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meta.datatype being set incorrectly in INPUT_CHECK.nf for sample sheets generated by fetchngs #106

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BethYates opened this issue Jul 30, 2024 · 0 comments
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@BethYates
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Description of the bug

When setting the meta.datatype value in the create_data_channels_from_fetchngs function the default value of "illumina" is selected. This is because each row of the samplesheet csv file passed to the function has not been split correctly. This issue can be fixed by modifying the
.splitCsv operator in this block of code

 FETCHNGSSAMPLESHEET_CHECK ( samplesheet )
            .csv
            .splitCsv ( header:true, sep:',' )
            .branch { row ->
                paired: row.fastq_2
                    [[id: row.run_accession, row:row], [row.fastq_1, row.fastq_2]]
                not_paired: true
            }
            .set { reads_pairedness } 

to include the option quote:'"'

Command used and terminal output

No response

Relevant files

samplesheet.csv

System information

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@BethYates BethYates added the bug Something isn't working label Jul 30, 2024
@muffato muffato closed this as completed Jul 31, 2024
@muffato muffato moved this from Todo to Done in Genome After Party Dec 11, 2024
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