diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1809eaf3..d9e783ad 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -48,6 +48,7 @@ jobs:
             profile: "conda"
           - isMaster: false
             profile: "singularity"
+      fail-fast: false # run all tests even if one fails
 
     steps:
       - name: Check out pipeline code
@@ -88,4 +89,4 @@ jobs:
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results_${{ matrix.test_name }}
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results_${{ matrix.test_name }}_${{ matrix.profile }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 29bb29f3..e53dde61 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Make output of FluteMLE optional as when some pathways produce bugs some channels are then empty ([#190](https://github.com/nf-core/crisprseq/pull/190))
 - Fix a typo in crisprcleanr/normalize, when a user inputs a file ([#192](https://github.com/nf-core/crisprseq/pull/192))
 
+### General
+
+- Run pipeline tests with docker, singularity and conda on CI ([#185](https://github.com/nf-core/crisprseq/pull/185))
+
 ## [v2.2.1 Romarin Curie - patch](https://github.com/nf-core/crisprseq/releases/tag/2.2.1) - [23.07.2024]
 
 ### Fixed
diff --git a/README.md b/README.md
index 3b6be505..e55f34a9 100644
--- a/README.md
+++ b/README.md
@@ -104,6 +104,10 @@ nextflow run nf-core/crisprseq --input samplesheet.csv --analysis <targeted/scre
 > [!WARNING]
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
+> [!WARNING]
+> Since Nextflow 23.07.0, Nextflow no longer mounts the host's HOME directory when using Apptainer or Singularity. MAGeCKFlute needs HOME directory write access. As a workaround, you can revert to the old behavior by setting the environment variable NXF_APPTAINER_HOME_MOUNT or NXF_SINGULARITY_HOME_MOUNT to true in the machine from which you launch the pipeline.
+> `export NXF_SINGULARITY_HOME_MOUNT=true; nextflow run nf-core/crisprseq --input samplesheet.csv --analysis screening --outdir <OUTDIR> -profile <singularity/aptainer>`
+
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/crisprseq/usage) and the [parameter documentation](https://nf-co.re/crisprseq/parameters).
 
 ## Pipeline output
diff --git a/conf/modules.config b/conf/modules.config
index 2078be96..12cb3fe4 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -317,7 +317,7 @@ process {
     }
 
     withName: MEDAKA {
-        ext.args = '-m r941_min_high_g303'
+        ext.args = { "-m ${model}" }
         ext.prefix = { "${reads.baseName}_medakaConsensus" }
     }
 
diff --git a/modules.json b/modules.json
index b4762749..ae97beb5 100644
--- a/modules.json
+++ b/modules.json
@@ -95,7 +95,8 @@
                     "racon": {
                         "branch": "master",
                         "git_sha": "f5ed3ac0834b68e80a00a06a61d04ce8e896f275",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/racon/racon.diff"
                     },
                     "samtools/index": {
                         "branch": "master",
diff --git a/modules/local/mageck/flutemle.nf b/modules/local/mageck/flutemle.nf
index e620c446..a95775a0 100644
--- a/modules/local/mageck/flutemle.nf
+++ b/modules/local/mageck/flutemle.nf
@@ -3,10 +3,10 @@ process MAGECK_FLUTEMLE {
     tag "$prefix"
     label 'process_high'
 
-    conda "bioconda::bioconductor-mageckflute=2.2.0"
+    conda "bioconda::bioconductor-mageckflute==2.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.2.0--r42hdfd78af_0':
-        'biocontainers/bioconductor-mageckflute:2.2.0--r42hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.6.0--r43hdfd78af_0':
+        'biocontainers/bioconductor-mageckflute:2.6.0--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gene_summary)
diff --git a/modules/local/mageck/graphrra.nf b/modules/local/mageck/graphrra.nf
index 69f48ae7..b22dfcee 100644
--- a/modules/local/mageck/graphrra.nf
+++ b/modules/local/mageck/graphrra.nf
@@ -2,10 +2,10 @@ process MAGECK_GRAPHRRA {
     tag "$meta.treatment"
     label 'process_single'
 
