fix: make variable naming consistent with ISA standard

cubi_isa_templates/isatab-bulk_rnaseq/cookiecutter.json

@@ -1,6 +1,6 @@
 {
   "investigation_title": "Investigation Title",
-  "sample_names": "sample1,sample2",
+  "source_names": "sample1,sample2",
   "a_measurement_type": [
       "transcription profiling"
   ],

cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt

@@ -1,5 +1,5 @@
 Sample Name	Protocol REF	Parameter Value[Concentration]	Performer	Date	Protocol REF	Parameter Value[Library source]	Parameter Value[Library strategy]	Parameter Value[Library selection]	Parameter Value[Library layout]	Parameter Value[Library kit]	Parameter Value[Target insert size]	Parameter Value[Wet-lab insert size]	Parameter Value[Barcode kit]	Parameter Value[Barcode name]	Performer	Date	Protocol REF	Parameter Value[Platform]	Parameter Value[Instrument model]	Parameter Value[Base quality encoding]	Parameter Value[Library prefix]	Performer	Date	Extract Name
-{% set sample_names = cookiecutter.sample_names.split(",") -%}
-{% for sample_name in sample_names -%}
-{{sample_name|replace("-", "_")}}	RNA extraction				Library construction												Nucleic acid sequencing				{{sample_name}}			{{sample_name}}
+{% set source_names = cookiecutter.source_names.split(",") -%}
+{% for source_name in source_names -%}
+{{source_name|replace("-", "_")}}	RNA extraction				Library construction												Nucleic acid sequencing				{{source_name}}			{{source_name}}
 {% endfor -%}

cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt

@@ -1,5 +1,5 @@
 Source Name	Characteristics[Organism]	Term Source REF	Term Accession Number	Characteristics[Source type]	Characteristics[external reference]	Characteristics[Group]	Protocol REF	Parameter Value[Method]	Performer	Date	Sample Name	Characteristics[Origin]	Characteristics[Condition]	Characteristics[Treatment]
-{% set sample_names = cookiecutter.sample_names.split(",") -%}
-{% for sample_name in sample_names -%}
-{{sample_name|replace("-", "_")}}	Homo sapiens	NCBITAXON	http://purl.bioontology.org/ontology/NCBITAXON/9606				Sample collection				{{sample_name|replace("-", "_")}}			
+{% set source_names = cookiecutter.source_names.split(",") -%}
+{% for source_name in source_names -%}
+{{source_name|replace("-", "_")}}	Homo sapiens	NCBITAXON	http://purl.bioontology.org/ontology/NCBITAXON/9606				Sample collection				{{source_name|replace("-", "_")}}			
 {% endfor -%}

cubi_isa_templates/isatab-generic/cookiecutter.json

@@ -1,6 +1,6 @@
 {
   "investigation_title": "Investigation Title",
-  "sample_names": "alpha,beta,gamma",
+  "source_names": "alpha,beta,gamma",
   "a_measurement_type": [
       "transcription profiling"
   ],
@@ -50,7 +50,7 @@
   "assay_prefix": "{{cookiecutter.s_file_name|lower}}",
   "a_measurement_abbreviation": "{% if cookiecutter.a_measurement_type == 'transcription profiling' %}mRNA_seq{% else %}UNKNOWN{% endif %}",
   "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}",
-  "sample_type": "x-charite-medgen-blood-book-id",
+  "source_type": "x-charite-medgen-blood-book-id",
   "lib_strategy": "{% if cookiecutter.a_measurement_abbreviation == 'mRNA_seq' %}RNA-seq{% else %}UNKNOWN{% endif %}",
   "lib_selection": "{% if cookiecutter.a_measurement_abbreviation == 'mRNA_seq' %}PolyA{% else %}UNKNOWN{% endif %}",
   "lib_layout": [ "PAIRED", "SINGLE" ],

cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt

@@ -1,5 +1,5 @@
 Sample Name	Protocol REF	Parameter Value[Concentration measurement]	Performer	Date	Extract Name	Characteristics[Concentration]	Unit	Term Source REF	Term Accession Number	Protocol REF	Parameter Value[Provider name]	Parameter Value[Provider contact]	Parameter Value[Provider project ID]	Parameter Value[Provider sample ID]	Parameter Value[Provider QC status]	Parameter Value[Requestor contact]	Parameter Value[Requestor project]	Parameter Value[Requestor sample ID]	Parameter Value[Concentration measurement]	Parameter Value[Library source]	Parameter Value[Library strategy]	Parameter Value[Library selection]	Parameter Value[Library layout]	Parameter Value[Library kit]	Parameter Value[Target insert size]	Parameter Value[Wet-lab insert size]	Parameter Value[Barcode kit]	Parameter Value[Barcode kit catalogue ID]	Parameter Value[Barcode name]	Parameter Value[Barcode sequence]	Performer	Date	Extract Name	Characteristics[Folder name]	Characteristics[Concentration]	Unit	Term Source REF	Term Accession Number	Protocol REF	Parameter Value[Platform]	Parameter Value[Instrument model]	Parameter Value[Base quality encoding]	Parameter Value[Center name]	Parameter Value[Center contact]	Performer	Date	Raw Data File	Extract Name
-{% set sample_names = cookiecutter.sample_names.split(",") -%}
-{%- for sample_name in sample_names -%}
-{{sample_name|replace("-", "_")}}-N1	Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}}				{{sample_name|replace("-", "_")}}-N1-RNA1					Library construction {{cookiecutter.a_measurement_abbreviation}}										TRANSCRIPTOMIC	{{cookiecutter.lib_strategy}}	{{cookiecutter.lib_selection}}	{{cookiecutter.lib_layout}}	{{cookiecutter.lib_kits[cookiecutter.lib_kit].name}}									{{sample_name|replace("-", "_")}}-N1-RNA1-{{cookiecutter.a_measurement_abbreviation}}1	{{sample_name}}					Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}}	ILLUMINA	{{cookiecutter.instrument}}	Phred+33						{{sample_name|replace("-", "_")}}
+{% set source_names = cookiecutter.source_names.split(",") -%}
+{%- for source_name in source_names -%}
+{{source_name|replace("-", "_")}}-N1	Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}}				{{source_name|replace("-", "_")}}-N1-RNA1					Library construction {{cookiecutter.a_measurement_abbreviation}}										TRANSCRIPTOMIC	{{cookiecutter.lib_strategy}}	{{cookiecutter.lib_selection}}	{{cookiecutter.lib_layout}}	{{cookiecutter.lib_kits[cookiecutter.lib_kit].name}}									{{source_name|replace("-", "_")}}-N1-RNA1-{{cookiecutter.a_measurement_abbreviation}}1	{{source_name}}					Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}}	ILLUMINA	{{cookiecutter.instrument}}	Phred+33						{{source_name|replace("-", "_")}}
 {% endfor %}

cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt

@@ -1,5 +1,5 @@
 Source Name	Characteristics[UUID]	Characteristics[External links]	Characteristics[Batch]	Characteristics[Organism]	Term Source REF	Term Accession Number	Characteristics[Sex]	Characteristics[Disease status]	Characteristics[OMIM disease]	Term Source REF	Term Accession Number	Characteristics[Orphanet disease]	Term Source REF	Term Accession Number	Characteristics[HPO terms]	Term Source REF	Term Accession Number	Comment[Disease notes]	Protocol REF	Performer	Sample Name	Characteristics[External links]	Characteristics[Cell origin]	Term Source REF	Term Accession Number	Characteristics[Cell type]	Term Source REF	Term Accession Number
-{% set sample_names = cookiecutter.sample_names.split(",") -%}
-{%- for sample_name in sample_names -%}
-{{sample_name|replace("-", "_")}}		{{cookiecutter.sample_type}}:{{sample_name}}	{{cookiecutter.batch}}	{{cookiecutter.organisms[cookiecutter.organism].name}}	NCBITAXON	http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter.organisms[cookiecutter.organism].taxon}}	UNKNOWN	UNKNOWN											Sample collection		{{sample_name|replace("-", "_")}}-N1							
+{% set source_names = cookiecutter.source_names.split(",") -%}
+{%- for source_name in source_names -%}
+{{source_name|replace("-", "_")}}		{{cookiecutter.source_type}}:{{source_name}}	{{cookiecutter.batch}}	{{cookiecutter.organisms[cookiecutter.organism].name}}	NCBITAXON	http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter.organisms[cookiecutter.organism].taxon}}	UNKNOWN	UNKNOWN											Sample collection		{{source_name|replace("-", "_")}}-N1							
 {% endfor %}

