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* New ISA template for StemCellCore * Fix indentation * Added 'Expansion ID' to default meta_source variables * Further improvements to default values * Better study & assay default names * Added extra template for stem cell core bulk * Incorporate CellPLex changes from isa-singelcell branch. * Split stem cell core template into bulk and single cell. Merged/cherry-picked changes from isa-singlecell branch (for both single cell & stem cell sc templates) * Updated stem cell core templates: added Cell culture step & better selection & definition of default columns. Renamed Sequencing run to Sequencing batch for single cell templates * Changed default configuration set in investigation to bih_cancer to enable IGV buttons * fix flake8
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22 changes: 14 additions & 8 deletions
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...cookiecutter.i_dir_name}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt
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{% set sample_names = cookiecutter.sample_names.split(",") -%} | ||
{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%} | ||
{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} | ||
{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} | ||
Sample Name Protocol REF Parameter Value[Dissociation method] Parameter Value[Cell count]{%+ for meta in dissociation_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Protocol REF Parameter Value[Library kit] Parameter Value[Library type] Parameter Value[Multiplex genotype] Parameter Value[Multiplex sample] Parameter Value[Multiplex oligo]{%+ for meta in library_construction_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Extract Name Protocol REF Parameter Value[Sequencing run] Parameter Value[Library prefix] Parameter Value[Barcode kit] Parameter Value[Barcode name]{%+ for meta in sequencing_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Library Name | ||
{% for sample_name in sample_names -%} | ||
{{sample_name|replace("-", "_")}} Dissociation {%+ for meta in dissociation_meta %} {% endfor %} Library construction {{cookiecutter.lib_kit}} Gene Expression {%+ for meta in library_construction_meta %} {% endfor %} {{sample_name}}_GEX Nucleic acid sequencing {{sample_name}}_GEX {%+ for meta in sequencing_meta %} {% endfor %} {{sample_name}} | ||
{% endfor -%} | ||
{% set sample_names = cookiecutter.sample_names.split(",") -%} | ||
{% set features = cookiecutter.library_type.split("+") -%} | ||
{% if cookiecutter.sample_multiplexing == "CellPlex" -%}{{ features.append("CellPlex") or "" }}{% endif -%} | ||
{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%} | ||
{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} | ||
{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} | ||
Sample Name Protocol REF Parameter Value[Dissociation method] Parameter Value[Cell count]{%+ for meta in dissociation_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Protocol REF Parameter Value[Library kit] Parameter Value[Library type] Parameter Value[Multiplex genotype] Parameter Value[Multiplex sample] Parameter Value[Multiplex oligo]{%+ for meta in library_construction_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Extract Name Protocol REF Parameter Value[Sequencing batch] Parameter Value[Fastq prefix] Parameter Value[Barcode kit] Parameter Value[Barcode name]{%+ for meta in sequencing_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Library Name | ||
{% for sample_name in sample_names -%} | ||
{% for f_name in features -%} | ||
{% set feature = cookiecutter._library_types[f_name].full -%} | ||
{% set abr = cookiecutter._library_types[f_name].short -%} | ||
{{sample_name|replace("-", "_")}} Dissociation {%+ for meta in dissociation_meta %} {% endfor %} Library construction {{cookiecutter.lib_kit}} {{feature}} {{cookiecutter.genotype_multiplexing == 'yes'}} {{cookiecutter.sample_multiplexing}} {%+ for meta in library_construction_meta %} {% endfor %} {{sample_name}}_{{abr}} Nucleic acid sequencing {{sample_name}}_{{abr}} {%+ for meta in sequencing_meta %} {% endfor %} {{sample_name}} | ||
{% endfor -%} | ||
{% endfor -%} |
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cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/cookiecutter.json
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{ | ||
"group": "CoreRnD", | ||
"study_title": "Study Title", | ||
"sample_numbers": "0001,0002", | ||
"investigation_title": "{{cookiecutter.group}} - {{cookiecutter.study_title}}", | ||
"source_type": ["hiPSC", "tissue"], | ||
"cellline": "", | ||
"cellculture_meta": "Expansion ID,Media,Matrix", | ||
"model_type": ["2D", "3D"], | ||
"sample_meta": "Experiment Name,Experiment Identifier,Tissue type,Differentiation duration,Condition,Treatment,Treatment duration", | ||
"a_measurement_type": "transcription profiling", | ||
"a_technology_type": "nucleotide sequencing", | ||
"library_kit": "mRNA", | ||
"library_construction_meta": "Library selection,Target insert size", | ||
"sequencing_meta": "Platform,Instrument model,No. targeted reads,Paired-End", | ||
"i_dir_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", | ||
