35,4 @@ workflow test_wf {
       assert output_list.size() == 1 : "output channel should contain one event"
       assert output_list[0][0] == "foo" : "Output ID should be same as input ID"
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/ingestion/cellranger_multi/integration_test.sh b/src/workflows/ingestion/cellranger_multi/integration_test.sh
index 3eab6f6cc47..b0b084027f9 100755
--- a/src/workflows/ingestion/cellranger_multi/integration_test.sh
+++ b/src/workflows/ingestion/cellranger_multi/integration_test.sh
@@ -1,32 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=22.10.3
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/cellranger_multi/test.nf \
   -entry test_wf \
-  -resume \
-  -profile no_publish,docker \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
-
+  -c src/workflows/utils/integration_tests.config
 
 nextflow \
   run . \
   -main-script src/workflows/ingestion/cellranger_multi/test.nf \
   -entry test_wf2 \
-  -resume \
-  -profile no_publish,docker \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
\ No newline at end of file
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/ingestion/cellranger_multi/test.nf b/src/workflows/ingestion/cellranger_multi/test.nf
index dff8beb29ce..cb15b3cfcec 100644
--- a/src/workflows/ingestion/cellranger_multi/test.nf
+++ b/src/workflows/ingestion/cellranger_multi/test.nf
@@ -3,23 +3,36 @@ nextflow.enable.dsl=2
 include { cellranger_multi } from params.rootDir + "/target/nextflow/workflows/ingestion/cellranger_multi/main.nf"
 include { cellranger_multi_test } from params.rootDir + "/target/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
         id: "foo",
-        input:[resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_GEX_1_subset_S1_L001_R1_001.fastq.gz"),
-               resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_GEX_1_subset_S1_L001_R2_001.fastq.gz"),
-               resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_AB_subset_S2_L004_R1_001.fastq.gz"),
-               resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_AB_subset_S2_L004_R2_001.fastq.gz"),
-               resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_VDJ_subset_S1_L001_R1_001.fastq.gz"),
-               resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_VDJ_subset_S1_L001_R2_001.fastq.gz")],
+        input:[
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_GEX_1_subset_S1_L001_R1_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_GEX_1_subset_S1_L001_R2_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_AB_subset_S2_L004_R1_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_AB_subset_S2_L004_R2_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_VDJ_subset_S1_L001_R1_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_VDJ_subset_S1_L001_R2_001.fastq.gz")
+        ],
         gex_reference: resources_test.resolve("reference_gencodev41_chr1/reference_cellranger.tar.gz"),
         vdj_reference: resources_test.resolve("10x_5k_anticmv/raw/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0.tar.gz"),
         feature_reference: resources_test.resolve("10x_5k_anticmv/raw/feature_reference.csv"),
-        library_id: ["5k_human_antiCMV_T_TBNK_connect_GEX_1_subset", "5k_human_antiCMV_T_TBNK_connect_AB_subset", "5k_human_antiCMV_T_TBNK_connect_VDJ_subset"],
-        library_type: ["Gene Expression", "Antibody Capture", "VDJ"]
+        library_id: [
+          "5k_human_antiCMV_T_TBNK_connect_GEX_1_subset",
+          "5k_human_antiCMV_T_TBNK_connect_AB_subset",
+          "5k_human_antiCMV_T_TBNK_connect_VDJ_subset"
+        ],
+        library_type: [
+          "Gene Expression",
+          "Antibody Capture",
+          "VDJ"
+        ]
       ]
     ])
     | map{ state -> [state.id, state] }
@@ -43,8 +56,9 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // Test cell multiplexing
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "foo",
@@ -74,4 +88,4 @@ workflow test_wf2 {
       assert output_list.size() == 3 : "output channel should contain three events"
       assert (output_list.collect{it[0]} as Set) == (["Liver_BC1andOvarian_BC2", "Pancreas_BC4", "Colorectal_BC3"] as Set) : "Output ID should be same as input ID"
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/ingestion/cellranger_postprocessing/integration_test.sh b/src/workflows/ingestion/cellranger_postprocessing/integration_test.sh
index 823787b8828..3ca259c913b 100755
--- a/src/workflows/ingestion/cellranger_postprocessing/integration_test.sh
+++ b/src/workflows/ingestion/cellranger_postprocessing/integration_test.sh
@@ -1,7 +1,5 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
@@ -14,9 +12,7 @@ nextflow \
   -entry test_wf \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt \
-  -resume
+  -c src/workflows/utils/integration_tests.config
 
