Update tb profiler v6.2.0 (#36)

* update variable name changes

* update tbprofiler version

* remove reporting allele fraction

* update variable names used in updated report

* update all variable names

bin/check_snpit_against_tbprofiler.py

@@ -44,17 +44,17 @@ def main(args):
 
     if snpit_results['Species'] == 'N/A':
         tbprofiler_report = json.load(open(args.tbprofiler_report))
-        pct_reads_mapped = tbprofiler_report['qc']['pct_reads_mapped']
-        if tbprofiler_report['main_lin'] == 'lineage4' and pct_reads_mapped >= args.min_percent_reads_mapped:
+        pct_reads_mapped = tbprofiler_report['qc']['percent_reads_mapped']
+        if tbprofiler_report['main_lineage'] == 'lineage4' and pct_reads_mapped >= args.min_percent_reads_mapped:
             snpit_results['Species'] = 'M. tuberculosis'
-            snpit_results['Lineage'] = tbprofiler_report['main_lin'].replace('lineage', 'Lineage ')
+            snpit_results['Lineage'] = tbprofiler_report['main_lineage'].replace('lineage', 'Lineage ')
             snpit_results['Percentage'] = 'N/A'
     elif snpit_results['Percentage'] != 'N/A' and snpit_results['Percentage'] < args.min_snpit_percentage:
         tbprofiler_report = json.load(open(args.tbprofiler_report))
-        pct_reads_mapped = tbprofiler_report['qc']['pct_reads_mapped']
-        if tbprofiler_report['main_lin'] == 'lineage4' and pct_reads_mapped >= args.min_percent_reads_mapped:
+        pct_reads_mapped = tbprofiler_report['qc']['percent_reads_mapped']
+        if tbprofiler_report['main_lineage'] == 'lineage4' and pct_reads_mapped >= args.min_percent_reads_mapped:
             snpit_results['Species'] = 'M. tuberculosis'
-            snpit_results['Lineage'] = tbprofiler_report['main_lin'].replace('lineage', 'Lineage ')
+            snpit_results['Lineage'] = tbprofiler_report['main_lineage'].replace('lineage', 'Lineage ')
             snpit_results['Name'] = 'N/A'
             snpit_results['Percentage'] = 'N/A'
 

environments/environment.yml

@@ -6,5 +6,5 @@ channels:
 dependencies:
   - python=3
   - fastp=0.23.2
-  - tb-profiler=4.3.0
+  - tb-profiler=6.2.0
   - qualimap=2.2.2d

modules/tbprofiler.nf

@@ -66,9 +66,8 @@ process tbprofiler {
       --platform ${params.platform} \
       --mapper ${params.mapper} \
       --caller ${params.caller} \
-      --min_depth ${params.min_depth} \
+      --depth ${params.min_depth} \
       --af ${params.min_af_used_for_calling} \
-      --reporting_af ${params.min_af_used_for_prediction} \
       --read1 ${reads_1} \
       --read2 ${reads_2} \
       --prefix ${sample_id} \
@@ -78,7 +77,7 @@ process tbprofiler {
     mv bam/${sample_id}.bam ./${sample_id}_tbprofiler.bam
     mv bam/${sample_id}.bam.bai ./${sample_id}_tbprofiler.bam.bai
 
-    mv vcf/${sample_id}.targets.csq.vcf.gz ./${sample_id}_tbprofiler_targets.vcf.gz
+    mv vcf/${sample_id}.targets.vcf.gz ./${sample_id}_tbprofiler_targets.vcf.gz
     gunzip ./${sample_id}_tbprofiler_targets.vcf.gz
 
     mv vcf/${sample_id}.vcf.gz ./${sample_id}_tbprofiler_whole_genome.vcf.gz