"s_file_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", | ||
"assay_prefix": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", | ||
"assay_name": "GEX_{{cookiecutter.a_measurement_type|replace(' ', '_')}}" | ||
} |
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...cookiecutter.i_dir_name}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt
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{% set sample_numbers = cookiecutter.sample_numbers.split(",") -%} | ||
{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} | ||
{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} | ||
Sample Name Protocol REF Parameter Value[Passed] Protocol REF Parameter Value[Extraction kit] Parameter Value[RNA amount (ng)] Parameter Value[Tapestation QC RIN] Performer Date Extract Name Protocol REF Parameter Value[Library kit] Parameter Value[Library type]{%+ for meta in library_construction_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Protocol REF Parameter Value[Sequencing run] Parameter Value[Barcode kit] Parameter Value[Barcode name]{%+ for meta in sequencing_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Library Name | ||
{% for sample_no in sample_numbers -%} | ||
GEX-BLK_{{sample_no}} OverallQC RNA extraction GEX-BLK_{{sample_no}} Library construction {{cookiecutter.library_kit}} Gene expression {%+ for meta in library_construction_meta %} {% endfor %} Nucleic acid sequencing {%+ for meta in sequencing_meta %} {% endfor %} GEX-BLK_{{sample_no}} | ||
{% endfor -%} |
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cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.i_dir_name}}/i_Investigation.txt
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ONTOLOGY SOURCE REFERENCE | ||
Term Source Name UO OBI NCBITAXON OMIM HP ORPHA | ||
Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO | ||
Term Source Version 48 35 10 12 570 2.8 | ||
Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology | ||
INVESTIGATION | ||
Investigation Identifier "" | ||
Investigation Title {{cookiecutter.investigation_title}} | ||
Investigation Description "" | ||
Investigation Submission Date "" | ||
Investigation Public Release Date "" | ||
Comment[Created With Configuration] bih_cancer | ||
Comment[Last Opened With Configuration] bih_cancer | ||
INVESTIGATION PUBLICATIONS | ||
Investigation PubMed ID | ||
Investigation Publication DOI | ||
Investigation Publication Author List | ||
Investigation Publication Title | ||
Investigation Publication Status | ||
Investigation Publication Status Term Accession Number | ||
Investigation Publication Status Term Source REF | ||
INVESTIGATION CONTACTS | ||
Investigation Person Last Name | ||
Investigation Person First Name | ||
Investigation Person Mid Initials | ||
Investigation Person Email | ||
Investigation Person Phone | ||
Investigation Person Fax | ||
Investigation Person Address | ||
Investigation Person Affiliation | ||
Investigation Person Roles | ||
Investigation Person Roles Term Accession Number | ||
Investigation Person Roles Term Source REF | ||
STUDY | ||
Study Identifier {{cookiecutter.i_dir_name}} | ||
Study Title {{cookiecutter.investigation_title}} | ||
Study Description "" | ||
Comment[Study Grant Number] "" | ||
Comment[Study Funding Agency] "" | ||
Study Submission Date "" | ||
Study Public Release Date "" | ||
Study File Name s_{{cookiecutter.s_file_name}}.txt | ||
STUDY DESIGN DESCRIPTORS | ||
Study Design Type | ||
Study Design Type Term Accession Number | ||
Study Design Type Term Source REF | ||
STUDY PUBLICATIONS | ||
Study PubMed ID | ||
Study Publication DOI | ||
Study Publication Author List | ||
Study Publication Title | ||
Study Publication Status | ||
Study Publication Status Term Accession Number | ||
Study Publication Status Term Source REF | ||
STUDY FACTORS | ||
Study Factor Name | ||
Study Factor Type | ||
Study Factor Type Term Accession Number | ||
Study Factor Type Term Source REF | ||
STUDY ASSAYS | ||
Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt | ||
Study Assay Measurement Type {{cookiecutter.a_measurement_type}} | ||
Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000424 | ||
Study Assay Measurement Type Term Source REF OBI | ||
Study Assay Technology Type {{cookiecutter.a_technology_type}} | ||
Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 | ||
Study Assay Technology Type Term Source REF OBI | ||
Study Assay Technology Platform Illumina | ||
STUDY PROTOCOLS | ||
{% set cellculture_meta = cookiecutter.cellculture_meta.split(",") -%} | ||
{% set sample_meta = cookiecutter.sample_meta.split(",") -%} | ||
{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} | ||
{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} | ||
Study Protocol Name OverallQC Cell culture Differentiation Sample collection RNA extraction Library construction Nucleic acid sequencing | ||
Study Protocol Type OverallQC Cell culture Differentiation Sample collection RNA extraction Library construction Nucleic acid sequencing | ||
Study Protocol Type Term Accession Number "" "" "" "" "" "" "" | ||
Study Protocol Type Term Source REF "" "" "" "" "" "" "" | ||
Study Protocol Description "" "" "" "" "" "" "" | ||