 nextflow \
   run . \
@@ -24,6 +20,4 @@ nextflow \
   -entry test_wf2 \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt \
-  -resume
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/ingestion/cellranger_postprocessing/test.nf b/src/workflows/ingestion/cellranger_postprocessing/test.nf
index 5c0f6580823..ce75512477a 100644
--- a/src/workflows/ingestion/cellranger_postprocessing/test.nf
+++ b/src/workflows/ingestion/cellranger_postprocessing/test.nf
@@ -4,9 +4,11 @@ include { cellranger_postprocessing } from params.rootDir + "/target/nextflow/wo
 include { from_10xh5_to_h5mu } from params.rootDir + "/target/nextflow/convert/from_10xh5_to_h5mu/main.nf"
 include { cellranger_postprocessing_test } from params.rootDir + "/target/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -55,9 +57,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
 
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -101,4 +102,4 @@ workflow test_wf2 {
     | map { output_list ->
       assert output_list.size() == 1 : "output channel should contain one event"
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/ingestion/conversion/integration_test.sh b/src/workflows/ingestion/conversion/integration_test.sh
index e2d19fda942..d551d4360d6 100755
--- a/src/workflows/ingestion/conversion/integration_test.sh
+++ b/src/workflows/ingestion/conversion/integration_test.sh
@@ -5,13 +5,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=24.04.4
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/conversion/test.nf \
   -entry test_wf \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
\ No newline at end of file
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/ingestion/conversion/test.nf b/src/workflows/ingestion/conversion/test.nf
index b31ee6b4a44..8c383361058 100644
--- a/src/workflows/ingestion/conversion/test.nf
+++ b/src/workflows/ingestion/conversion/test.nf
@@ -3,9 +3,11 @@ nextflow.enable.dsl=2
 include { conversion } from params.rootDir + "/target/nextflow/workflows/ingestion/conversion/main.nf"
 include { conversion_test } from params.rootDir + "/target/nextflow/test_workflows/ingestion/conversion_test/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -52,4 +54,4 @@ workflow test_wf {
     | map { output_list ->
       assert output_list.size() == 4 : "output channel should contain four events"
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/ingestion/demux/integration_test.sh b/src/workflows/ingestion/demux/integration_test.sh
index bb48efe7817..ef155d14cbd 100755
--- a/src/workflows/ingestion/demux/integration_test.sh
+++ b/src/workflows/ingestion/demux/integration_test.sh
@@ -1,23 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q 'workflows/ingestion/demux'
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/demux/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
-  -with-trace work/trace.txt \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
\ No newline at end of file
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/ingestion/demux/test.nf b/src/workflows/ingestion/demux/test.nf
index ef5a942f0b4..366fa9d963d 100644
--- a/src/workflows/ingestion/demux/test.nf
+++ b/src/workflows/ingestion/demux/test.nf
@@ -3,8 +3,11 @@ nextflow.enable.dsl=2
 
 include { demux } from params.rootDir + "/target/nextflow/workflows/ingestion/demux/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   // or when running from s3:
   Channel.fromList([
@@ -50,4 +53,4 @@ workflow test_wf {
     | map { output_list ->
       assert output_list.size() == 3 : "There should be three outputs"
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/ingestion/make_reference/integration_test.sh b/src/workflows/ingestion/make_reference/integration_test.sh
index 873336b45aa..d390fc78cce 100755
--- a/src/workflows/ingestion/make_reference/integration_test.sh
+++ b/src/workflows/ingestion/make_reference/integration_test.sh
@@ -1,20 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=23.04.2
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/make_reference/test.nf \
   -entry test_wf \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/ingestion/make_reference/test.nf b/src/workflows/ingestion/make_reference/test.nf
index c5a04aef667..80c0d314989 100644
--- a/src/workflows/ingestion/make_reference/test.nf
+++ b/src/workflows/ingestion/make_reference/test.nf
@@ -2,9 +2,11 @@ nextflow.enable.dsl=2
 
