diff --git a/tests/test_alfa/test.sh b/tests/test_alfa/test.sh
index 5e417f4b8b3cce6444bcdbca2225f29c6b4597f1..538973426f2338833e1330271384ad83e2a7750e 100755
--- a/tests/test_alfa/test.sh
+++ b/tests/test_alfa/test.sh
@@ -34,6 +34,7 @@ snakemake \
     --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
     --verbose \
     --notemp \
+    --no-hooks \
     results/ALFA/ALFA_plots_mqc.png
 
 # Check md5 sum of some output files
diff --git a/tests/test_create_dag_image/test.sh b/tests/test_create_dag_image/test.sh
index c5fc8dd8c7fcb3e7f230ef81ca437333a4540add..1c954dd3f80399aec892d7ab90b9ac75fd104063 100755
--- a/tests/test_create_dag_image/test.sh
+++ b/tests/test_create_dag_image/test.sh
@@ -27,5 +27,6 @@ snakemake \
     --dryrun \
     --verbose \
     --notemp \
+    --no-hooks \
     | dot -Tsvg > "../../images/dag_test_workflow.svg"
 
diff --git a/tests/test_create_rule_graph/test.sh b/tests/test_create_rule_graph/test.sh
index 2fa3db75f436a96902ff617ddb144920d13fe5e6..287e08d9d4831c79c0bff172f36653dd2012ca66 100755
--- a/tests/test_create_rule_graph/test.sh
+++ b/tests/test_create_rule_graph/test.sh
@@ -27,5 +27,6 @@ snakemake \
     --dryrun \
     --verbose \
     --notemp \
+    --no-hooks \
     | dot -Tsvg > "../../images/rule_graph.svg"
 
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index 92429556e2a1db6434184fade06aac4a0130337b..9bfdb92d52fcbe9ddece85178267dcc32eb9ddf2 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -20,7 +20,6 @@ ea36f062eedc7f54ceffea2b635a25a8  results/star_indexes/homo_sapiens/75/STAR_inde
 500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate1.fastq
 e90e31db1ce51d930645eb74ff70d21b  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate2.fastq
 1c0796d7e0bdab0e99780b2e11d80c19  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate2.fastq
-d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.SJ.out.tab
 9896744dd90ff3eef00c91fa1f721366  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc_data.txt
 6946ba80af318b9c1052b264dc674a51  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc.fo
 2603f3031242e97411a71571f6ad9e53  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/summary.txt
@@ -45,18 +44,9 @@ b28aac49f537b8cba364b6422458ad28  results/samples/synthetic_10_reads_paired_synt
 69b70e3f561b749bf10b186dd2480a8a  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_sequence_quality.png
 b28aac49f537b8cba364b6422458ad28  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_tile_quality.png
 5b950b5dfe3c7407e9aac153db330a38  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/sequence_length_distribution.png
-2e77276535976efccb244627231624bf  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/abundance.tsv
-d013650f813b815a790c9e6a51c7559b  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/pseudoalignments.bam
 d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.kallisto.pseudo.sam
-981b59830d74d300bb5dd3e602e0d86f  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/lib_format_counts.json
-989d6ee63b728fced9ec0249735ab83d  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/ambig_info.tsv
-3407f87245d0003e0ffbfdf6d8c04f20  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/expected_bias
-92bcd0592d22a6a58d0360fc76103e56  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias
-92bcd0592d22a6a58d0360fc76103e56  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias_3p
-d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/unmapped_names.txt
 500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_adapters_mate1.fastq
 500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_polya_mate1.fastq
-d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.SJ.out.tab
 fdb8c6ddd39b606414b2785d6ec2da8a  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc_data.txt
 3cb70940acdcca512207bd8613085538  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc.fo
 fc276a1711cc35f7a9d5328bdbbab810  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/summary.txt
@@ -69,15 +59,7 @@ e4c1a39967ec9547a2e4c71c97982ee0  results/samples/synthetic_10_reads_mate_1_synt
 69b70e3f561b749bf10b186dd2480a8a  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_sequence_quality.png
 b28aac49f537b8cba364b6422458ad28  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_tile_quality.png
 5b950b5dfe3c7407e9aac153db330a38  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/sequence_length_distribution.png
-50a9b89a9f1da2c438cb0041b64faa0e  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/abundance.tsv
-fd8242418230a4edb33350be2e4f1d78  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/pseudoalignments.bam
 d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.kallisto.pseudo.sam
-d6ae863b39ca6ec5d0f63c03036f9dda  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/lib_format_counts.json
-989d6ee63b728fced9ec0249735ab83d  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/ambig_info.tsv
-3407f87245d0003e0ffbfdf6d8c04f20  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/expected_bias
-92bcd0592d22a6a58d0360fc76103e56  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias
-92bcd0592d22a6a58d0360fc76103e56  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias_3p
-d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/unmapped_names.txt
 3ce47cb1d62482c5d62337751d7e8552  results/transcriptome/homo_sapiens/transcriptome.fa
 6b44c507f0a1c9f7369db0bb1deef0fd  results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
 2caebc23faf78fdbbbdbb118d28bd6b5  results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 00f6d964b053fb2506116de7c1c19d5014567392..d1a87ae3eb230127f0c1122915a77a9fc3ebe52a 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -7,9 +7,6 @@ cleanup () {
     rm -rf .config/
     rm -rf .fontconfig/
     rm -rf .java/
-    rm -rf .snakemake/
-    rm -rf logs/
-    rm -rf results/
     rm -rf snakemake_report.html
     cd $user_dir
     echo "Exit status: $rc"
@@ -34,6 +31,7 @@ snakemake \
     --use-singularity \
     --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
     --notemp \
+    --no-hooks \
     --verbose
 
