Create two dictionary files for converting LabKey table to Snakemake inputs

scripts/input_dict.tsv → scripts/input_dict_caption.tsv

@@ -48,4 +48,4 @@ Library preparation kit	library_kit
 Cycles	cycles
 Molecule	molecule
 Contaminant sequences	contaminant_seqs
-Name of BioAnalyzer file	bioanalyser_file
\ No newline at end of file
+Name of BioAnalyzer file	bioanalyser_file

scripts/input_dict_field_key.tsv

+labkey	snakemake
+Entry_Date	entry_date
+Path_Fastq_Files	fastq_path
+Condition_Name	condition
+Replicate_Name	replicate_name
+Single_Paired	seqmode
+Mate1_File	fq1
+Mate2_File	fq2
+Mate1_Direction	mate1_direction
+Mate2_Direction	mate2_direction
+Mate1_5p_Adapter	fq1_5p
+Mate1_3p_Adapter	fq1_3p
+Mate2_5p_Adapter	fq2_5p
+Mate2_3p_Adapter	fq2_3p
+Fragment_Length_Mean	mean
+Fragment_Length_SD	sd
+Quality_Control_Flag	quality_control_flag
+Checksum_Raw_FASTQ_Mate1	mate1_checksum
+Checksum_Raw_FASTQ_Mate2	mate2_checksum
+File_Name_Metadata_File	metadata
+Name_Quality_Control_File_Mate1	mate1_quality
+Name_Quality_Control_File_Mate2	mate2_quality
+Organism	organism
+TaxonID	taxon_id
+Strain_Isolate_Breed_Ecotype	strain_name
+Strain_Isolate_Breed_Ecotype_ID	strain_id
+Biomaterial_Provider	biomaterial_provider
+Source_Tissue_Name	source_name
+Tissue_Code	tissue_code
+Additional_Tissue_Description	tissue_description
+Genotype_Short_Name	genotype_name
+Genotype_Description	genotype_description
+Disease_Short_Name	disease_name
+Disease_Description	disease_description
+Treatment_Short_Name	treatment
+Treatment_Description	treatment_description
+Gender	gender
+Age	age
+Developmental_Stage	development_stage
+Passage_Number	passage_number
+Sample_Preparation_Date	sample_prep_date
+Prepared_By	prepared_by
+Documentation	documentation
+Protocol_File	protocol_file
+Sequencing_Date	seq_date
+Sequencing_Instrument	seq_instrument
+Library_preparation_kit	library_kit
+Cycles	cycles
+Molecule	molecule
+Contaminant_Sequences	contaminant_seqs
+BioAnalyzer_File	bioanalyser_file

tests/test_scripts_labkey_to_snakemake/test.sh

@@ -14,7 +14,7 @@ cd $script_dir
 # Run tests
 python "../../scripts/labkey_to_snakemake.py" \
     --input_table="input_table.tsv" \
-    --input_dict="../../scripts/input_dict.tsv" \
+    --input_dict="../../scripts/input_dict_caption.tsv" \
     --config_file="config.yaml" \
     --samples_table="samples.tsv" \
     --genomes_path="."