Progress using rdf model to link fastqs with flowcell/lib metadata.

[htsworkflow.git] / htsworkflow / templates / geo_submission.soft

diff --git a/htsworkflow/templates/geo_submission.soft b/htsworkflow/templates/geo_submission.soft
index ae2ac5760946a14d414fd87730812e477bdafb87..8ae3ed9ef78e0d737f1d7cada296a740e2ff553d 100644 (file)
--- a/htsworkflow/templates/geo_submission.soft
+++ b/htsworkflow/templates/geo_submission.soft
@@ -1,11 +1,34 @@
-Soft template
-!Platform_title = Illumina Genome Analyzer (Homo sapiens)
-!Platform_geo_accession = GPL9052
-{% for sample in samples %}{% for row in sample %}{%if forloop.first %}
+{% for name, value in series %}
+{{name}}={{value}}{% endfor %}{% for row in samples %}
 ^SAMPLE={{row.name}}
+!Sample_type=SRA
 !Sample_title={{row.name}}
-!Sample_organism_ch1 = {{ row.species_name }}
-!Sample_taxid_ch1 = {{ row.taxon_id }}
-{% spaceless %}{% if row.cell %}!Sample_characteristics_ch1 = cell: {{ row.cell }}
-{% endif %}{% endspaceless %}{% endif %}
-!Sample_supplementary_file_{{forloop.counter}}={{row.filename}}{% endfor %}{% endfor %}
\ No newline at end of file
+!Sample_series_id={{ series_id }}
+!Sample_channel_count=1
+!Sample_organism_ch1={{ row.species_name }}
+!Sample_taxid_ch1={{ row.taxon_id }}
+!Sample_source_name_ch1={{row.cell}}
+!Sample_library_strategy={{ row.experiment_type }}
+!Sample_library_source={{row.library_source}}
+!Sample_library_selection={{ row.library_selection }}
+!Sample_growth_protocol_ch1={{ row.growthProtocol|safe }}
+!Sample_extract_protocol={{ row.extractProtocol|safe }}
+!Sample_data_processing={{ row.dataProtocol|safe }}
+!Sample_molecule_ch1={{ row.extractMolecule }}
+!Sample_characteristics_ch1=labExpId: {{ row.library_id }}{% if row.replicate %}
+!Sample_characteristics_ch1=replicate: {{ row.replicate }}{% endif %}{% if row.cell %}
+!Sample_characteristics_ch1=cell: {{ row.cell }}{% endif %}{% if row.readType %}
+!Sample_characteristics_ch1=readType: {{ row.readType }}{% endif %}{% if row.antibody %}
+!Sample_characteristics_ch1=cell: {{ row.antibody }}{% endif %}{% for run in row.run %}{% if run.image_software %}
+!Sample_characteristics_ch1=Illumina image processing pipeline version: {{ run.image_software }}-{{ run.image_version }}{% endif %}{% if run.basecall_software %}
+!Sample_characteristics_ch1=Illumina base-calling pipeline version: {{ run.basecall_software }}-{{ run.basecall_version }}{% endif %}{% endfor %}{% for raw in row.raw %}
+!Sample_raw_file_{{forloop.counter}}={{ raw.filename }}
+!Sample_raw_file_type_{{forloop.counter}}={{raw.file_type_label}}
+!Sample_raw_file_insert_size_{{forloop.counter}}={{ row.insertLength }}
+!Sample_raw_file_read_length_{{forloop.counter}}={{raw.read_length}}
+!Sample_raw_file_instrument_model_{{forloop.counter}}={{raw.sequencer_model}}
+!Sample_raw_file_checksum_{{forloop.counter}}={{raw.md5sum}}
+!sample_raw_file_single_or_paired-end_{{forloop.counter}}={{raw.flowcell_type}}{% endfor %}{% for sup in row.supplimental %}
+!Sample_supplementary_file_{{forloop.counter}}={{sup.filename}}
+!Sample_supplementary_file_checksum_{{forloop.counter}}={{sup.md5sum}}
+{% endfor %}{% endfor %}