 include { make_reference } from params.rootDir + "/target/nextflow/workflows/ingestion/make_reference/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
diff --git a/src/workflows/integration/bbknn_leiden/integration_test.sh b/src/workflows/integration/bbknn_leiden/integration_test.sh
index f10544167a0..79c3106c251 100755
--- a/src/workflows/integration/bbknn_leiden/integration_test.sh
+++ b/src/workflows/integration/bbknn_leiden/integration_test.sh
@@ -1,25 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/bbknn_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/bbknn_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf2 \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
\ No newline at end of file
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/integration/bbknn_leiden/test.nf b/src/workflows/integration/bbknn_leiden/test.nf
index ced193b8ac2..5a1eba9a5f8 100644
--- a/src/workflows/integration/bbknn_leiden/test.nf
+++ b/src/workflows/integration/bbknn_leiden/test.nf
@@ -2,8 +2,12 @@ nextflow.enable.dsl=2
 
 include { bbknn_leiden } from params.rootDir + "/target/nextflow/workflows/integration/bbknn_leiden/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
+
   output_ch =
     Channel.fromList([
       [
@@ -44,7 +48,9 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
+
   output_ch =
     Channel.fromList([
       [
@@ -73,4 +79,4 @@ workflow test_wf2 {
       assert output_list.size() == 1 : "output channel should contain 1 event."
       assert output_list.collect{it[0]} == ["test_output_arg"]
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/integration/harmony_leiden/integration_test.sh b/src/workflows/integration/harmony_leiden/integration_test.sh
index 4521dd8ecc6..1dfb63b199f 100755
--- a/src/workflows/integration/harmony_leiden/integration_test.sh
+++ b/src/workflows/integration/harmony_leiden/integration_test.sh
@@ -1,27 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/harmony_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/harmony_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf2 \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/integration/harmony_leiden/test.nf b/src/workflows/integration/harmony_leiden/test.nf
index c1833ff95c9..e5c0d025a5d 100644
--- a/src/workflows/integration/harmony_leiden/test.nf
+++ b/src/workflows/integration/harmony_leiden/test.nf
@@ -2,8 +2,11 @@ nextflow.enable.dsl=2
 
 include { harmony_leiden } from params.rootDir + "/target/nextflow/workflows/integration/harmony_leiden/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = 
     Channel.fromList([
@@ -52,7 +55,8 @@ workflow test_wf {
 
 
 workflow test_wf2 {
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = 
     Channel.fromList([
diff --git a/src/workflows/integration/scanorama_leiden/integration_test.sh b/src/workflows/integration/scanorama_leiden/integration_test.sh
index 0c154a12ead..0c1c6db0fc9 100755
--- a/src/workflows/integration/scanorama_leiden/integration_test.sh
+++ b/src/workflows/integration/scanorama_leiden/integration_test.sh
@@ -6,20 +6,18 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/scanorama_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
+  -c src/workflows/utils/integration_tests.config
 
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/scanorama_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf2 \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/integration/scanorama_leiden/test.nf b/src/workflows/integration/scanorama_leiden/test.nf
index 91283f6f571..4803001c1de 100644
--- a/src/workflows/integration/scanorama_leiden/test.nf
+++ b/src/workflows/integration/scanorama_leiden/test.nf
@@ -2,9 +2,11 @@ nextflow.enable.dsl=2
 
