Incorporate the changes in the nf-core/mag samplesheet for its generation#183
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Incorporate the changes in the nf-core/mag samplesheet for its generation#183
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By default, we evaluate whether there are more than two FastQ files available in the column download_links by checking the presence of a semicolon. If there is a semicolon, the first entry is used as R1 and the second entry as R2. However, in the case that a third FastQ file is uploaded, such as the merged reads or singletons, the first FastQ file does not contain the paired reads but the second and third do. This implements the check whether there are three FastQ files to pick the correct paired FastQ files for the assembly.
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Closes #179. |
jfy133
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Feb 6, 2026
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Awesome thanks Alex!
If we do a quick release after the Hackathon can include the mag protocol paper ;)
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short_read_platformandlong_read_platformdownload_linkscorrectly when three FastQ files per sample exist