523 lines
16 KiB
Plaintext
523 lines
16 KiB
Plaintext
#create project directory
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task create_dir {
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String workdir
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command <<<
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if [ ! -d ${workdir} ];then
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mkdir -p ${workdir}/log
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fi
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>>>
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}
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task annovar {
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String prefix
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String output_dir
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String ref
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String vcf
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command <<<
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if [ ! -d ${output_dir}/mutation ];then
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mkdir ${output_dir}/mutation
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fi
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table_annovar.pl \
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${vcf} \
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/dataseq/jmdna/software/annovar/humandb/ \
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-buildver hg19 -nastring . -vcfinput -remove -otherinfo \
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-protocol refGene,avsnp150,cosmic91,clinvar_20220320,1000g2015aug_all,1000g2015aug_eas,esp6500siv2_all,exac03nontcga,gnomad_genome,dbnsfp35c,cytoBand \
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-argument '-splicing_threshold 2 -hgvs',,,,,,,,,, \
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--intronhgvs 50 \
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-operation g,f,f,f,f,f,f,f,f,f,r \
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--outfile ${output_dir}/mutation/${prefix}
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>>>
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output {
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String anno = "${output_dir}/mutation/${prefix}.hg19_multianno.txt"
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}
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}
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task dealwithsnvindel {
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String name
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String anno
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String project
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String output_dir
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String umi
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String tumor_rmdup_bam
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command <<<
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if [ ! -d ${output_dir}/mutation ];then
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mkdir ${output_dir}/mutation
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fi
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if ${umi} ;then
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filter_snpindel_common.pl \
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${anno} \
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${project} \
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c \
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${output_dir}/mutation/${name}.snp.indel.Somatic.anno.hg19_multianno_filtered_pre.txt \
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${output_dir}/mutation/${name}.snp.indel.Germline.anno.hg19_multianno_filtered.txt \
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${output_dir}/mutation/${name}.snp.indel.anno.hg19_multianno_tag.txt
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filter_snpindel_umi_correct_f1r1.py \
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${output_dir}/mutation/${name}.snp.indel.Somatic.anno.hg19_multianno_filtered_pre.txt \
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${tumor_rmdup_bam} \
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${output_dir}/mutation/${name}.snp.indel.Somatic.anno.hg19_multianno_filtered.txt
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else
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filter_snpindel_common.pl \
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${anno} \
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${project} \
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t \
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${output_dir}/mutation/${name}.snp.indel.Somatic.anno.hg19_multianno_filtered.txt \
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${output_dir}/mutation/${name}.snp.indel.Germline.anno.hg19_multianno_filtered.txt \
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${output_dir}/mutation/${name}.snp.indel.anno.hg19_multianno_tag.txt
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fi
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>>>
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output {
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String snvindel_filtered= "${output_dir}/mutation/${name}.snp.indel.Somatic.anno.hg19_multianno_filtered.txt"
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String germline_filtered = "${output_dir}/mutation/${name}.snp.indel.Germline.anno.hg19_multianno_filtered.txt"
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}
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}
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task tmb {
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String codesDir
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String name
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String output_dir
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String somatic_anno
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command <<<
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perl ${codesDir}/tmb.pl ${output_dir} ${name}
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>>>
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output {
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String tmb="${output_dir}/mutation/${name}.tmb.txt"
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}
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}
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task fusion {
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String name
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String ref
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String codesDir
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String output_dir
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String rmdupBam
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String cancer
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String project
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String tumor_bamdst_depth
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command <<<
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if [ ! -d ${output_dir}/fusion ];then
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mkdir ${output_dir}/fusion
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fi
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# Extract the discordant paired-end alignments.
