htsworkflow/templates/geo_submission.soft

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