-    conda "bioconda::bioconductor-mageckflute=2.2.0"
+    conda "bioconda::bioconductor-mageckflute==2.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mageckflute:2.2.0--r42hdfd78af_0':
-        'biocontainers/bioconductor-mageckflute:2.2.0--r42hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-mageckflute:2.6.0--r43hdfd78af_0':
+        'biocontainers/bioconductor-mageckflute:2.6.0--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gene_summary)
diff --git a/modules/local/matricescreation.nf b/modules/local/matricescreation.nf
index 9470b5da..55f77e3b 100644
--- a/modules/local/matricescreation.nf
+++ b/modules/local/matricescreation.nf
@@ -1,7 +1,7 @@
 process MATRICESCREATION {
     label 'process_single'
 
-    conda 'r-ggplot2=3.4.3 bioconductor-shortread=1.58.0 r-ggpubr=0.6.0 r-ggmsa=1.0.2 r-seqmagick=0.1.6 r-tidyr=1.3.0 r-ggseqlogo=0.1 r-cowplot=1.1.1 r-seqinr=4.2_30 r-optparse=1.7.3 r-dplyr=1.1.2 r-plyr=1.8.8 r-stringr=1.5.0 r-plotly=4.10.2'
+    conda 'conda-forge::r-base==4.0'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-6de07928379e6eface08a0019c4a1d6b5192e805:0d77388f37ddd923a087f7792e30e83ab54c918c-0' :
         'biocontainers/mulled-v2-6de07928379e6eface08a0019c4a1d6b5192e805:0d77388f37ddd923a087f7792e30e83ab54c918c-0' }"
diff --git a/modules/local/orient_reference.nf b/modules/local/orient_reference.nf
index 28ec7641..5e176368 100644
--- a/modules/local/orient_reference.nf
+++ b/modules/local/orient_reference.nf
@@ -2,7 +2,8 @@ process ORIENT_REFERENCE {
     tag "$meta.id"
     label 'process_single'
 
-    conda "r-seqinr=4.2_16 bioconductor-biostrings=2.62.0 bioconductor-shortread=1.52.0"
+    // jpeg is required in the conda container to fix a "libjpeg.so.9: No such file or directory" error
+    conda "r-seqinr=4.2_16 bioconductor-biostrings=2.62.0 bioconductor-shortread=1.52.0 jpeg=9d"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-63136bce0d642de81864be727b6b42a26026e33b:d3ce5caf7bcbf6cecedcf51b0135646831c01e77-0' :
         'biocontainers/mulled-v2-63136bce0d642de81864be727b6b42a26026e33b:d3ce5caf7bcbf6cecedcf51b0135646831c01e77-0' }"
diff --git a/modules/local/venndiagram.nf b/modules/local/venndiagram.nf
index c9cab983..13675f1c 100644
--- a/modules/local/venndiagram.nf
+++ b/modules/local/venndiagram.nf
@@ -3,7 +3,7 @@ process VENNDIAGRAM {
     label 'process_low'
 
 
-    conda "bioconda::r-venndiagram=1.6.16"
+    conda "conda-forge::r-ggvenn=0.1.10"
     container "ghcr.io/qbic-pipelines/rnadeseq:dev"
 
     input:
diff --git a/modules/nf-core/medaka/environment.yml b/modules/nf-core/medaka/environment.yml
index 20e2cbbe..4f200e1e 100644
--- a/modules/nf-core/medaka/environment.yml
+++ b/modules/nf-core/medaka/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::medaka=1.4.4
+  - bioconda::medaka=1.11.3 # Updating version due to unable to find tensorflow with the previous version
diff --git a/modules/nf-core/medaka/main.nf b/modules/nf-core/medaka/main.nf
index a092aeb3..3afefba9 100644
--- a/modules/nf-core/medaka/main.nf
+++ b/modules/nf-core/medaka/main.nf
@@ -4,11 +4,12 @@ process MEDAKA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0' :
-        'biocontainers/medaka:1.4.4--py38h130def0_0' }"
+        'https://depot.galaxyproject.org/singularity/medaka:1.11.3--py38h2e44183_0' :
+        'biocontainers/medaka:1.11.3--py38h2e44183_0' }"
 