 include { scanorama_leiden } from params.rootDir + "/target/nextflow/workflows/integration/scanorama_leiden/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -46,8 +48,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -77,4 +79,4 @@ workflow test_wf2 {
       assert output_list.size() == 1 : "output channel should contain 1 event"
       assert output_list.collect{it[0]} == ["test_output_arg"]
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/integration/scgpt_leiden/integration_test.sh b/src/workflows/integration/scgpt_leiden/integration_test.sh
index c37e71f6d9b..001299c408e 100755
--- a/src/workflows/integration/scgpt_leiden/integration_test.sh
+++ b/src/workflows/integration/scgpt_leiden/integration_test.sh
@@ -1,29 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q scgpt_leiden
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/scgpt_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/scgpt_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf2 \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/integration/scgpt_leiden/test.nf b/src/workflows/integration/scgpt_leiden/test.nf
index 2c1ddd3a544..9973b74df9b 100644
--- a/src/workflows/integration/scgpt_leiden/test.nf
+++ b/src/workflows/integration/scgpt_leiden/test.nf
@@ -2,33 +2,36 @@ nextflow.enable.dsl=2
 
 include { scgpt_leiden } from params.rootDir + "/target/nextflow/workflows/integration/scgpt_leiden/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-    resources_test = file("${params.rootDir}/resources_test/scgpt")
+
+  resources_test = file(params.resources_test)
 
     output_ch = Channel.fromList([
         [
-            id: "simple_execution_test",
-            input: resources_test.resolve("test_resources/Kim2020_Lung_subset_preprocessed.h5mu"),
-            model: resources_test.resolve("source/best_model.pt"),
-            model_config: resources_test.resolve("source/args.json"),
-            model_vocab: resources_test.resolve("source/vocab.json"),
-            input_layer: "log_normalized",
-            obs_batch_label: "sample",
-            n_hvg: 400,
-            seed: 1,
-            leiden_resolution: [1.0, 0.25]
+          id: "simple_execution_test",
+          input: resources_test.resolve("scgpt/test_resources/Kim2020_Lung_subset_preprocessed.h5mu"),
+          model: resources_test.resolve("scgpt/source/best_model.pt"),
+          model_config: resources_test.resolve("scgpt/source/args.json"),
+          model_vocab: resources_test.resolve("scgpt/source/vocab.json"),
+          input_layer: "log_normalized",
+          obs_batch_label: "sample",
+          n_hvg: 400,
+          seed: 1,
+          leiden_resolution: [1.0, 0.25]
         ],
         [
-            id: "no_leiden_resolutions_test",
-            input: resources_test.resolve("test_resources/Kim2020_Lung_subset_preprocessed.h5mu"),
-            model: resources_test.resolve("source/best_model.pt"),
-            model_config: resources_test.resolve("source/args.json"),
-            model_vocab: resources_test.resolve("source/vocab.json"),
-            obs_batch_label: "sample",
-            n_hvg: 400,
-            seed: 1,
-            input_layer: "log_normalized",
-            leiden_resolution: []
+          id: "no_leiden_resolutions_test",
+          input: resources_test.resolve("scgpt/test_resources/Kim2020_Lung_subset_preprocessed.h5mu"),
+          model: resources_test.resolve("scgpt/source/best_model.pt"),
+          model_config: resources_test.resolve("scgpt/source/args.json"),
+          model_vocab: resources_test.resolve("scgpt/source/vocab.json"),
+          obs_batch_label: "sample",
+          n_hvg: 400,
+          seed: 1,
+          input_layer: "log_normalized",
+          leiden_resolution: []
         ]
     ])
     | map{ state -> [state.id, state] }
@@ -58,7 +61,8 @@ workflow test_wf {
 