 # Create a Snakemake report after the workflow execution
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index 02aaf7229c1c0d8c5f0330d1e733840ed1d5f220..c6c84103ee873c4546487b6b9ed7af58be2f6112 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -36,6 +36,7 @@ snakemake \
     --use-singularity \
     --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
     --notemp \
+    --no-hooks \
     --verbose
 
 # Create a Snakemake report after the workflow execution
diff --git a/tests/test_integration_workflow_multiple_lanes/expected_output.md5 b/tests/test_integration_workflow_multiple_lanes/expected_output.md5
index 7a6ae82d02eb20ee568017f8150bc7a671dadc4c..c52d4c0603f6580840d9bb829a48bb5f5a1dbc18 100644
--- a/tests/test_integration_workflow_multiple_lanes/expected_output.md5
+++ b/tests/test_integration_workflow_multiple_lanes/expected_output.md5
@@ -20,7 +20,6 @@ ea36f062eedc7f54ceffea2b635a25a8  results/star_indexes/homo_sapiens/75/STAR_inde
 500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate1.fastq
 e90e31db1ce51d930645eb74ff70d21b  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate2.fastq
 1c0796d7e0bdab0e99780b2e11d80c19  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate2.fastq
-d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.SJ.out.tab
 9896744dd90ff3eef00c91fa1f721366  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc_data.txt
 6946ba80af318b9c1052b264dc674a51  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc.fo
 2603f3031242e97411a71571f6ad9e53  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/summary.txt
@@ -45,18 +44,9 @@ b28aac49f537b8cba364b6422458ad28  results/samples/synthetic_10_reads_paired_synt
 69b70e3f561b749bf10b186dd2480a8a  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_sequence_quality.png
 b28aac49f537b8cba364b6422458ad28  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_tile_quality.png
 5b950b5dfe3c7407e9aac153db330a38  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/sequence_length_distribution.png
-2e77276535976efccb244627231624bf  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/abundance.tsv
-d013650f813b815a790c9e6a51c7559b  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/pseudoalignments.bam
 d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.kallisto.pseudo.sam
-981b59830d74d300bb5dd3e602e0d86f  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/lib_format_counts.json
-989d6ee63b728fced9ec0249735ab83d  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/ambig_info.tsv
-3407f87245d0003e0ffbfdf6d8c04f20  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/expected_bias
-92bcd0592d22a6a58d0360fc76103e56  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias
-92bcd0592d22a6a58d0360fc76103e56  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias_3p
-d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/unmapped_names.txt
 500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_adapters_mate1.fastq
 500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_polya_mate1.fastq
-d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.SJ.out.tab
 fdb8c6ddd39b606414b2785d6ec2da8a  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc_data.txt
 3cb70940acdcca512207bd8613085538  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc.fo
 fc276a1711cc35f7a9d5328bdbbab810  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/summary.txt
@@ -69,15 +59,7 @@ e4c1a39967ec9547a2e4c71c97982ee0  results/samples/synthetic_10_reads_mate_1_synt
 69b70e3f561b749bf10b186dd2480a8a  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_sequence_quality.png
 b28aac49f537b8cba364b6422458ad28  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_tile_quality.png
 5b950b5dfe3c7407e9aac153db330a38  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/sequence_length_distribution.png
-50a9b89a9f1da2c438cb0041b64faa0e  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/abundance.tsv
-fd8242418230a4edb33350be2e4f1d78  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/pseudoalignments.bam
 d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.kallisto.pseudo.sam
-d6ae863b39ca6ec5d0f63c03036f9dda  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/lib_format_counts.json
-989d6ee63b728fced9ec0249735ab83d  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/ambig_info.tsv
-3407f87245d0003e0ffbfdf6d8c04f20  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/expected_bias
-92bcd0592d22a6a58d0360fc76103e56  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias
-92bcd0592d22a6a58d0360fc76103e56  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias_3p
-d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/unmapped_names.txt
 3ce47cb1d62482c5d62337751d7e8552  results/transcriptome/homo_sapiens/transcriptome.fa
 6b44c507f0a1c9f7369db0bb1deef0fd  results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
 2caebc23faf78fdbbbdbb118d28bd6b5  results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
diff --git a/tests/test_integration_workflow_multiple_lanes/test.local.sh b/tests/test_integration_workflow_multiple_lanes/test.local.sh
index 9804f337de0760003d0acbd048f5f680157b9cd1..fd45fa49fe29f11f480e19ca38860a54f1ef5edc 100755
--- a/tests/test_integration_workflow_multiple_lanes/test.local.sh
+++ b/tests/test_integration_workflow_multiple_lanes/test.local.sh
@@ -34,6 +34,7 @@ snakemake \
     --use-singularity \
     --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
     --notemp \
+    --no-hooks \
     --verbose
 