     input:
     tuple val(meta), path(reads), path(assembly)
+    path model
 
     output:
     tuple val(meta), path("*_medakaConsensus.fasta"), emit: assembly
diff --git a/modules/nf-core/medaka/medaka.diff b/modules/nf-core/medaka/medaka.diff
index 7f8752ac..7f161da7 100644
--- a/modules/nf-core/medaka/medaka.diff
+++ b/modules/nf-core/medaka/medaka.diff
@@ -1,4 +1,13 @@
 Changes in module 'nf-core/medaka'
+--- modules/nf-core/medaka/environment.yml
++++ modules/nf-core/medaka/environment.yml
+@@ -4,4 +4,4 @@
+   - bioconda
+   - defaults
+ dependencies:
+-  - bioconda::medaka=1.4.4
++  - bioconda::medaka=1.11.3 # Updating version due to unable to find tensorflow with the previous version
+
 --- modules/nf-core/medaka/main.nf
 +++ modules/nf-core/medaka/main.nf
 @@ -11,8 +11,8 @@
diff --git a/modules/nf-core/racon/main.nf b/modules/nf-core/racon/main.nf
index de29e355..7cff3057 100644
--- a/modules/nf-core/racon/main.nf
+++ b/modules/nf-core/racon/main.nf
@@ -11,8 +11,8 @@ process RACON {
     tuple val(meta), path(reads), path(assembly), path(paf)
 
     output:
-    tuple val(meta), path('*_assembly_consensus.fasta.gz') , emit: improved_assembly
-    path "versions.yml"          , emit: versions
+    tuple val(meta), path('*_assembly_consensus.fasta.gz'), emit: improved_assembly
+    path "versions.yml"                                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,11 +21,11 @@ process RACON {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    racon -t "$task.cpus" \\
-        "${reads}" \\
-        "${paf}" \\
+    racon -t $task.cpus \\
+        ${reads} \\
+        ${paf} \\
         $args \\
-        "${assembly}" > \\
+        ${assembly} > \\
         ${prefix}_assembly_consensus.fasta
 
     gzip -n ${prefix}_assembly_consensus.fasta
diff --git a/modules/nf-core/racon/racon.diff b/modules/nf-core/racon/racon.diff
new file mode 100644
index 00000000..27994bdb
--- /dev/null
+++ b/modules/nf-core/racon/racon.diff
@@ -0,0 +1,32 @@
+Changes in module 'nf-core/racon'
+--- modules/nf-core/racon/main.nf
++++ modules/nf-core/racon/main.nf
+@@ -11,8 +11,8 @@
+     tuple val(meta), path(reads), path(assembly), path(paf)
+ 
+     output:
+-    tuple val(meta), path('*_assembly_consensus.fasta.gz') , emit: improved_assembly
+-    path "versions.yml"          , emit: versions
++    tuple val(meta), path('*_assembly_consensus.fasta.gz'), emit: improved_assembly
++    path "versions.yml"                                   , emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+@@ -21,11 +21,11 @@
+     def args = task.ext.args ?: ''
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     """
+-    racon -t "$task.cpus" \\
+-        "${reads}" \\
+-        "${paf}" \\
++    racon -t $task.cpus \\
++        ${reads} \\
++        ${paf} \\
+         $args \\
+-        "${assembly}" > \\
++        ${assembly} > \\
+         ${prefix}_assembly_consensus.fasta
+ 
+     gzip -n ${prefix}_assembly_consensus.fasta
+
+************************************************************
diff --git a/modules/nf-core/vsearch/cluster/main.nf b/modules/nf-core/vsearch/cluster/main.nf
index 0aca4446..ce74abeb 100644
--- a/modules/nf-core/vsearch/cluster/main.nf
+++ b/modules/nf-core/vsearch/cluster/main.nf
@@ -11,19 +11,19 @@ process VSEARCH_CLUSTER {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path('*.aln.gz')                , optional: true, emit: aln
-    tuple val(meta), path('*.biom.gz')               , optional: true, emit: biom
-    tuple val(meta), path('*.mothur.tsv.gz')         , optional: true, emit: mothur
-    tuple val(meta), path('*.otu.tsv.gz')            , optional: true, emit: otu
-    tuple val(meta), path('*.bam')                   , optional: true, emit: bam
-    tuple val(meta), path('*.out.tsv.gz')            , optional: true, emit: out
-    tuple val(meta), path('*.blast.tsv.gz')          , optional: true, emit: blast
-    tuple val(meta), path('*.uc.tsv.gz')             , optional: true, emit: uc
-    tuple val(meta), path('*.centroids.fasta.gz')    , optional: true, emit: centroids
-    tuple val(meta), path('*.clusters.fasta*.gz')    , optional: true, emit: clusters
-    tuple val(meta), path('*.profile.txt.gz')        , optional: true, emit: profile
-    tuple val(meta), path('*.msa.fasta.gz')          , optional: true, emit: msa
-    path "versions.yml"                              , emit: versions
+    tuple val(meta), path('*.aln.gz')            , optional: true, emit: aln
+    tuple val(meta), path('*.biom.gz')           , optional: true, emit: biom
+    tuple val(meta), path('*.mothur.tsv.gz')     , optional: true, emit: mothur
+    tuple val(meta), path('*.otu.tsv.gz')        , optional: true, emit: otu
+    tuple val(meta), path('*.bam')               , optional: true, emit: bam
+    tuple val(meta), path('*.out.tsv.gz')        , optional: true, emit: out
+    tuple val(meta), path('*.blast.tsv.gz')      , optional: true, emit: blast
+    tuple val(meta), path('*.uc.tsv.gz')         , optional: true, emit: uc
+    tuple val(meta), path('*.centroids.fasta.gz'), optional: true, emit: centroids
+    tuple val(meta), path('*_clusters*')         , optional: true, emit: clusters
+    tuple val(meta), path('*.profile.txt.gz')    , optional: true, emit: profile
+    tuple val(meta), path('*.msa.fasta.gz')      , optional: true, emit: msa
+    path "versions.yml"                                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -41,7 +41,7 @@ process VSEARCH_CLUSTER {
                     args3.contains("--biomout") ? "biom" :
                     args3.contains("--blast6out") ? "blast.tsv" :
                     args3.contains("--centroids") ? "centroids.fasta" :
-                    args3.contains("--clusters") ? "clusters.fasta" :
+                    args3.contains("--clusters") ? "clusters" :
                     args3.contains("--mothur_shared_out") ? "mothur.tsv" :
                     args3.contains("--msaout") ? "msa.fasta" :
                     args3.contains("--otutabout") ? "otu.tsv" :
@@ -54,7 +54,7 @@ process VSEARCH_CLUSTER {
     """
     vsearch \\
         $args2 $fasta \\
-        $args3 ${prefix}.${out_ext} \\
+        $args3 ${prefix}_${out_ext} \\
         --threads $task.cpus \\
         $args
 