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samtools view -b -F 1294 ${rmdupBam} > ${output_dir}/fusion/${name}.discordants.bam
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# Extract the split-read alignments
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samtools view -h ${rmdupBam} \
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| /dataseq/jmdna/software/lumpy-sv/scripts/extractSplitReads_BwaMem -i stdin \
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| samtools view -Sb - \
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> ${output_dir}/fusion/${name}.splitters.bam
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lumpyexpress \
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-B ${rmdupBam} \
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-S ${output_dir}/fusion/${name}.splitters.bam \
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-D ${output_dir}/fusion/${name}.discordants.bam \
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-o ${output_dir}/fusion/${name}.fusion.vcf
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perl ${codesDir}/fusion.filter.pl ${output_dir}/fusion/${name}.fusion.vcf ${output_dir}/fusion/${name}.fusion.filter.vcf
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svtyper \
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-B ${rmdupBam} \
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-i ${output_dir}/fusion/${name}.fusion.filter.vcf \
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-T ${ref} \
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-o ${output_dir}/fusion/${name}.fusion.gt.vcf
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# table_annovar.pl \
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# ${output_dir}/fusion/${name}.fusion.gt.vcf \
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# /dataseq/jmdna/software/annovar/humandb/ \
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# -buildver hg19 -nastring . -vcfinput -remove -otherinfo \
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# -protocol refGene \
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# -operation g \
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# --outfile ${output_dir}/fusion/${name}.fusion
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# perl ${codesDir}/fusion.reanno.pl ${tumor_bamdst_depth} ${output_dir} ${name}
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# perl /home/jm001/test_duantao/database_update/codes/682/fusion_targetTherapy.pl ${codesDir} ${name} ${output_dir} ${project} ${cancer}
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>>>
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output {
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String fusion = "${output_dir}/fusion/${name}.fusion.pos.txt"
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}
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}
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task tumor_content {
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String name
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String tumor_pileup
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String normal_pileup
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String ref
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String output_dir
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String codesDir
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String gc_wiggle = "/dataseq/jmdna/codes/pancancer_controlsample/hg19.gc200Base.txt.gz"
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command <<<
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sequenza-utils bam2seqz \
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-p -gc ${gc_wiggle} \
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-F ${ref} \
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-n ${normal_pileup} \
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-t ${tumor_pileup} \
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| gzip > ${output_dir}/qc/target_${name}.200base.seqz.gz
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sequenza-utils seqz_binning -w 200 -s ${output_dir}/qc/target_${name}.200base.seqz.gz \
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| gzip > ${output_dir}/qc/target_${name}.200base.small.seqz.gz
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Rscript ${codesDir}/sequenza.R ${name} ${output_dir}/qc/target_${name}.200base.small.seqz.gz ${output_dir}/qc/sequenza || echo "sequenza failed!"
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>>>
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output {
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String purity = "${output_dir}/qc/sequenza/${name}_CP_contours.pdf"
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}
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}
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task cnvkit {
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String tumor
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String normal
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String tumor_rmdupBam
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String normal_rmdupBam
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String ref
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String bed
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String output_dir
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String cancer
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String codesDir
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String project
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String accessBed = "/dataseq/jmdna/software/cnvkit-0.9.7/data/access-5k-mappable.hg19.bed"
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String annotateGene = "/dataseq/jmdna/software/cnvkit-0.9.7/data/refFlat.txt"
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command <<<
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if [ ! -d ${output_dir}/cnvkit ];then
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mkdir ${output_dir}/cnvkit
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fi
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cnvkit.py batch \
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${tumor_rmdupBam} \
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--normal ${normal_rmdupBam} \
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--targets ${bed} \
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--fasta ${ref} \
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--access ${accessBed} \
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--output-reference ${output_dir}/cnvkit/${normal}_reference.cnn \
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--annotate ${annotateGene} \
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--drop-low-coverage --scatter --output-dir ${output_dir}/cnvkit
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cnvkit.py scatter \
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${output_dir}/cnvkit/${tumor}.rmdup.cnr -s ${output_dir}/cnvkit/${tumor}.rmdup.cns \
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--y-max 3 --y-min -3 \
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--title ${tumor}.cns \
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-o ${output_dir}/cnvkit/${tumor}.cnv.png
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perl ${codesDir}/log2_cn.pl ${output_dir}/cnvkit/${tumor}.rmdup.cns ${output_dir}/cnvkit/${tumor}.rmdup.cns.cn
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perl /home/jm001/test_duantao/database_update/codes/682/cnv_targetTherapy.pl ${codesDir} ${tumor} ${output_dir} ${project} ${cancer}
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>>>
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output {
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String cns = "${output_dir}/cnvkit/${tumor}.rmdup.cns"
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String png = "${output_dir}/cnvkit/${tumor}.cnv.png"
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}
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}
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task chemo {
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String codesDir
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String output_dir
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String project
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String normal
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String rmdupBam
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command <<<
