htsworkflow/templates/geo_submission.soft

   1 {% for name, value in series %}
   2 {{name}}={{value}}{% endfor %}{% for row in samples %}
   3 ^SAMPLE={{row.name}}
   4 !Sample_type=SRA
   5 !Sample_title={{row.name}}
   6 !Sample_series_id={{ series_id }}
   7 !Sample_channel_count=1
   8 !Sample_organism_ch1={{ row.species_name }}
   9 !Sample_taxid_ch1={{ row.taxon_id }}
  10 !Sample_source_name_ch1={{row.cell}}
  11 !Sample_library_strategy={{ row.experiment_type }}
  12 !Sample_library_source={{row.library_source}}
  13 !Sample_library_selection={{ row.library_selection }}
  14 !Sample_growth_protocol_ch1={{ row.growthProtocol|safe }}
  15 !Sample_extract_protocol={{ row.extractProtocol|safe }}
  16 !Sample_data_processing={{ row.dataProtocol|safe }}
  17 !Sample_molecule_ch1={{ row.extractMolecule }}
  18 !Sample_characteristics_ch1=labExpId: {{ row.library_id }}{% if row.replicate %}
  19 !Sample_characteristics_ch1=replicate: {{ row.replicate }}{% endif %}{% if row.cell %}
  20 !Sample_characteristics_ch1=cell: {{ row.cell }}{% endif %}{% if row.readType %}
  21 !Sample_characteristics_ch1=readType: {{ row.readType }}{% endif %}{% if row.antibody %}
  22 !Sample_characteristics_ch1=cell: {{ row.antibody }}{% endif %}{% for run in row.run %}{% if run.image_software %}
  23 !Sample_characteristics_ch1=Illumina image processing pipeline version: {{ run.image_software }}-{{ run.image_version }}{% endif %}{% if run.basecall_software %}
  24 !Sample_characteristics_ch1=Illumina base-calling pipeline version: {{ run.basecall_software }}-{{ run.basecall_version }}{% endif %}{% endfor %}{% for raw in row.raw %}
  25 !Sample_raw_file_{{forloop.counter}}={{ raw.filename }}
  26 !Sample_raw_file_type_{{forloop.counter}}={{raw.file_type_label}}
  27 !Sample_raw_file_insert_size_{{forloop.counter}}={{ row.insertLength }}
  28 !Sample_raw_file_read_length_{{forloop.counter}}={{raw.read_length}}
  29 !Sample_raw_file_instrument_model_{{forloop.counter}}={{raw.sequencer_model}}
  30 !Sample_raw_file_checksum_{{forloop.counter}}={{raw.md5sum}}
  31 !sample_raw_file_single_or_paired-end_{{forloop.counter}}={{raw.flowcell_type}}{% endfor %}{% for sup in row.supplimental %}
  32 !Sample_supplementary_file_{{forloop.counter}}={{sup.filename}}
  33 !Sample_supplementary_file_checksum_{{forloop.counter}}={{sup.md5sum}}
  34 {% endfor %}{% endfor %}