Merge pull request #96 from cidgoh/MZA_dev

Adding recombinant lineages and updating surveillance module for it
cidgoh · Apr 15, 2022 · 488f7ff · 488f7ff
2 parents 9dd19a8 + 24ecaeb
commit 488f7ff
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Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/assets/ncov_variants/variants_who.tsv b/assets/ncov_variants/variants_who.tsv
@@ -3,7 +3,7 @@ Alpha	B.1.1.7*,Q.*,XA,XC,AP.1,B.1.1.459	VOC	n/a	18-Dec-2020	n/a
 Beta	B.1.351,B.1.351.*	VOC	n/a	18-Dec-2020	n/a
 Gamma	P.1,P.1.*	VOC	n/a	11-Jan-2021	n/a
 Delta	B.1.617.2,AY.*	VOC	04-Apr-2021	11-May-2021	n/a
-Omicron	B.1.1.529,BA.*	VOC	n/a	26-Nov-2021	24-Nov-2021
+Omicron	B.1.1.529,BA.*,XE	VOC	n/a	26-Nov-2021	24-Nov-2021
 Lambda	C.37,C.37.1	VOI	14-Jun-2021	n/a	n/a
 Mu	B.1.621,B.1.621.1	VOI	30-Aug-2021	n/a	n/a
 Kappa	B.1.617.1	VUM	4-Apr-2021	n/a	20-Sep-2021
@@ -12,3 +12,4 @@ Unnamed	C.1.2	VUM	n/a	n/a	01-Sep-2021
 Unnamed	B.1.640	VUM	n/a	n/a	22-Nov-2021
 Unnamed	B.1.640.1	VUM	n/a	n/a	22-Nov-2021
 Unnamed	B.1.640.2	VUM	n/a	n/a	22-Nov-2021
+Recombinant_XD	XD	VUM	n/a	n/a	09-Mar-2022
diff --git a/bin/surveillance_report_pdf.py b/bin/surveillance_report_pdf.py
@@ -179,10 +179,10 @@ def summarize_mutations(tsv, functions_dataframe):
     # adding if condition
     # if there are no commas
     # anywhere in the 'ao' column, calculate AF straight out
+    #if df['Alternate Allele Obs'][df['Alternate Allele Obs'].astype(
+    #        str).str.contains("n/a")].empty:
+    #    df['Alternate Frequency'] = np.nan
     if df['Alternate Allele Obs'][df['Alternate Allele Obs'].astype(
-            str).str.contains("n/a")].empty:
-        df['Alternate Frequency'] = np.nan
-    elif df['Alternate Allele Obs'][df['Alternate Allele Obs'].astype(
             str).str.contains(",")].empty:
         df['Alternate Frequency'] = round(
             df['Alternate Allele Obs'].astype(
@@ -394,7 +394,7 @@ def write_mutation_summary(df):
     tf = TableFormatter()
     tf.size = "scriptsize"
     if not args.user:
-        tf.table_spec = "{|p{1.2cm}|p{2.5cm}|p{3.3cm}|p{1.8cm}|p{1.8cm}|p{1.0cm}|p{1.3cm}|p{1.3cm}|p{1.3cm}|}"
+        tf.table_spec = "{|p{1.2cm}|p{2.5cm}|p{3.3cm}|p{1.8cm}|p{1.5cm}|p{1.0cm}|p{1.6cm}|p{1.3cm}|p{1.3cm}|}"
     else:
         tf.table_spec = "{|p{1.2cm}|p{2.5cm}|p{3.3cm}|p{1.8cm}|p{1.0cm}|p{1.3cm}|p{1.3cm}|p{1.3cm}|}"
 

diff --git a/modules/nf-core/modules/pangolin/main.nf b/modules/nf-core/modules/pangolin/main.nf
@@ -5,10 +5,10 @@ process PANGOLIN {
     publishDir "${params.outdir}/${params.prefix}/${task.process.replaceAll(":","_")}", pattern: "*.csv", mode: 'copy'
 
 
-    conda (params.enable_conda ? 'bioconda::pangolin=3.1.17' : null)
+    conda (params.enable_conda ? 'bioconda::pangolin=4.0.5' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pangolin:3.1.17--pyhdfd78af_1' :
-        'quay.io/biocontainers/pangolin:3.1.17--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/pangolin%3A4.0.5--pyhdfd78af_0' :
+        'quay.io/biocontainers/pangolin:4.0.5--pyhdfd78af_0' }"
 
     input:
     path(fasta)