 
 workflow test_wf2 {
-  resources_test = file("${params.rootDir}/resources_test/scgpt")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -93,4 +97,4 @@ workflow test_wf2 {
       assert output_list.size() == 1 : "output channel should contain 1 event"
       assert output_list.collect{it[0]} == ["test_output_arg"]
     }
-  }
\ No newline at end of file
+  }
diff --git a/src/workflows/integration/scvi_leiden/integration_test.sh b/src/workflows/integration/scvi_leiden/integration_test.sh
index b59198c68de..d9577b5dd48 100755
--- a/src/workflows/integration/scvi_leiden/integration_test.sh
+++ b/src/workflows/integration/scvi_leiden/integration_test.sh
@@ -1,19 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/scvi_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/integration/scvi_leiden/test.nf b/src/workflows/integration/scvi_leiden/test.nf
index ee0b8127979..da86ae21001 100644
--- a/src/workflows/integration/scvi_leiden/test.nf
+++ b/src/workflows/integration/scvi_leiden/test.nf
@@ -2,9 +2,11 @@ nextflow.enable.dsl=2
 
 include { scvi_leiden } from params.rootDir + "/target/nextflow/workflows/integration/scvi_leiden/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
diff --git a/src/workflows/integration/totalvi_leiden/integration_test.sh b/src/workflows/integration/totalvi_leiden/integration_test.sh
index cc7acf52ee8..0e6ed54fa65 100755
--- a/src/workflows/integration/totalvi_leiden/integration_test.sh
+++ b/src/workflows/integration/totalvi_leiden/integration_test.sh
@@ -1,18 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=23.04.2
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/totalvi_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/integration/totalvi_leiden/test.nf b/src/workflows/integration/totalvi_leiden/test.nf
index 84926ce76b7..a7aa7d4636f 100644
--- a/src/workflows/integration/totalvi_leiden/test.nf
+++ b/src/workflows/integration/totalvi_leiden/test.nf
@@ -2,9 +2,11 @@ nextflow.enable.dsl=2
 
 include { totalvi_leiden } from params.rootDir + "/target/nextflow/workflows/integration/totalvi_leiden/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-    // allow changing the resources_test dir
-    resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
     output_ch = Channel.fromList([
       [
@@ -47,11 +49,6 @@ workflow test_wf {
       ]
     ])
     | map{ state -> [state.id, state] }
-    | map {id, state -> 
-      copy = state.reference.copyTo("${id}_reference.h5mu")
-      def new_state = state + ["reference": copy]
-      [id, new_state]
-    }
     | totalvi_leiden
     | view { output ->
       assert output.size() == 2 : "Outputs should contain two elements; [id, state]"
diff --git a/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml b/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml
index 585e2fa763b..4817ae2cf64 100644
--- a/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml
+++ b/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml
@@ -92,6 +92,6 @@ test_resources:
   - type: nextflow_script
     path: test.nf
     entrypoint: test_wf
-  - path: ..//resources_test/concat_test_data
+  - path: /resources_test/concat_test_data
 runners:
-  - type: nextflow
\ No newline at end of file
+  - type: nextflow
diff --git a/src/workflows/multiomics/dimensionality_reduction/integration_test.sh b/src/workflows/multiomics/dimensionality_reduction/integration_test.sh
index 7aab614f582..49dbba787c3 100755
--- a/src/workflows/multiomics/dimensionality_reduction/integration_test.sh
+++ b/src/workflows/multiomics/dimensionality_reduction/integration_test.sh
@@ -1,19 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/multiomics/dimensionality_reduction/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
\ No newline at end of file
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/multiomics/dimensionality_reduction/test.nf b/src/workflows/multiomics/dimensionality_reduction/test.nf
index ddbface6e9a..b99991f61ab 100644
--- a/src/workflows/multiomics/dimensionality_reduction/test.nf
+++ b/src/workflows/multiomics/dimensionality_reduction/test.nf
@@ -3,9 +3,11 @@ nextflow.enable.dsl=2
 include { dimensionality_reduction } from params.rootDir + "/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf"
 include { dimensionality_reduction_test } from params.rootDir + "/target/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf" 
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   input_ch = Channel.fromList([
       [
@@ -55,4 +57,4 @@ workflow test_wf {
     | dimensionality_reduction_test
 
