diff --git a/scripts/input_dict.tsv b/scripts/input_dict_caption.tsv similarity index 97% rename from scripts/input_dict.tsv rename to scripts/input_dict_caption.tsv index a309c29bbdc8dc59f21ebd3314b6d78b009fa7b5..6f043f835084ef9286e1584994f06a40e0011214 100644 --- a/scripts/input_dict.tsv +++ b/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 diff --git a/scripts/input_dict_field_key.tsv b/scripts/input_dict_field_key.tsv new file mode 100644 index 0000000000000000000000000000000000000000..0a54bf629b963f485871fb3fea39cd7e4ae184d0 --- /dev/null +++ b/scripts/input_dict_field_key.tsv @@ -0,0 +1,51 @@ +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 diff --git a/tests/test_scripts_labkey_to_snakemake/test.sh b/tests/test_scripts_labkey_to_snakemake/test.sh index 68d740d6993586142ec3d25e68e2be5245e89029..c168305bebc4ca9eb08697daef89ab0be94b658b 100755 --- a/tests/test_scripts_labkey_to_snakemake/test.sh +++ b/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="."