Study Protocol URI "" "" "" "" "" "" "" | ||
Study Protocol Version "" "" "" "" "" "" "" | ||
Study Protocol Parameters Name Passed Passage{% for meta in cellculture_meta %};{{meta}}{% endfor %} Protocol numbers;Culture type;Differentiation dates;No. of passages;Well format;Day SampleType;Collection reagent Extraction kit;RNA amount (ng);Tapestation QC RIN Library kit;Library type{% for meta in library_construction_meta -%};{{meta}}{% endfor %} Sequencing run;Barcode kit;Barcode name{% for meta in sequencing_meta -%};{{meta}}{% endfor %} | ||
Study Protocol Parameters Name Term Accession Number "" "{% for meta in cellculture_meta %};{% endfor %}" ";;;;;" ";" ";;" ";{% for meta in library_construction_meta -%};{% endfor %}" ";;{% for meta in sequencing_meta -%};{% endfor %}" | ||
Study Protocol Parameters Name Term Source REF "" "{% for meta in cellculture_meta %};{% endfor %}" ";;;;;" ";" ";;" ";{% for meta in library_construction_meta -%};{% endfor %}" ";;{% for meta in sequencing_meta -%};{% endfor %}" | ||
Study Protocol Components Name "" "" "" "" "" "" "" | ||
Study Protocol Components Type "" "" "" "" "" "" "" | ||
Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" | ||
Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" | ||
STUDY CONTACTS | ||
Study Person Last Name | ||
Study Person First Name | ||
Study Person Mid Initials | ||
Study Person Email | ||
Study Person Phone | ||
Study Person Fax | ||
Study Person Address | ||
Study Person Affiliation | ||
Study Person Roles | ||
Study Person Roles Term Accession Number | ||
Study Person Roles Term Source REF |
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...isatab-stem_cell_core_bulk/{{cookiecutter.i_dir_name}}/s_{{cookiecutter.s_file_name}}.txt
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{% set sample_numbers = cookiecutter.sample_numbers.split(",") -%} | ||
{% set cellculture_meta = cookiecutter.cellculture_meta.split(",") -%} | ||
{% set sample_meta = cookiecutter.sample_meta.split(",") -%} | ||
Source Name Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Source Type] Characteristics[Cellline] Characteristics[Genetic modfications] Protocol REF Parameter Value[Passage]{%+ for meta in cellculture_meta %} Parameter Value[{{meta}}]{% endfor %} Protocol REF Parameter Value[Protocol numbers] Parameter Value[Culture type] Parameter Value[Differentiation dates] Parameter Value[No. of passages] Parameter Value[Well format] Parameter Value[Day] Performer Protocol REF Parameter Value[SampleType] Parameter Value[Collection reagent] Performer Date Sample Name{%+ for meta in sample_meta %} Characteristics[{{meta}}]{% endfor %} | ||
{% for sample_no in sample_numbers -%} | ||
{{cookiecutter.cellline}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 {{cookiecutter.source_type}} {{cookiecutter.cellline}} Cell culture {%+ for meta in cellculture_meta %} {% endfor %} Differentiation {{cookiecutter.model_type}} Sample collection GEX-BLK_{{sample_no}}{%+ for meta in sample_meta %} {% endfor %} | ||
{% endfor -%} |
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cubi_tk/isa_tpl/isatab-stem_cell_core_sc/cookiecutter.json
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{ | ||
"group": "CoreRnD", | ||
"study_title": "Study Title", | ||
"sample_names": "sample1,sample2", | ||
"investigation_title": "{{cookiecutter.group}} - {{cookiecutter.study_title}}", | ||
"source_type": ["hiPSC", "tissue"], | ||
"cellline": "", | ||
"cellculture_meta": "Expansion ID,Media,Matrix", | ||
"model_type": ["3D", "2D"], | ||
"sample_meta": "Experiment Name,Experiment Identifier,Tissue type,Differentiation duration,Condition,Treatment,Treatment duration", | ||
"a_measurement_type": "transcription profiling", | ||
"a_technology_type": "nucleotide sequencing", | ||
"library_kit": [ | ||
"SC3Pv3", | ||
"SC3Pv2", | ||
"SC5P-PE", | ||
"SC5P-R2", | ||
"threeprime", | ||
"fiveprime" | ||
], | ||
"dissociation_meta": "Cell count,Removal debris,Removal dead cell,Cell fixation,Cell viability,No. cells used", | ||
"library_construction_meta": "RNA amount,QC cell load recovery,QC tape fragment size,Library concentration (ng/µl)", | ||
"sequencing_meta": "Platform,Instrument model,No. targeted reads", | ||
"_library_types": { | ||
"GEX": {"full" : "Gene Expression", "short": "GEX"}, | ||
"antibody": {"full" : "Antibody Capture", "short": "surface"}, | ||
"VDJ": {"full" : "VDJ-T", "short": "TCR"}, | ||
"other": {"full" : "other", "short": "XXX"}, | ||
"another": {"full" : "foobar", "short": "YYY"}, | ||
"CellPlex": {"full": "Multiplexing Capture", "short": "MPX"} | ||
}, | ||
"library_type": ["GEX", "GEX+antibody", "GEX+VDJ", "GEX+other", "GEX+antibody+VDJ", "GEX+other+another"], | ||
"sample_multiplexing": ["No", "CellPlex", "TotalSeq", "Other"], | ||
"genotype_multiplexing": ["no", "yes"], | ||
"i_dir_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", | ||
"s_file_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", | ||
"assay_prefix": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", | ||
"assay_name": "{{cookiecutter.library_type}}_{{cookiecutter.a_measurement_type|replace(' ', '_')}}" | ||
} |
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