updated alignment_protocol field in the script, doc, and the example templates

9 files changed, 9 insertions, 9 deletions

diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html
index b49830b..aea74ad 100644
--- a/doc/blog/using-covid-19-pubseq-part3.html
+++ b/doc/blog/using-covid-19-pubseq-part3.html
@@ -589,7 +589,7 @@ virus:
 
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0009173</span>,http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0009173</span>]
-    sequence_assembly_method: Protocol used for assembly
+    alignment_protocol: Protocol used for assembly
     sequencing_coverage: [<span style="color: #8bc34a;">70.0</span>, <span style="color: #8bc34a;">100.0</span>]
     additional_technology_information: Optional free text field for additional information
 
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index d0d6c7f..c98bf27 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -234,7 +234,7 @@ a more elaborate example (note most fields are optional) may look like
 
   technology:
       sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173]
-      sequence_assembly_method: Protocol used for assembly
+      alignment_protocol: Protocol used for assembly
       sequencing_coverage: [70.0, 100.0]
       additional_technology_information: Optional free text field for additional information
 
diff --git a/example/esr_example.yaml b/example/esr_example.yaml
index 48b11e4..b3e97d5 100644
--- a/example/esr_example.yaml
+++ b/example/esr_example.yaml
@@ -24,7 +24,7 @@ virus:
 
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION
-    sequence_assembly_method: https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics
+    alignment_protocol: https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics
     additional_technology_information: "Artic V3 workflow"
 
 submitter:
diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml
index 54736f8..cd8890d 100644
--- a/example/maximum_metadata_example.yaml
+++ b/example/maximum_metadata_example.yaml
@@ -35,7 +35,7 @@ virus:
 
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173]
-    sequence_assembly_method: Protocol used for assembly
+    alignment_protocol: Protocol used for assembly
     sequencing_coverage: [70.0, 100.0]
     additional_technology_information: Optional free text field for additional information
 
diff --git a/example/uthsc_example.yaml b/example/uthsc_example.yaml
index 956faf1..3bdbf6f 100644
--- a/example/uthsc_example.yaml
+++ b/example/uthsc_example.yaml
@@ -24,7 +24,7 @@ virus:
 
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632] // Nanopore MinION
-    sequence_assembly_method: guppy
+    alignment_protocol: guppy
     additional_technology_information: Optional free text field for additional information
 
 submitter:
diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
index 364090e..87b348b 100755
--- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
@@ -190,7 +190,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
 
                 for info_to_check, field_in_yaml in zip(
                     ['Assembly Method', 'Coverage', 'Sequencing Technology'],
-                    ['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology']
+                    ['alignment_protocol', 'sequencing_coverage', 'sample_sequencing_technology']
                 ):
                     if info_to_check in GBSeq_comment_text:
                         tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
diff --git a/scripts/esr_samples/template.yaml b/scripts/esr_samples/template.yaml
index 98f08a6..3ca1de3 100644
--- a/scripts/esr_samples/template.yaml
+++ b/scripts/esr_samples/template.yaml
@@ -14,7 +14,7 @@ virus:
 
 technology:
     sample_sequencing_technology: ["http://www.ebi.ac.uk/efo/EFO_0008632"]
-    sequence_assembly_method: "https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics"
+    alignment_protocol: "https://github.com/ESR-NZ/NZ_SARS-CoV-2_genomics"
     additional_technology_information: "Artic V3 workflow"
 
 submitter:
diff --git a/scripts/uthsc_samples/template.yaml b/scripts/uthsc_samples/template.yaml
index 07e0828..c81bd28 100644
--- a/scripts/uthsc_samples/template.yaml
+++ b/scripts/uthsc_samples/template.yaml
@@ -22,7 +22,7 @@ virus:
 
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632]
-    sequence_assembly_method: https://bio.tools/BWA#!
+    alignment_protocol: https://bio.tools/BWA#!
     additional_technology_information: "Oxford Nanopore MiniIon RNA long reads"
 
 submitter:
diff --git a/test/data/input/TN_UT2.yaml b/test/data/input/TN_UT2.yaml
index 9c4370d..236110d 100644
--- a/test/data/input/TN_UT2.yaml
+++ b/test/data/input/TN_UT2.yaml
@@ -22,7 +22,7 @@ virus:
 
 technology:
     sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632]
-    sequence_assembly_method: https://bio.tools/BWA#!
+    alignment_protocol: https://bio.tools/BWA#!
     additional_technology_information: Oxford Nanopore MiniIon RNA long reads
 
 submitter: