118 lines
3.3 KiB
Plaintext
Executable File
118 lines
3.3 KiB
Plaintext
Executable File
# statistics
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task run_statistics {
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String name
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String output_dir
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String rmdupBam
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String ref
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String bed
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command {
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if [ ! -d ${output_dir}/qc/${name}_bamdst ];then
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mkdir -p ${output_dir}/qc/${name}_bamdst
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fi
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samtools flagstat -@ 10 ${rmdupBam} >${output_dir}/qc/${name}.rmdup.flagstat
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samtools stats --reference ${ref} -t ${bed} -@ 10 ${rmdupBam} > ${output_dir}/qc/${name}.rmdup.stat
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bamdst -p ${bed} -o ${output_dir}/qc/${name}_bamdst ${rmdupBam}
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qc_stat.py ${output_dir}/qc/${name}.json ${output_dir}/qc/${name}_bamdst/ ${output_dir}/qc/${name}_qc.txt
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# InsertAndDepthStat.R \
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# ${output_dir}/qc/${name}_InsertAndDepthStat \
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# ${output_dir}/qc/${name}_bamdst/insertsize.plot \
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# ${output_dir}/qc/${name}_bamdst/depth_distribution.plot
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}
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}
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task run_statistics_umi {
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String name
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String output_dir
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String sortedBam
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String rmdupBam
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String genecore_json
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String ref
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String bed
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command {
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if [ ! -d ${output_dir}/qc/${name}_bamdst ];then
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mkdir -p ${output_dir}/qc/${name}_bamdst
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mkdir -p ${output_dir}/qc/${name}_sorted_bamdst
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fi
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samtools flagstat -@ 10 ${rmdupBam} >${output_dir}/qc/${name}.rmdup.flagstat
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samtools stats --reference ${ref} -t ${bed} -@ 10 ${rmdupBam} > ${output_dir}/qc/${name}.rmdup.stat
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bamdst -p ${bed} -o ${output_dir}/qc/${name}_bamdst ${rmdupBam}
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bamdst -p ${bed} -o ${output_dir}/qc/${name}_sorted_bamdst ${sortedBam}
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qc_stat_umi.py ${output_dir}/qc/${name}.json ${output_dir}/qc/${name}_bamdst/ ${output_dir}/qc/${name}_sorted_bamdst/ ${genecore_json} ${output_dir}/qc/${name}_qc.txt
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# InsertAndDepthStat.R \
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# ${output_dir}/qc/${name}_InsertAndDepthStat \
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# ${output_dir}/qc/${name}_bamdst/insertsize.plot \
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# ${output_dir}/qc/${name}_bamdst/depth_distribution.plot
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}
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}
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workflow statistics {
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Boolean run=true
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Boolean umi
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String tumor
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String tumor_rmdup_bam
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String tumor_sorted_bam
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String? normal
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String? normal_rmdup_bam
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String genecore_json
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String ref
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String bed
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String output_dir
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if (run) {
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if (umi) {
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call run_statistics_umi as runstatistics_umi_tumor {
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input:
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name=tumor,
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output_dir=output_dir,
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rmdupBam=tumor_rmdup_bam,
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genecore_json=genecore_json,
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sortedBam=tumor_sorted_bam,
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ref=ref,
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bed=bed
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}
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}
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if (!umi) {
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call run_statistics as runstatistics_tumor {
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input:
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name=tumor,
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output_dir=output_dir,
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rmdupBam=tumor_rmdup_bam,
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ref=ref,
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bed=bed
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}
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}
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if (defined(normal)) {
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call run_statistics as runstatistics_normal {
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input:
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name=normal,
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output_dir=output_dir,
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rmdupBam=normal_rmdup_bam,
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ref=ref,
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bed=bed
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}
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}
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}
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output {
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String tumor_bamdst_depth = "${output_dir}/qc/${tumor}_bamdst/depth.tsv.gz"
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}
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} |