 
-}
\ No newline at end of file
+}
diff --git a/src/workflows/multiomics/process_batches/integration_test.sh b/src/workflows/multiomics/process_batches/integration_test.sh
index 8835e0175c9..6790505773a 100755
--- a/src/workflows/multiomics/process_batches/integration_test.sh
+++ b/src/workflows/multiomics/process_batches/integration_test.sh
@@ -1,26 +1,18 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-viash ns build -q process_batches
-
-export NXF_VER=24.04.4
-
 nextflow \
   run . \
   -main-script src/workflows/multiomics/process_batches/test.nf \
   -entry test_wf \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
-
+  -c src/workflows/utils/integration_tests.config
 
 nextflow \
   run . \
@@ -28,5 +20,4 @@ nextflow \
   -entry test_wf2 \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/multiomics/process_batches/test.nf b/src/workflows/multiomics/process_batches/test.nf
index 3a8caf0c63b..6a684892538 100644
--- a/src/workflows/multiomics/process_batches/test.nf
+++ b/src/workflows/multiomics/process_batches/test.nf
@@ -5,11 +5,12 @@ include { process_batches } from targetDir + "/workflows/multiomics/process_batc
 include { workflow_test } from targetDir + "/test_workflows/multiomics/process_batches/workflow_test/main.nf"
 include { workflow_test2 } from targetDir + "/test_workflows/multiomics/process_batches/workflow_test2/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
 
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
-  
+  resources_test = file(params.resources_test)
+
   input_ch = Channel.fromList([
       [
           id: "test",
@@ -53,8 +54,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   input_ch = Channel.fromList([
       [
@@ -93,4 +94,4 @@ workflow test_wf2 {
     )
 
   
-}
\ No newline at end of file
+}
diff --git a/src/workflows/multiomics/process_samples/integration_test.sh b/src/workflows/multiomics/process_samples/integration_test.sh
index 786c1ae6fcc..7d62e019398 100755
--- a/src/workflows/multiomics/process_samples/integration_test.sh
+++ b/src/workflows/multiomics/process_samples/integration_test.sh
@@ -8,15 +8,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=23.10.3
-
-viash ns build -q '^workflows'
-
 nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -26,7 +21,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config \
@@ -37,7 +31,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config \
@@ -48,7 +41,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config \
@@ -57,9 +49,8 @@ nextflow \
 nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
-  -entry test_wf2 \
-  -resume \
   -profile docker,no_publish \
+  -entry test_wf2 \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
@@ -67,7 +58,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf3 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -76,7 +66,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf4 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -85,7 +74,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf5 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -94,7 +82,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf6 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -103,7 +90,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf7 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
\ No newline at end of file
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/multiomics/process_samples/test.nf b/src/workflows/multiomics/process_samples/test.nf
index 62cf0326c27..982da9ca3ca 100644
--- a/src/workflows/multiomics/process_samples/test.nf
+++ b/src/workflows/multiomics/process_samples/test.nf
@@ -5,9 +5,11 @@ include { remove_modality }  from targetDir + '/filter/remove_modality/main.nf'
 include { move_layer } from targetDir + '/transform/move_layer/main.nf' 
 include { process_samples } from targetDir + "/workflows/multiomics/process_samples/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -42,8 +44,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -94,8 +96,8 @@ workflow test_wf2 {
 }
 
 workflow test_wf3 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   input_ch = Channel.fromList([
       [
@@ -156,8 +158,8 @@ workflow test_wf3 {
 }
 
 workflow test_wf4 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -187,8 +189,8 @@ workflow test_wf4 {
 }
 
 workflow test_wf5 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -235,8 +237,8 @@ workflow test_wf5 {
 }
 
 workflow test_wf6 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -298,8 +300,8 @@ workflow test_wf6 {
 // }
 
