diff --git a/README.md b/README.md index 6c76bbc5b907fb7fc7b5a6a9703b3bb852c42592..c8dca57c41d6a461ce6617bd42ddca6604f5634e 100644 --- a/README.md +++ b/README.md @@ -257,7 +257,7 @@ help screen with option '--help' for further options and information): python scripts/prepare_inputs.py \ --labkey-domain="my.labkey.service.io" --labkey-domain="/my/project/path" - --input-to-output-mapping="scripts/prepare_inputs.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" \ diff --git a/scripts/prepare_inputs.labkey_to_snakemake.dict.tsv b/scripts/prepare_inputs.dict.tsv similarity index 100% rename from scripts/prepare_inputs.labkey_to_snakemake.dict.tsv rename to scripts/prepare_inputs.dict.tsv diff --git a/scripts/prepare_inputs.py b/scripts/prepare_inputs.py index 4ac90ab8d0d1aaa7abd67732b1fb4a6d2c9e7dec..1efc031f7767dafb393e8a549c3f6ce1fcd42443 100755 --- a/scripts/prepare_inputs.py +++ b/scripts/prepare_inputs.py @@ -61,7 +61,7 @@ def parse_cli_args() -> argparse.Namespace: type=argparse.FileType('r'), default=os.path.join( os.path.dirname(__file__), - 'prepare_inputs.labkey_to_snakemake.dict.tsv', + 'prepare_inputs.dict.tsv', ), help="lookup table with mappings from input (LabKey or LabKey-like) " "to output (Snakemake) table; default: '%(default)s'", diff --git a/tests/test_scripts_prepare_inputs_labkey/test.sh b/tests/test_scripts_prepare_inputs_labkey/test.sh index 45aea366c65749a6ba848bd7624e207f8cbaaedd..3f8b721e5632b38e8d131c64decf976fcdadc90c 100755 --- a/tests/test_scripts_prepare_inputs_labkey/test.sh +++ b/tests/test_scripts_prepare_inputs_labkey/test.sh @@ -33,7 +33,7 @@ EOF python "../../scripts/prepare_inputs.py" \ --labkey-domain="${LABKEY_HOST}" \ --labkey-path="/Zavolan Group/TEST_LABKEY" \ - --input-to-output-mapping="../../scripts/prepare_inputs.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" \ diff --git a/tests/test_scripts_prepare_inputs_table/test.sh b/tests/test_scripts_prepare_inputs_table/test.sh index e9bc935e677577b387ce80a40b73bc71aa3f47ce..ebd9391f2303cfe8e251c127d5748faa68ea7ba8 100755 --- a/tests/test_scripts_prepare_inputs_table/test.sh +++ b/tests/test_scripts_prepare_inputs_table/test.sh @@ -22,7 +22,7 @@ cd $script_dir/ # Run tests python "../../scripts/prepare_inputs.py" \ - --input-to-output-mapping="../../scripts/prepare_inputs.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" \