Merge pull request #62 from microbiomedata/61-eukaryotic_evaluation-h…

…as-completeness-and-contamination-as-strings 61 eukaryotic evaluation has completeness and contamination as strings
microbiomedata · Nov 18, 2024 · 5a922a1 · 5a922a1
2 parents 58292e3 + 3ef4994
commit 5a922a1
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Showing 5 changed files with 8 additions and 7 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+.idea/
diff --git a/Docker/Dockerfile b/Docker/Dockerfile
@@ -2,7 +2,7 @@ FROM doejgi/mbin:v1.0.1
 ## python 3.9.12
 
 LABEL maintainer="[email protected]"
-LABEL version="1.0.3"
+LABEL version="1.0.4"
 LABEL software="NMDC_MAG_Pipeline"
 LABEL tags="bioinformatics"
 

diff --git a/Docker/mbin_stats.py b/Docker/mbin_stats.py
@@ -76,17 +76,17 @@ def parse_eukcc(file, bin_list):
             if 'completeness' not in line:
                 content = line.rstrip().split("\t")
                 binname = content[0].replace('.fa','')
-                eukcc[binname]['completeness'] = content[1]
-                eukcc[binname]['contamination'] = content[2]
+                eukcc[binname]['completeness'] = float(content[1])
+                eukcc[binname]['contamination'] = float(content[2])
                 eukcc[binname]['ncbi_lineage_tax_ids'] = content[3]
                 eukcc[binname]['ncbi_lineage'] = content[4]
 
     for bin in bin_list:
         if bin['bin_name'] in eukcc:
             if 'eukaryotic_evaluation' not in bin:
                 bin['eukaryotic_evaluation']= dict()
-            bin['eukaryotic_evaluation']['completeness'] = eukcc[bin['bin_name']]['completeness']
-            bin['eukaryotic_evaluation']['contamination'] = eukcc[bin['bin_name']]['contamination']
+            bin['eukaryotic_evaluation']['completeness'] = float(eukcc[bin['bin_name']]['completeness'])
+            bin['eukaryotic_evaluation']['contamination'] = float(eukcc[bin['bin_name']]['contamination'])
             bin['eukaryotic_evaluation']['ncbi_lineage_tax_ids'] = eukcc[bin['bin_name']]['ncbi_lineage_tax_ids']
             bin['eukaryotic_evaluation']['ncbi_lineage'] = eukcc[bin['bin_name']]['ncbi_lineage']
         update_bin_list.append(bin)

diff --git a/mbin_nmdc.wdl b/mbin_nmdc.wdl
@@ -24,7 +24,7 @@ workflow nmdc_mags {
         String checkm_db="/refdata/checkM_DB/checkm_data_2015_01_16"
         String eukcc2_db="/refdata/EUKCC2_DB/eukcc2_db_ver_1.2"
         String package_container = "microbiomedata/nmdc_mbin_vis:0.7.0"
-        String container = "microbiomedata/nmdc_mbin@sha256:49e218e9de783d3f307740dd02c9e0213bfaff0b8095abc89eb111a962388430"
+        String container = "microbiomedata/nmdc_mbin@sha256:2d9d79740eef27b2959d00c34fa5816ff911ec7c4dc80fedb110ab170ce0b868"
     }
     call stage {
         input:

diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-v1.3.11
+v1.3.12