cubi_isa_templates/isatab-germline/cookiecutter.json

@@ -1,6 +1,6 @@
 {
   "investigation_title": "Investigation Title",
-  "sample_names": "index,mother,father",
+  "source_names": "index,mother,father",
   "a_measurement_type": [
       "exome sequencing",
       "genome sequencing",
@@ -66,7 +66,7 @@
   "a_technology_type": "nucleotide sequencing",
   "a_measurement_abbreviation": "{% if cookiecutter.a_measurement_type == 'exome sequencing' %}WES{% else %}WGS{% endif %}",
   "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}",
-  "sample_type": "x-charite-medgen-blood-book-id",
+  "source_type": "x-charite-medgen-blood-book-id",
   "lib_strategy": "{% if cookiecutter.a_measurement_abbreviation == 'WES' %}WXS{% else %}WGS{% endif %}",
   "lib_selection": "{% if cookiecutter.a_measurement_abbreviation == 'WES' %}Hybrid Selection{% else %}RANDOM{% endif %}",
   "lib_layout": "PAIRED",

cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt

@@ -1,5 +1,5 @@
 Sample Name	Protocol REF	Parameter Value[Concentration measurement]	Performer	Date	Extract Name	Characteristics[Concentration]	Unit	Term Source REF	Term Accession Number	Protocol REF	Parameter Value[Provider name]	Parameter Value[Provider contact]	Parameter Value[Provider project ID]	Parameter Value[Provider sample ID]	Parameter Value[Provider QC status]	Parameter Value[Requestor contact]	Parameter Value[Requestor project]	Parameter Value[Requestor sample ID]	Parameter Value[Concentration measurement]	Parameter Value[Library source]	Parameter Value[Library strategy]	Parameter Value[Library selection]	Parameter Value[Library layout]	Parameter Value[Library kit]	Comment[Library kit catalogue ID]	Parameter Value[Target insert size]	Parameter Value[Wet-lab insert size]	Parameter Value[Barcode kit]	Parameter Value[Barcode kit catalogue ID]	Parameter Value[Barcode name]	Parameter Value[Barcode sequence]	Performer	Date	Extract Name	Characteristics[Folder name]	Characteristics[Concentration]	Unit	Term Source REF	Term Accession Number	Protocol REF	Parameter Value[Platform]	Parameter Value[Instrument model]	Parameter Value[Base quality encoding]	Parameter Value[Center name]	Parameter Value[Center contact]	Performer	Date	Raw Data File
-{% set sample_names = cookiecutter.sample_names.split(",") -%}
-{%- for sample_name in sample_names -%}
-{{sample_name|replace("-", "_")}}-N1	Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}}				{{sample_name|replace("-", "_")}}-N1-DNA1					Library construction {{cookiecutter.a_measurement_abbreviation}}										GENOMIC	{{cookiecutter.lib_strategy}}	{{cookiecutter.lib_selection}}	{{cookiecutter.lib_layout}}	{{cookiecutter.lib_kits[cookiecutter.lib_kit].name}}	{{cookiecutter.lib_kits[cookiecutter.lib_kit].cat_id}}									{{sample_name|replace("-", "_")}}-N1-DNA1-{{cookiecutter.a_measurement_abbreviation}}1	{{sample_name}}					Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}}	ILLUMINA	{{cookiecutter.instrument}}	Phred+33					
+{% set source_names = cookiecutter.source_names.split(",") -%}
+{%- for source_name in source_names -%}
+{{source_name|replace("-", "_")}}-N1	Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}}				{{source_name|replace("-", "_")}}-N1-DNA1					Library construction {{cookiecutter.a_measurement_abbreviation}}										GENOMIC	{{cookiecutter.lib_strategy}}	{{cookiecutter.lib_selection}}	{{cookiecutter.lib_layout}}	{{cookiecutter.lib_kits[cookiecutter.lib_kit].name}}	{{cookiecutter.lib_kits[cookiecutter.lib_kit].cat_id}}									{{source_name|replace("-", "_")}}-N1-DNA1-{{cookiecutter.a_measurement_abbreviation}}1	{{source_name}}					Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}}	ILLUMINA	{{cookiecutter.instrument}}	Phred+33					
 {% endfor %}

cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt

@@ -1,5 +1,5 @@
 Source Name	Characteristics[UUID]	Characteristics[External links]	Characteristics[Batch]	Characteristics[Family]	Characteristics[Organism]	Term Source REF	Term Accession Number	Characteristics[Mother]	Characteristics[Father]	Comment[Family notes]	Characteristics[Sex]	Characteristics[Disease status]	Characteristics[OMIM disease]	Term Source REF	Term Accession Number	Characteristics[Orphanet disease]	Term Source REF	Term Accession Number	Characteristics[HPO terms]	Term Source REF	Term Accession Number	Comment[Disease notes]	Protocol REF	Performer	Sample Name	Characteristics[External links]	Characteristics[Cell origin]	Term Source REF	Term Accession Number	Characteristics[Cell type]	Term Source REF	Term Accession Number
-{% set sample_names = cookiecutter.sample_names.split(",") -%}
-{%- for sample_name in sample_names -%}
-{{sample_name|replace("-", "_")}}		{{cookiecutter.sample_type}}:{{sample_name}}	{{cookiecutter.batch}}	FAM_{{sample_name|replace("-", "_")}}	Homo sapiens	NCBITAXON	http://purl.bioontology.org/ontology/NCBITAXON/9606	0	0		UNKNOWN	UNKNOWN											Sample collection		{{sample_name|replace("-", "_")}}-N1							
+{% set source_names = cookiecutter.source_names.split(",") -%}
+{%- for source_name in source_names -%}
+{{source_name|replace("-", "_")}}		{{cookiecutter.source_type}}:{{source_name}}	{{cookiecutter.batch}}	FAM_{{source_name|replace("-", "_")}}	Homo sapiens	NCBITAXON	http://purl.bioontology.org/ontology/NCBITAXON/9606	0	0		UNKNOWN	UNKNOWN											Sample collection		{{source_name|replace("-", "_")}}-N1							
 {% endfor %}

cubi_isa_templates/isatab-microarray/cookiecutter.json

@@ -1,6 +1,6 @@
 {
   "investigation_title": "Investigation Title",
-  "sample_names": "alpha,beta,gamma",
+  "source_names": "alpha,beta,gamma",
   "a_measurement_type": [
       "transcription profiling"
   ],

cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt

@@ -1,5 +1,5 @@
 Sample Name	Protocol REF	Performer	Date	Extract Name	Protocol REF	Performer	Date	Labeled Extract Name	Label	Protocol REF	Performer	Date	Hybridization Assay Name	Array Design REF	Protocol REF	Performer	Date	Scan Name	Image File	Array Data File	Array Data Matrix File	Protocol REF	Performer	Date	Normalization Name	Derived Array Data File	Protocol REF	Performer	Date	Data Transformation Name	Derived Array Data Matrix File
-{% set sample_names = cookiecutter.sample_names.split(",") -%}																															
-{%- for sample_name in sample_names -%}																															
-{{sample_name|replace("-", "_")}}-S1	Nucleic acid extraction			{{sample_name|replace("-", "_")}}-S1-E1	Labeling					Nucleic acid hybridization			{{sample_name|replace("-", "_")}}-S1-E1-H1	{{cookiecutter.array_design_ref}}	Data collection			{{sample_name|replace("-", "_")}}-S1-E1-H1				Normalization data transformation					Data transformation				
+{% set source_names = cookiecutter.source_names.split(",") -%}																															
+{%- for source_name in source_names -%}																															
+{{source_name|replace("-", "_")}}-S1	Nucleic acid extraction			{{source_name|replace("-", "_")}}-S1-E1	Labeling					Nucleic acid hybridization			{{source_name|replace("-", "_")}}-S1-E1-H1	{{cookiecutter.array_design_ref}}	Data collection			{{source_name|replace("-", "_")}}-S1-E1-H1				Normalization data transformation					Data transformation				
 {% endfor %}

cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt

@@ -1,5 +1,5 @@
 Source Name	Characteristics[Organism]	Term Source REF	Term Accession Number	Protocol REF	Performer	Date	Sample Name	Factor Value[time of differentiation]	Unit	Term Source REF	Term Accession Number
-{% set sample_names = cookiecutter.sample_names.split(",") -%}											
-{%- for sample_name in sample_names -%}											
-{{sample_name|replace("-", "_")}}	{{cookiecutter.organisms[cookiecutter.organism].name}}	NCBITAXON	http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter.organisms[cookiecutter.organism].taxon}}	Sample collection			{{sample_name|replace("-", "_")}}-S1		day	OBI	http://purl.obolibrary.org/obo/UO_0000033
+{% set source_names = cookiecutter.source_names.split(",") -%}											
+{%- for source_name in source_names -%}											
+{{source_name|replace("-", "_")}}	{{cookiecutter.organisms[cookiecutter.organism].name}}	NCBITAXON	http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter.organisms[cookiecutter.organism].taxon}}	Sample collection			{{source_name|replace("-", "_")}}-S1		day	OBI	http://purl.obolibrary.org/obo/UO_0000033
 {% endfor %}

cubi_isa_templates/isatab-ms_meta_biocrates/cookiecutter.json

@@ -5,7 +5,7 @@
   "study_id": "{{cookiecutter.study_title|lower|replace(' ', '_')}}",
   "study_file_name": "{{cookiecutter.study_id}}",
 
