Merge pull request #10 from UMCUGenetics/release/v2.0.0

Release/v2.0.0

Kinship/Dockerfile

@@ -0,0 +1,10 @@
+FROM --platform=linux/amd64 continuumio/miniconda3
+
+LABEL base_image="continuumio/miniconda3"
+LABEL version="1.0.0"
+LABEL extra.binaries="vcftools, plink, king"
+
+RUN conda config --add channels bioconda && \
+    conda config --add channels conda-forge && \
+    conda install -y vcftools=0.1.14 plink=1.90b4 king=2.2.7
+

Utils/Kinship.nf → Kinship/Kinship.nf

@@ -1,7 +1,7 @@
 process Kinship {
-    // Custom process to run Kinship tools
     tag {"Kinship ${analysis_id}"}
     label 'Kinship'
+    container = 'docker.io/umcugenbioinf/kinship:1.0.0'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -13,10 +13,10 @@ process Kinship {
 
     script:
         """
-        ${params.vcftools_path}/vcftools --vcf ${vcf_file} --plink
-        ${params.plink_path}/plink --file out --make-bed --noweb
-        ${params.king_path}/king -b plink.bed --kinship
+        vcftools --vcf ${vcf_file} --plink
+        plink --file out --make-bed --noweb
+        king -b plink.bed --kinship
         cp king.kin0 ${analysis_id}.kinship
-        python ${baseDir}/CustomModules/Utils/check_kinship.py ${analysis_id}.kinship ${ped_file} > ${analysis_id}.kinship_check.out
+        python ${baseDir}/CustomModules/Kinship/check_kinship.py ${analysis_id}.kinship ${ped_file} > ${analysis_id}.kinship_check.out
         """
 }

MipsTrimDedup/MipsTrimDedup.nf

@@ -18,6 +18,6 @@ process MipsTrimDedup {
         rg_id = "${sample_id}_MergedTrimmedDedup"
 
         """
-        python ${params.mips_trim_dedup_path}/mips_trim_dedup.py -d ${params.dxtracks_path}/${params.mips_design_file}  -l ${params.mips_uuid_length} -ur ${params.mips_uuid_read} -r1 ${r1_args} -r2 ${r2_args}
+        python2 ${params.mips_trim_dedup_path}/mips_trim_dedup.py -d ${params.dxtracks_path}/${params.mips_design_file}  -l ${params.mips_uuid_length} -ur ${params.mips_uuid_read} -r1 ${r1_args} -r2 ${r2_args}
         """
 }

Utils/CreateHSmetricsSummary.nf

@@ -12,6 +12,6 @@ process CreateHSmetricsSummary {
 
     script:
         """
-        python ${baseDir}/CustomModules/Utils/create_hsmetrics_summary.py ${hsmetrics_files} > HSMetrics_summary.txt
+        python2 ${baseDir}/CustomModules/Utils/create_hsmetrics_summary.py ${hsmetrics_files} > HSMetrics_summary.txt
         """
 }

Utils/GetStatsFromFlagstat.nf

@@ -12,6 +12,6 @@ process GetStatsFromFlagstat {
 
     script:
         """
-        python ${baseDir}/CustomModules/Utils/get_stats_from_flagstat.py ${flagstat_files} > run_stats.txt
+        python2 ${baseDir}/CustomModules/Utils/get_stats_from_flagstat.py ${flagstat_files} > run_stats.txt
         """
 }

Utils/ParseChildFromFullTrio.nf

@@ -15,6 +15,6 @@ process ParseChildFromFullTrio {
     script:
         def sample_ids = sample_id.join(" ")
         """
-        python ${baseDir}/CustomModules/Utils/parse_child_from_fulltrio.py ${ped_file} ${sample_ids} | tr -d '\n'
+        python2 ${baseDir}/CustomModules/Utils/parse_child_from_fulltrio.py ${ped_file} ${sample_ids} | tr -d '\n'
         """
 }

Utils/parse_child_from_fulltrio.py

@@ -1,6 +1,31 @@
 #! /usr/bin/env python
 import argparse
-from check_kinship import parse_ped
+
+
+def parse_ped(ped_file):
+    samples = {}  # 'sample_id': {'family': 'fam_id', 'parents': ['sample_id', 'sample_id']}
+
+    for line in ped_file:
+        ped_data = line.strip().split()
+        family, sample, father, mother, sex, phenotype = ped_data
+
+        # Create samples
+        if sample not in samples:
+            samples[sample] = {'family': family, 'parents': [], 'children': []}
+        if father != '0' and father not in samples:
+            samples[father] = {'family': family, 'parents': [], 'children': []}
+        if mother != '0' and mother not in samples:
+            samples[mother] = {'family': family, 'parents': [], 'children': []}
+
+        # Save sample relations
+        if father != '0':
+            samples[sample]['parents'].append(father)
+            samples[father]['children'].append(sample)
+        if mother != '0':
+            samples[sample]['parents'].append(mother)
+            samples[mother]['children'].append(sample)
+    return samples
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description='Check kinship output based on ped file.')