diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..62c8935 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +.idea/ \ No newline at end of file diff --git a/Docker/Dockerfile b/Docker/Dockerfile index 5e246bc..13f8753 100644 --- a/Docker/Dockerfile +++ b/Docker/Dockerfile @@ -2,7 +2,7 @@ FROM doejgi/mbin:v1.0.1 ## python 3.9.12 LABEL maintainer="chienchi@lanl.gov" -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 index 2b19c30..8853f03 100755 --- a/Docker/mbin_stats.py +++ b/Docker/mbin_stats.py @@ -76,8 +76,8 @@ 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] @@ -85,8 +85,8 @@ def parse_eukcc(file, 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 index 72cba18..2212aea 100755 --- 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 index 69f9380..65c670f 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -v1.3.11 +v1.3.12