-  "sample_names": "alpha,beta,gamma",
+  "source_names": "alpha,beta,gamma",
 
   "organism": [
     "Homo sapiens",

cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt

@@ -1,6 +1,6 @@
 Sample Name	Protocol REF	Parameter Value[Post extraction]	Parameter Value[Derivatization]	Parameter Value[Phase]	Performer	Date	Extract Name	Characteristics[Concentration]	Unit	Term Source REF	Term Accession Number	Protocol REF	Performer	Date	Protocol REF	Parameter Value[Scan polarity]	Parameter Value[Scan m/z range]	Parameter Value[Instrument]	Term Source REF	Term Accession Number	Parameter Value[Ion source]	Term Source REF	Term Accession Number	Parameter Value[Mass analyzer]	Term Source REF	Term Accession Number	Parameter Value[Detector]	Term Source REF	Term Accession Number	Parameter Value[Aquisition mode]	Term Source REF	Term Accession Number	Parameter Value[Aquisition software name]	Parameter Value[Aquisition software version]	Parameter Value[Aquisition parameter]	Performer	Date	MS Assay Name	Raw Spectral Data File	Comment[Batch]	Comment[Well position]	Comment[Sample type]	Protocol REF	Parameter Value[Analysis software name]	Parameter Value[Analysis software version]	Metabolite Assignment File	Protocol REF	Parameter Value[Software name]	Parameter Value[Software version]	Parameter Value[Report file]	Performer	Date
-{% set sample_names = cookiecutter.sample_names.split(",") -%}																																																				
-{%- for sample_name in sample_names -%}																																																				
-{{sample_name|replace("-", "_")}}-N1	Extraction {{cookiecutter.assay_measurement_abbreviation_LC}}						{{sample_name|replace("-", "_")}}-N1-Meta1					Flow Injection Analysis {{cookiecutter.assay_measurement_abbreviation_FIA}}			Mass spectrometry {{cookiecutter.assay_measurement_abbreviation_FIA}}			{{cookiecutter.instruments[cookiecutter.instrument].term}}	{{cookiecutter.instruments[cookiecutter.instrument].source}}	{{cookiecutter.instruments[cookiecutter.instrument].accession}}																		{{sample_name|replace("-", "_")}}-N1-Meta1-{{cookiecutter.assay_measurement_abbreviation_FIA}}1					Data transformation {{cookiecutter.assay_measurement_abbreviation_FIA}}	Biocrates MetIDQ	{{cookiecutter.biocrates_metidq_version}}		Quality Control {{cookiecutter.assay_measurement_abbreviation_FIA}}	MeTaQuaC	{{cookiecutter.metaquac_version}}			
+{% set source_names = cookiecutter.source_names.split(",") -%}																																																				
+{%- for source_name in source_names -%}																																																				
+{{source_name|replace("-", "_")}}-N1	Extraction {{cookiecutter.assay_measurement_abbreviation_LC}}						{{source_name|replace("-", "_")}}-N1-Meta1					Flow Injection Analysis {{cookiecutter.assay_measurement_abbreviation_FIA}}			Mass spectrometry {{cookiecutter.assay_measurement_abbreviation_FIA}}			{{cookiecutter.instruments[cookiecutter.instrument].term}}	{{cookiecutter.instruments[cookiecutter.instrument].source}}	{{cookiecutter.instruments[cookiecutter.instrument].accession}}																		{{source_name|replace("-", "_")}}-N1-Meta1-{{cookiecutter.assay_measurement_abbreviation_FIA}}1					Data transformation {{cookiecutter.assay_measurement_abbreviation_FIA}}	Biocrates MetIDQ	{{cookiecutter.biocrates_metidq_version}}		Quality Control {{cookiecutter.assay_measurement_abbreviation_FIA}}	MeTaQuaC	{{cookiecutter.metaquac_version}}			
 {% endfor %}