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Fix paths to Snakefile for slurm test scripts

Merged BIOPZ-Gypas Foivos requested to merge bug/snakemake-report-with-slurm-run into dev
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@@ -26,7 +26,7 @@ cd $script_dir
@@ -26,7 +26,7 @@ cd $script_dir
# Run tests
# Run tests
snakemake \
snakemake \
--snakefile="../../Snakefile" \
--snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--configfile="../input_files/config.yaml" \
--cluster-config="../input_files/cluster.json" \
--cluster-config="../input_files/cluster.json" \
--cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
--cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
@@ -41,7 +41,7 @@ snakemake \
@@ -41,7 +41,7 @@ snakemake \
# Create a Snakemake report after the workflow execution
# Create a Snakemake report after the workflow execution
snakemake \
snakemake \
--snakefile="../../Snakefile" \
--snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--configfile="../input_files/config.yaml" \
--report="snakemake_report.html"
--report="snakemake_report.html"
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