From e791ce60e4268a60f212aad423734031aa9e44f9 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Fri, 23 Oct 2020 14:19:52 +0200
Subject: [PATCH] add --no-hooks for CI tests, mark output files of salmon for
multiqc, adjust files for md5 check.
---
tests/test_alfa/test.sh | 1 +
tests/test_create_dag_image/test.sh | 1 +
tests/test_create_rule_graph/test.sh | 1 +
.../expected_output.md5 | 18 ------------------
tests/test_integration_workflow/test.local.sh | 4 +---
tests/test_integration_workflow/test.slurm.sh | 1 +
.../expected_output.md5 | 18 ------------------
.../test.local.sh | 1 +
.../test.slurm.sh | 1 +
workflow/rules/paired_end.snakefile.smk | 16 +++++++++++++++-
workflow/rules/single_end.snakefile.smk | 16 +++++++++++++++-
11 files changed, 37 insertions(+), 41 deletions(-)
diff --git a/tests/test_alfa/test.sh b/tests/test_alfa/test.sh
index 5e417f4..5389734 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 c5fc8dd..1c954dd 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 2fa3db7..287e08d 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 9242955..9bfdb92 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 00f6d96..d1a87ae 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 02aaf72..c6c8410 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 7a6ae82..c52d4c0 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 9804f33..fd45fa4 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 a0517fd..74ba028 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 a756856..9337ad0 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 a1c62e4..3bf1aaa 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"
--
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