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Commit 4951350e authored by BIOPZ-Iborra de Toledo Paula's avatar BIOPZ-Iborra de Toledo Paula
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Updated test folder. Working local and slurm execution

parent 8dee761a
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1 merge request!1WIP: Updated workflow
......@@ -16,6 +16,4 @@
scripts_dir: "../scripts"
local_log: "logs/local"
cluster_log: "logs/cluster"
...
......@@ -7,4 +7,4 @@ results/homo_sapiens/GRCh38.98_chrY/exons.gtf
results/homo_sapiens/GRCh38.98_chrY/transcriptome.fa
results/homo_sapiens/GRCh38.98_chrY/exons.bed
results/homo_sapiens/GRCh38.98_chrY/headerOfCollapsedFasta.sam
results/homo_sapiens/GRCh38.98_chrY/genome_index_segemehl.idx
results/homo_sapiens/GRCh38.98_chrY/genome_index_segemehl.idx
\ No newline at end of file
......@@ -7,4 +7,4 @@ f37a213f94d11bf2260f50f2c9f199d2 results/homo_sapiens/GRCh38.98_chrY/genome.pro
5ab1c2f39ab35fabc6673c73beb3097b results/homo_sapiens/GRCh38.98_chrY/transcriptome.fa
51ac61c61825929f8f05c4b4f821f04d results/homo_sapiens/GRCh38.98_chrY/exons.bed
7027e0b45c8e46ef79f1cb234fa3b839 results/homo_sapiens/GRCh38.98_chrY/headerOfCollapsedFasta.sam
11b0b7c50160aa8837dd92eda516c124 results/homo_sapiens/GRCh38.98_chrY/genome_index_segemehl.idx
11b0b7c50160aa8837dd92eda516c124 results/homo_sapiens/GRCh38.98_chrY/genome_index_segemehl.idx
\ No newline at end of file
......@@ -18,7 +18,7 @@ user_dir=$PWD
script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
cd $script_dir
# Run tests
# Run tests
snakemake \
--snakefile="../snakemake/Snakefile" \
--configfile="config.yaml" \
......
......@@ -18,7 +18,7 @@ user_dir=$PWD
script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
cd $script_dir
# Run tests
# Run tests
snakemake \
--snakefile="../snakemake/Snakefile" \
--configfile="config.yaml" \
......
......@@ -40,5 +40,4 @@ md5sum --check "expected_output.md5"
# -name \*\.gz \
# -exec gunzip '{}' \;
# > expected_output.files
# md5sum $(cat expected_output.files) > expected_output.md5
# md5sum $(cat expected_output.files) > expected_output.md5
\ No newline at end of file
......@@ -55,5 +55,4 @@ md5sum --check "expected_output.md5"
# -name \*\.gz \
# -exec gunzip '{}' \;
# > expected_output.files
# md5sum $(cat expected_output.files) > expected_output.md5
# md5sum $(cat expected_output.files) > expected_output.md5
\ No newline at end of file
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