Need to set 'keep_flowcell_layout' to true for wrapica collection of runinfo xml

[alexiswl]

Tested with

num_lanes = get_num_lanes_from_run_info(
        project_id="9ec02c1f-53ba-47a5-854d-e6b53101adb7",
        data_id="fil.7d86703bc9e2424c441d08dcf9e059fc"  #/ilmn-runs/bssh_aps2-sh-prod_4515537/RunInfo.xml
    )
)

print(num_lanes)

v2_samplesheet_dict = v2_samplesheet_reader(
    StringIO(
        read_icav2_file_contents_to_string(
            project_id="9ec02c1f-53ba-47a5-854d-e6b53101adb7",
            data_id="fil.b4534c47c0d5481075d308dcfabfb3a9"  #/ilmn-runs/bssh_aps2-sh-prod_4515537/SampleSheet.csv
        )
    )
)

# And now append the lane attribute to every
v2_samplesheet_dict['bclconvert_data'] = list(flatten(
    map(
        lambda bclconvert_data_row_iter: list(
            map(
                lambda lane_iter: {
                    **bclconvert_data_row_iter,
                    **{"lane": lane_iter + 1}
                },
                range(num_lanes)
            )
        ),
        v2_samplesheet_dict['bclconvert_data']
    ),
))

print(
    json.dumps(
        v2_samplesheet_dict,
        indent=4
    )
)

Returns

4

{
    "header": {
        "file_format_version": 2,
    ....
}

[victorskl]

Easy win!