diff --git a/modules/nf-core/vsearch/cluster/vsearch-cluster.diff b/modules/nf-core/vsearch/cluster/vsearch-cluster.diff
index 8f1977e4..df715174 100644
--- a/modules/nf-core/vsearch/cluster/vsearch-cluster.diff
+++ b/modules/nf-core/vsearch/cluster/vsearch-cluster.diff
@@ -1,7 +1,56 @@
 Changes in module 'nf-core/vsearch/cluster'
 --- modules/nf-core/vsearch/cluster/main.nf
 +++ modules/nf-core/vsearch/cluster/main.nf
-@@ -60,7 +60,7 @@
+@@ -11,19 +11,19 @@
+     tuple val(meta), path(fasta)
+ 
+     output:
+-    tuple val(meta), path('*.aln.gz')                , optional: true, emit: aln
+-    tuple val(meta), path('*.biom.gz')               , optional: true, emit: biom
+-    tuple val(meta), path('*.mothur.tsv.gz')         , optional: true, emit: mothur
+-    tuple val(meta), path('*.otu.tsv.gz')            , optional: true, emit: otu
+-    tuple val(meta), path('*.bam')                   , optional: true, emit: bam
+-    tuple val(meta), path('*.out.tsv.gz')            , optional: true, emit: out
+-    tuple val(meta), path('*.blast.tsv.gz')          , optional: true, emit: blast
+-    tuple val(meta), path('*.uc.tsv.gz')             , optional: true, emit: uc
+-    tuple val(meta), path('*.centroids.fasta.gz')    , optional: true, emit: centroids
+-    tuple val(meta), path('*.clusters.fasta*.gz')    , optional: true, emit: clusters
+-    tuple val(meta), path('*.profile.txt.gz')        , optional: true, emit: profile
+-    tuple val(meta), path('*.msa.fasta.gz')          , optional: true, emit: msa
+-    path "versions.yml"                              , emit: versions
++    tuple val(meta), path('*.aln.gz')            , optional: true, emit: aln
++    tuple val(meta), path('*.biom.gz')           , optional: true, emit: biom
++    tuple val(meta), path('*.mothur.tsv.gz')     , optional: true, emit: mothur
++    tuple val(meta), path('*.otu.tsv.gz')        , optional: true, emit: otu
++    tuple val(meta), path('*.bam')               , optional: true, emit: bam
++    tuple val(meta), path('*.out.tsv.gz')        , optional: true, emit: out
++    tuple val(meta), path('*.blast.tsv.gz')      , optional: true, emit: blast
++    tuple val(meta), path('*.uc.tsv.gz')         , optional: true, emit: uc
++    tuple val(meta), path('*.centroids.fasta.gz'), optional: true, emit: centroids
++    tuple val(meta), path('*_clusters*')         , optional: true, emit: clusters
++    tuple val(meta), path('*.profile.txt.gz')    , optional: true, emit: profile
++    tuple val(meta), path('*.msa.fasta.gz')      , optional: true, emit: msa
++    path "versions.yml"                                          , emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+@@ -41,7 +41,7 @@
+                     args3.contains("--biomout") ? "biom" :
+                     args3.contains("--blast6out") ? "blast.tsv" :
+                     args3.contains("--centroids") ? "centroids.fasta" :
+-                    args3.contains("--clusters") ? "clusters.fasta" :
++                    args3.contains("--clusters") ? "clusters" :
+                     args3.contains("--mothur_shared_out") ? "mothur.tsv" :
+                     args3.contains("--msaout") ? "msa.fasta" :
+                     args3.contains("--otutabout") ? "otu.tsv" :
+@@ -54,13 +54,13 @@
+     """
+     vsearch \\
+         $args2 $fasta \\
+-        $args3 ${prefix}.${out_ext} \\
++        $args3 ${prefix}_${out_ext} \\
+         --threads $task.cpus \\
+         $args
  