 # Create a Snakemake report after the workflow execution
diff --git a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
index a0517fddf6d6815d954bebce7b01e385b9b2073a..74ba028f9ef4ac85543657916adbfbe45de25c9e 100755
--- a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
+++ b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh
@@ -36,6 +36,7 @@ snakemake \
     --use-singularity \
     --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
     --notemp \
+    --no-hooks \
     --verbose
 
 # Create a Snakemake report after the workflow execution
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index a756856ef49bf9a3e7c7ec824e353becdc860659..9337ad0c4bf1d927e76d23ed191467769386d42b 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -323,7 +323,21 @@ rule pe_quantification_salmon:
             "samples",
             "{sample}",
             "{sample}.salmon.pe",
-            "quant.sf")
+            "quant.sf"),
+        meta_info = os.path.join(
+            config["output_dir"],
+            "samples",
+            "{sample}",
+            "{sample}.salmon.pe",
+            "aux_info",
+            "meta_info.json"),
+        flenDist = os.path.join(
+            config["output_dir"],
+            "samples",
+            "{sample}",
+            "{sample}.salmon.pe",
+            "libParams",
+            "flenDist.txt")
 
     shadow: "full"
 
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index a1c62e459c7b6c51f1fa323e0e29c3c60135e667..3bf1aaa20ae92840bdf5e2342e033f3141d0b97d 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -260,7 +260,21 @@ rule quantification_salmon:
             "samples",
             "{sample}",
             "{sample}.salmon.se",
-            "quant.sf")
+            "quant.sf"),
+        meta_info = os.path.join(
+            config["output_dir"],
+            "samples",
+            "{sample}",
+            "{sample}.salmon.se",
+            "aux_info",
+            "meta_info.json"),
+        flenDist = os.path.join(
+            config["output_dir"],
+            "samples",
+            "{sample}",
+            "{sample}.salmon.se",
+            "libParams",
+            "flenDist.txt")
 
     shadow: "full"