 workflow test_wf7 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -345,4 +347,4 @@ workflow test_wf7 {
     assert output_list.size() == 1 : "output channel should contain one event"
     assert output_list[0][0] == "merged" : "Output ID should be 'merged'"
   }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/multiomics/split_modalities/integration_test.sh b/src/workflows/multiomics/split_modalities/integration_test.sh
index a6b30d4aea1..eaecdca1bb6 100755
--- a/src/workflows/multiomics/split_modalities/integration_test.sh
+++ b/src/workflows/multiomics/split_modalities/integration_test.sh
@@ -4,12 +4,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-
-
-nextflow run . \
-    -main-script src/workflows/multiomics/split_modalities/test.nf \
-    -entry test_wf \
-    -resume \
-    -profile docker \
-    -c src/workflows/utils/labels_ci.config \
-    -c src/workflows/utils/integration_tests.config
\ No newline at end of file
+nextflow \
+  run . \
+  -main-script src/workflows/multiomics/split_modalities/test.nf \
+  -entry test_wf \
+  -profile docker,no_publish \
+  -c src/workflows/utils/labels_ci.config \
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/multiomics/split_modalities/test.nf b/src/workflows/multiomics/split_modalities/test.nf
index 28277d06b6f..acc988deb89 100644
--- a/src/workflows/multiomics/split_modalities/test.nf
+++ b/src/workflows/multiomics/split_modalities/test.nf
@@ -3,9 +3,11 @@ nextflow.enable.dsl=2
 include { split_modalities } from params.rootDir + "/target/nextflow/dataflow/split_modalities/main.nf"
 include { split_modalities_test } from params.rootDir + "/target/nextflow/test_workflows/multiomics/split_modalities_test/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -32,4 +34,4 @@ workflow test_wf {
       "orig_input": "orig_input",
     ]
   )
-}
\ No newline at end of file
+}
diff --git a/src/workflows/prot/prot_multisample/integration_test.sh b/src/workflows/prot/prot_multisample/integration_test.sh
index f0078e0ddd8..46633a8f3f2 100755
--- a/src/workflows/prot/prot_multisample/integration_test.sh
+++ b/src/workflows/prot/prot_multisample/integration_test.sh
@@ -6,12 +6,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-viash ns build -q prot_multisample
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/prot/prot_multisample/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
\ No newline at end of file
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/prot/prot_multisample/test.nf b/src/workflows/prot/prot_multisample/test.nf
index 4c26573fa4b..9a35e0bd2c7 100644
--- a/src/workflows/prot/prot_multisample/test.nf
+++ b/src/workflows/prot/prot_multisample/test.nf
@@ -2,9 +2,11 @@ nextflow.enable.dsl=2
 
 include { prot_multisample } from params.rootDir + "/target/nextflow/workflows/prot/prot_multisample/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
diff --git a/src/workflows/prot/prot_singlesample/integration_test.sh b/src/workflows/prot/prot_singlesample/integration_test.sh
index 07ef39ef582..22f68c0d0e0 100755
--- a/src/workflows/prot/prot_singlesample/integration_test.sh
+++ b/src/workflows/prot/prot_singlesample/integration_test.sh
@@ -6,15 +6,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q prot_singlesample
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/multiomics/prot_singlesample/test.nf \
-  -profile docker,no_publish \
-  -resume \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
\ No newline at end of file
+  -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/prot/prot_singlesample/test.nf b/src/workflows/prot/prot_singlesample/test.nf
index a458bed6fd9..e2d4569655a 100644
--- a/src/workflows/prot/prot_singlesample/test.nf
+++ b/src/workflows/prot/prot_singlesample/test.nf
@@ -2,9 +2,11 @@ nextflow.enable.dsl=2
 