      if [[ $args3 == "--clusters" ]]
      then
diff --git a/nextflow.config b/nextflow.config
index 76f078ee..5946cb46 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -43,7 +43,7 @@ params {
 
     // UMI parameters
     umi_bin_size               = 1
-    medaka_model               = 'r941_min_high_g303'
+    medaka_model               = 'https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g303_model.hdf5'
 
     // Vsearch options
     vsearch_minseqlength       = 55
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4b775892..a495b414 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -88,7 +88,7 @@
                 },
                 "medaka_model": {
                     "type": "string",
-                    "default": "r941_min_high_g303",
+                    "default": "https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g303_model.hdf5",
                     "fa_icon": "fas fa-font",
                     "description": "Medaka model (-m) to use according to the basecaller used."
                 }
diff --git a/templates/template_fluteMLE.R b/templates/template_fluteMLE.R
index 7aea697d..38abcdb0 100644
--- a/templates/template_fluteMLE.R
+++ b/templates/template_fluteMLE.R
@@ -4,6 +4,14 @@
     ####
     #### graphs mageck MLE
 
+    # Required to fix corrupted cache from Singularity container
+    library(BiocFileCache)
+    bfc <- BiocFileCache("~/.cache/R/ExperimentHub")
+    res <- bfcquery(bfc, "experimenthub.index.rds", field="rname", exact=TRUE)
+    bfcremove(bfc, rids=res\$rid)
+    library(ExperimentHub)
+    eh = ExperimentHub()
+
     library(MAGeCKFlute)
     library(clusterProfiler)
     library(ggplot2)
diff --git a/workflows/crisprseq_targeted.nf b/workflows/crisprseq_targeted.nf
index 55a88f51..c584fe24 100644
--- a/workflows/crisprseq_targeted.nf
+++ b/workflows/crisprseq_targeted.nf
@@ -507,7 +507,8 @@ workflow CRISPRSEQ_TARGETED {
         //
         MEDAKA (
             ch_clusters_sequence
-                .join(RACON_2.out.improved_assembly)
+                .join(RACON_2.out.improved_assembly),
+            Channel.value( file(params.medaka_model) )
         )
         ch_versions = ch_versions.mix(MEDAKA.out.versions.first())