From 8b8e277473b0074aecaa2ee79f0dd9289d02162b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?BIOPZ-B=C3=B6rsch=20Anastasiya?=
<anastasiya.boersch@unibas.ch>
Date: Fri, 7 Feb 2020 11:48:51 +0100
Subject: [PATCH] Create two dictionary files for converting LabKey table to
Snakemake inputs
---
...{input_dict.tsv => input_dict_caption.tsv} | 2 +-
scripts/input_dict_field_key.tsv | 51 +++++++++++++++++++
.../test_scripts_labkey_to_snakemake/test.sh | 2 +-
3 files changed, 53 insertions(+), 2 deletions(-)
rename scripts/{input_dict.tsv => input_dict_caption.tsv} (97%)
create mode 100644 scripts/input_dict_field_key.tsv
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 a309c29..6f043f8 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 0000000..0a54bf6
--- /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 68d740d..c168305 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="."
--
GitLab