 include { prot_singlesample } from params.rootDir + "/target/nextflow/workflows/prot/prot_singlesample/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -33,4 +35,4 @@ workflow test_wf {
       assert output_list[0][0] == "foo" : "Output ID should be same as input ID"
       assert (output_list.collect({it[1].output.getFileName().toString()}) as Set).equals(["foo.final.h5mu"] as Set)
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/qc/qc/integration_test.sh b/src/workflows/qc/qc/integration_test.sh
index 8ac821bf864..408ec36e9e3 100755
--- a/src/workflows/qc/qc/integration_test.sh
+++ b/src/workflows/qc/qc/integration_test.sh
@@ -1,22 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q '^workflows/qc/qc'
-
 nextflow \
   run . \
   -main-script src/workflows/qc/qc/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/qc/qc/test.nf b/src/workflows/qc/qc/test.nf
index c96a9b69f71..d380b8eec59 100644
--- a/src/workflows/qc/qc/test.nf
+++ b/src/workflows/qc/qc/test.nf
@@ -3,10 +3,11 @@ nextflow.enable.dsl=2
 include { qc } from params.rootDir + "/target/nextflow/workflows/qc/qc/main.nf"
 include { qc_test } from params.rootDir + "/target/nextflow/test_workflows/qc/qc_test/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = 
     Channel.fromList([
@@ -54,4 +55,4 @@ workflow test_wf {
       assert output_list.size() == 2 : "output channel should contain 2 events"
       assert output_list.collect{it[0]} == ["human_test", "mouse_test"]
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/rna/rna_multisample/integration_test.sh b/src/workflows/rna/rna_multisample/integration_test.sh
index 3b553ba9892..c11d688b97f 100755
--- a/src/workflows/rna/rna_multisample/integration_test.sh
+++ b/src/workflows/rna/rna_multisample/integration_test.sh
@@ -1,22 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-viash ns build -q rna_multisample
-
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/rna/rna_multisample/test.nf \
-  -profile docker,no_publish \
-  -resume \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/rna/rna_multisample/test.nf b/src/workflows/rna/rna_multisample/test.nf
index 956a8c6f90b..eb65dc4d058 100644
--- a/src/workflows/rna/rna_multisample/test.nf
+++ b/src/workflows/rna/rna_multisample/test.nf
@@ -2,9 +2,11 @@ nextflow.enable.dsl=2
 
 include { rna_multisample } from params.rootDir + "/target/nextflow/workflows/rna/rna_multisample/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
diff --git a/src/workflows/rna/rna_singlesample/integration_test.sh b/src/workflows/rna/rna_singlesample/integration_test.sh
index 2644ca4b352..43b6299cd11 100755
--- a/src/workflows/rna/rna_singlesample/integration_test.sh
+++ b/src/workflows/rna/rna_singlesample/integration_test.sh
@@ -1,30 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q rna_singlesample
-# viash ns build -q 'filter|publish|qc|metadata' --parallel --setup cb
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/rna/rna_singlesample/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
-nextflow run . \
+nextflow \
+  run . \
+  -entry test_wf2 \
   -main-script src/workflows/rna/rna_singlesample/test.nf \
   -profile docker,no_publish \
-  -entry test_wf2 \
-  -with-trace work/trace.txt \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
diff --git a/src/workflows/rna/rna_singlesample/test.nf b/src/workflows/rna/rna_singlesample/test.nf
index 645efdbf1d2..6c06d6677f1 100644
--- a/src/workflows/rna/rna_singlesample/test.nf
+++ b/src/workflows/rna/rna_singlesample/test.nf
@@ -2,9 +2,11 @@ nextflow.enable.dsl=2
 
 include { rna_singlesample } from params.rootDir + "/target/nextflow/workflows/rna/rna_singlesample/main.nf"
 
+params.resources_test = params.rootDir + "/resources_test"
+
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -52,8 +54,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
@@ -87,4 +89,4 @@ workflow test_wf2 {
       assert (output_list.collect({it[1].output.getFileName().toString()}) as Set).equals(["mitochondrial_test.final.h5mu"] as Set)
 
     }
-}
\ No newline at end of file
+}
diff --git a/src/workflows/test_workflows/qc/config.vsh.yaml b/src/workflows/test_workflows/qc/config.vsh.yaml
index dae7ca6b842..19648acd20b 100644
--- a/src/workflows/test_workflows/qc/config.vsh.yaml
+++ b/src/workflows/test_workflows/qc/config.vsh.yaml
@@ -39,4 +39,6 @@ engines:
         __merge__: /src/base/requirements/viashpy.yaml
 runners:
   - type: executable
-  - type: nextflow
\ No newline at end of file
+  - type: nextflow
+    directives:
+      label: [midmem, midcpu]
\ No newline at end of file