diff --git a/tools/artic/artic_minion.xml b/tools/artic/artic_minion.xml index 36210b55ecc..a36ce22bd58 100644 --- a/tools/artic/artic_minion.xml +++ b/tools/artic/artic_minion.xml @@ -416,7 +416,7 @@ For majority of users the default parameter values will result in a good consens - normalise: Increase this value to include more reads in the consensus generation step. This is per amplicon per strand, a value of a 100 would equate to an effective depth of 200. - primer match threshold: When matching a read to a primer site, the pipeline allows for some deviation from the primer location. This value represents the max nucleotide distance between primer site and alignment position. -.. _MPXV protocol: https://artic.network/mpxv/mpxv-bioinformatics-sop.html +.. _MPXV protocol: https://artic.network/fieldbioinformatics/fieldbioinformatics-sop.html .. _clair3: https://github.com/HKU-BAL/Clair3 .. _Rerio: https://github.com/nanoporetech/rerio .. _can read here: https://raw.githubusercontent.com/nanoporetech/rerio/refs/heads/master/LICENCE.txt diff --git a/tools/artic/tool-data/models.loc.sample b/tools/artic/tool-data/clair3_models.loc.sample similarity index 100% rename from tools/artic/tool-data/models.loc.sample rename to tools/artic/tool-data/clair3_models.loc.sample diff --git a/tools/artic/tool_data_table_conf.xml.sample b/tools/artic/tool_data_table_conf.xml.sample index ca6f03d6794..47b2e3c0500 100644 --- a/tools/artic/tool_data_table_conf.xml.sample +++ b/tools/artic/tool_data_table_conf.xml.sample @@ -10,8 +10,8 @@ value, dbkey, name, path - +
value, platform, sha256, path, source - +
diff --git a/tools/artic/tool_data_table_conf.xml.test b/tools/artic/tool_data_table_conf.xml.test index 4412b6dd4e2..2943f93b3eb 100644 --- a/tools/artic/tool_data_table_conf.xml.test +++ b/tools/artic/tool_data_table_conf.xml.test @@ -9,7 +9,7 @@ value, dbkey, name, path - +
value, platform, sha256, path, source