Merge branch 'fix_labkey_test' into 'dev'

fix(prepare_inputs): support relative paths

See merge request !68

.gitlab-ci.yml

@@ -12,8 +12,8 @@ test:
     # add code quality tests here
     # add unit tests here
     # add script tests here
-    # - bash tests/test_scripts_labkey_to_snakemake_table/test.sh
-    # - bash tests/test_scripts_labkey_to_snakemake_api/test.sh
+    - bash tests/test_scripts_prepare_inputs_table/test.sh
+    - bash tests/test_scripts_prepare_inputs_labkey/test.sh
     - bash tests/test_alfa/test.sh
     # add integration tests here
     - bash tests/test_create_dag_image/test.sh

README.md

@@ -254,10 +254,10 @@ replacing the placeholders with the appropriate values (check out the
 help screen with option '--help' for further options and information):
 
     ```bash
-    python scripts/labkey_to_snakemake.py \
+    python scripts/prepare_inputs.py \
         --labkey-domain="my.labkey.service.io"
         --labkey-domain="/my/project/path"
-        --input-to-output-mapping="scripts/labkey_to_snakemake.dict.tsv" \
+        --input-to-output-mapping="scripts/prepare_inputs.dict.tsv" \
         --resources-dir="/path/to/my/genome/resources" \
         --output-table="config/my_run/samples.tsv" \
         --config_file="config/my_run/config.yaml" \

tests/test_scripts_labkey_to_snakemake_table/expected_output.md5

-057cbd5757ca7f0b94909eeeca531af3  config.yaml
-34422785b7cc77d1aac73d25e767dc2d  samples.tsv

tests/test_scripts_labkey_to_snakemake_api/test.sh → tests/test_scripts_prepare_inputs_labkey/test.sh

@@ -30,10 +30,10 @@ password ${LABKEY_PASS}
 EOF
 
 # Run tests
-python "../../scripts/labkey_to_snakemake.py" \
+python "../../scripts/prepare_inputs.py" \
     --labkey-domain="${LABKEY_HOST}" \
     --labkey-path="/Zavolan Group/TEST_LABKEY" \
-    --input-to-output-mapping="../../scripts/labkey_to_snakemake.dict.tsv" \
+    --input-to-output-mapping="../../scripts/prepare_inputs.dict.tsv" \
     --resources-dir="../input_files" \
     --output-table="samples.tsv" \
     --config-file="config.yaml" \

tests/test_scripts_prepare_inputs_table/expected_output.md5

+40bd0f0fcecdd0d9bc932f63c2811478  config.yaml
+c8dcc5a203e9046806c4090525960151  samples.tsv

tests/test_scripts_labkey_to_snakemake_table/test.sh → tests/test_scripts_prepare_inputs_table/test.sh

@@ -21,13 +21,15 @@ script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
 cd $script_dir/
 
 # Run tests
-python "../../scripts/labkey_to_snakemake.py" \
-    --input-to-output-mapping="../../scripts/labkey_to_snakemake.dict.tsv" \
+python "../../scripts/prepare_inputs.py" \
+    --input-to-output-mapping="../../scripts/prepare_inputs.dict.tsv" \
     --resources-dir="../input_files" \
     --output-table="samples.tsv" \
     --config-file="config.yaml" \
     --multimappers='10' \
     --logo="../../images/logo.128px.png" \
+    --output-dir="" \
+    --no-process-paths \
     "input_table.tsv"