first commit

codescripts/merge_mendelian_vot.py

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+import pandas as pd
+import sys, argparse, os
+
+men = pd.read_table(sys.argv[1],header=None)
+vote = pd.read_table(sys.argv[2],low_memory=False)
+mut = pd.read_table(sys.argv[3],header=None)
+
+merged_df = pd.merge(vote, men,  how='inner', left_on=['CHROM','POS'], right_on = [0,1])
+merged_df['mendelian_check'] = 'MIE'
+merged_df.loc[merged_df[2]=='1:1:1','mendelian_check'] = 'MP'
+sub = merged_df[['CHROM','POS','LCL5_detected_num','mendelian_check',2]]
+sub.columns=['CHROM','POS','detected_num','mendelian','detail']
+genotype_sub = pd.merge(sub, mut,  how='inner', left_on=["CHROM","POS"], right_on = [0,1])
+genotype_sub = genotype_sub[['CHROM','POS','detected_num','mendelian','detail',2,3]]
+genotype_sub.to_csv(sys.argv[4],header=0,sep="\t",index=0)

inputs

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+{
+  "{{ project_name }}.right_200": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.right.200",
+  "{{ project_name }}.left_100": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.left.100",
+  "{{ project_name }}.disk_size": "100",
+  "{{ project_name }}.right_50": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.right.50",
+  "{{ project_name }}.chromo": "chr6",
+  "{{ project_name }}.right_150": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.right.150",
+  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
+  "{{ project_name }}.right_100": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.right.100",
+  "{{ project_name }}.left_150": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.left.150",
+  "{{ project_name }}.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
+  "{{ project_name }}.left_200": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.left.200",
+  "{{ project_name }}.left_50": "oss://pgx-result/renluyao/manuscript/small_variants_near_SV/chr6.ins.left.50",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"
+}

tasks/MIEpos2bed.wdl

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+task MIEpos2bed {
+	File mie_file
+	String chromo
+	String sample_name
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		cat ${mie_file} | awk '{print $1,$2,$2}' > ${sample_name}.${chromo}.allvariants.bed	
+
+		cat ${mie_file} | grep -v '1:1:1' | awk '{print $1,$2,$2}' > ${sample_name}.${chromo}.mie.bed			
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File mie_bed = "${sample_name}.${chromo}.mie.bed"
+		File all_bed = "${sample_name}.${chromo}.allvariants.bed"
+	}
+}

tasks/bedCoverage.wdl

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+task bedCoverage {
+	File mie_bed
+	File all_bed
+	File left_50
+	File left_100
+	File left_150
+	File left_200
+	File right_50
+	File right_100
+	File right_150
+	File right_200
+	String sample_name
+	String chromo
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+## MIE
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_50} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left50.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_100} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left100.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_150} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left150.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_200} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left200.coverage.txt
+
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_50} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right50.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_100} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right100.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_150} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right150.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_200} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right200.coverage.txt
+
+		paste ${sample_name}.${chromo}.mie.left50.coverage.txt ${sample_name}.${chromo}.mie.left100.coverage.txt ${sample_name}.${chromo}.mie.left150.coverage.txt ${sample_name}.${chromo}.mie.left200.coverage.txt ${sample_name}.${chromo}.mie.right50.coverage.txt ${sample_name}.${chromo}.mie.right100.coverage.txt ${sample_name}.${chromo}.mie.right150.coverage.txt ${sample_name}.${chromo}.mie.right200.coverage.txt > ${sample_name}.${chromo}.mie.coverage.txt
+
+# all variants
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_50} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left50.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_100} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left100.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_150} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left150.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_200} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left200.coverage.txt
+
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_50} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right50.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_100} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right100.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_150} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right150.coverage.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_200} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right200.coverage.txt
+
+		paste ${sample_name}.${chromo}.all.left50.coverage.txt ${sample_name}.${chromo}.all.left100.coverage.txt ${sample_name}.${chromo}.all.left150.coverage.txt ${sample_name}.${chromo}.all.left200.coverage.txt ${sample_name}.${chromo}.all.right50.coverage.txt ${sample_name}.${chromo}.all.right100.coverage.txt ${sample_name}.${chromo}.all.right150.coverage.txt ${sample_name}.${chromo}.all.right200.coverage.txt > ${sample_name}.${chromo}.all.coverage.txt
+
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File mie = "${sample_name}.${chromo}.mie.coverage.txt"
+		File all = "${sample_name}.${chromo}.all.coverage.txt"
+	}
+}

workflow.wdl

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+import "./tasks/MIEpos2bed.wdl" as MIEpos2bed
+import "./tasks/bedCoverage.wdl" as bedCoverage
+
+workflow {{ project_name }} {
+	File inputSamplesFile
+	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
+	File left_50
+	File left_100
+	File left_150
+	File left_200
+	File right_50
+	File right_100
+	File right_150
+	File right_200
+	String chromo
+	String docker
+	String cluster_config
+	String disk_size
+
+	scatter (sample in inputSamples){
+		call MIEpos2bed.MIEpos2bed as MIEpos2bed {
+			input:
+			mie_file=sample[0],
+			chromo=chromo,
+			sample_name=sample[1],
+			docker=docker,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+		}
+		call bedCoverage.bedCoverage as bedCoverage {
+			input:
+			mie_bed=MIEpos2bed.mie_bed,
+			all_bed=MIEpos2bed.all_bed,
+			left_50=left_50,
+			left_100=left_100,
+			left_150=left_150,
+			left_200=left_200,
+			right_50=right_50,
+			right_100=right_100,
+			right_150=right_150,
+			right_200=right_200,
+			sample_name=sample[1],
+			chromo=chromo,
+			docker=docker,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+		}
+	}
+}