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Bug in sra_ids_to_runinfo.py #46

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hukai916 opened this issue Oct 18, 2021 · 1 comment
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Bug in sra_ids_to_runinfo.py #46

hukai916 opened this issue Oct 18, 2021 · 1 comment
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@hukai916
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Hi,

This should be quick, basically, the function gse_to_srx() can't recognize GEO ids.
gsm_ids = [x.split('=')[1].strip() for x in fetch_url(url) if x.startswith('GSM')] should be
gsm_ids = [x.split('=')[1].strip() for x in fetch_url(url) if x.split('=')[1].strip().startswith('GSM')]

Thanks for creating fetchngs pipeline!

--Kai

@hukai916 hukai916 added the bug Something isn't working label Oct 18, 2021
drpatelh added a commit to drpatelh/nf-core-fetchngs that referenced this issue Oct 25, 2021
@drpatelh
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Thanks @hukai916 ! Your fix did the trick and will be added in #49

drpatelh added a commit that referenced this issue Oct 25, 2021
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