diff --git a/qiita_pet/support_files/doc/source/gettingstartedguide/index.rst b/qiita_pet/support_files/doc/source/gettingstartedguide/index.rst index c5b19a5ae..5c723c9a8 100755 --- a/qiita_pet/support_files/doc/source/gettingstartedguide/index.rst +++ b/qiita_pet/support_files/doc/source/gettingstartedguide/index.rst @@ -281,22 +281,24 @@ In order to submit your data to EBI, certain fields are required in your prepara For all valid values for instrument_model per platform, view the values in the table below: -+-----------------+----------------------------------------------------------------------------------------------------------+ -| Platform | Valid instrument_model options | -+=================+==========================================================================================================+ -| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, | -| | ``454 GS Junior`` or ``unspecified`` | -+-----------------+----------------------------------------------------------------------------------------------------------+ -| ``Illumina`` | ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, | -| | ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``, | -| | ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``, | -| | ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``, | -| | ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or `unspecified`` | -+-----------------+----------------------------------------------------------------------------------------------------------+ -| ``Ion_Torrent`` | ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL`` | -+-----------------+----------------------------------------------------------------------------------------------------------+ -| ``PacBio_SMRT`` | ``PacBio RS``, ``PacBio RS II``, ``Sequel ``, ``Sequel II`` | -+-----------------+----------------------------------------------------------------------------------------------------------+ ++---------------------+----------------------------------------------------------------------------------------------------------+ +| Platform | Valid instrument_model options | ++=====================+==========================================================================================================+ +| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, | +| | ``454 GS Junior`` or ``unspecified`` | ++---------------------+----------------------------------------------------------------------------------------------------------+ +| ``Illumina`` | ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, | +| | ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``, | +| | ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``, | +| | ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``, | +| | ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or ``unspecified`` | ++---------------------+----------------------------------------------------------------------------------------------------------+ +| ``Ion_Torrent`` | ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL`` | ++---------------------+----------------------------------------------------------------------------------------------------------+ +| ``PacBio_SMRT`` | ``PacBio RS``, ``PacBio RS II``, ``Sequel``, ``Sequel II`` | ++---------------------+----------------------------------------------------------------------------------------------------------+ +| ``Oxford_Nanopore`` | ``GridION`` | ++---------------------+----------------------------------------------------------------------------------------------------------+ Required fields for pre-processing target gene data diff --git a/qiita_ware/ebi.py b/qiita_ware/ebi.py index 5fcd19087..aad462c15 100644 --- a/qiita_ware/ebi.py +++ b/qiita_ware/ebi.py @@ -113,6 +113,7 @@ class EBISubmission(object): 'NEXTSEQ 500', 'NEXTSEQ 550', 'UNSPECIFIED'], + 'OXFORD_NANOPORE': ['GRIDION'], 'PACBIO_SMRT': ['PACBIO RS', 'PACBIO RS II', 'SEQUEL',