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if [ ! -d ${output_dir}/chemo ];then
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mkdir ${output_dir}/chemo
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fi
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${codesDir}/chemo/chemo_panel.py -p ${project} -o ${output_dir} --n ${normal}
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>>>
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}
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task msi {
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String bed
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String name
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String output_dir
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String tumor_rmdupBam
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String normal_rmdupBam
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command <<<
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if [ ! -d ${output_dir}/msi ];then
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mkdir ${output_dir}/msi
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fi
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msisensor2 msi -d /dataseq/jmdna/software/msisensor2/hg19.microsatellites.list \
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-n ${normal_rmdupBam} \
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-t ${tumor_rmdupBam} \
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-e ${bed} -b 10 -o ${output_dir}/msi/${name}.msi
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>>>
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output {
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String target="${output_dir}/MSI/${name}.msi"
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}
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}
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task hla {
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String inputDir
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String output_dir
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String normal
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command <<<
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if [ ! -d ${output_dir}/neoantigen ];then
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mkdir -p ${output_dir}/neoantigen/HLA
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fi
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razers3 -tc 10 -i 95 -m 1 -dr 0 \
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-o ${output_dir}/neoantigen/HLA/fished_1.bam /dataseq/jmdna/software/OptiType-1.3.5/data/hla_reference_dna.fasta \
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${inputDir}/*_${normal}_*1.fq.gz
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samtools bam2fq ${output_dir}/neoantigen/HLA/fished_1.bam > ${output_dir}/neoantigen/HLA/${normal}_1_fished.fastq
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rm ${output_dir}/neoantigen/HLA/fished_1.bam
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razers3 -tc 10 -i 95 -m 1 -dr 0 \
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-o ${output_dir}/neoantigen/HLA/fished_2.bam /dataseq/jmdna/software/OptiType-1.3.5/data/hla_reference_dna.fasta \
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${inputDir}/*_${normal}_*2.fq.gz
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samtools bam2fq ${output_dir}/neoantigen/HLA/fished_2.bam > ${output_dir}/neoantigen/HLA/${normal}_2_fished.fastq
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rm ${output_dir}/neoantigen/HLA/fished_2.bam
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/dataseq/jmdna/software/OptiType-1.3.5/OptiTypePipeline.py \
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-i ${output_dir}/neoantigen/HLA/${normal}_1_fished.fastq ${output_dir}/neoantigen/HLA/${normal}_2_fished.fastq \
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--dna -v --prefix ${normal} -o ${output_dir}/neoantigen/HLA/
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>>>
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output {
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String hla = "${output_dir}/neoantigen/HLA/${normal}_result.tsv"
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}
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}
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task neoantigen {
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String codesDir
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String output_dir
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String name
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String normal
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String somatic_hc_vcf
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String hla
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command <<<
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sh /home/jm001/test_duantao/database_update/test_project/20230814_test/predict_neoantigen.sh ${output_dir} ${name} ${name} ${codesDir}
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>>>
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output {
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String neoantigen = "${output_dir}/neoantigen/MHC_Class_I/${name}.all_epitopes.netchop.txt"
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}
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}
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task hereditary {
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String codesDir
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String name
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String output_dir
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String project
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String germline_filtered
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command <<<
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${codesDir}/hereditary/hereditary.py -p ${project} -o ${output_dir} --n ${name}
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>>>
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output {
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String hereditary_pre = "${output_dir}/hereditary/${name}.hereditary.pre.txt"
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}
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}
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task conpair {
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String codesDir
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String name
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String tumor_rmdupBam
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String normal_rmdupBam
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String output_dir
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String ref
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command <<<
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if [ ! -d ${output_dir}/conpair ];then
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mkdir -p ${output_dir}/conpair
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fi
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python3 /dataseq/jmdna/software/Conpair-master/scripts/run_gatk_pileup_for_sample.py \
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-M /dataseq/jmdna/software/Conpair-master/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed \
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-B ${tumor_rmdupBam} \
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-O ${output_dir}/conpair/${name}.tumor.gatk.mpileup \
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-R ${ref} \
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-G /dataseq/jmdna/software/GenomeAnalysisTK.3.7.jar
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python3 /dataseq/jmdna/software/Conpair-master/scripts/run_gatk_pileup_for_sample.py \
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-M /dataseq/jmdna/software/Conpair-master/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed \
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-B ${normal_rmdupBam} \
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-O ${output_dir}/conpair/${name}.normal.gatk.mpileup \
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-R ${ref} \
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-G /dataseq/jmdna/software/GenomeAnalysisTK.3.7.jar
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sed -i 's/^chr//g' ${output_dir}/conpair/${name}.tumor.gatk.mpileup
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sed -i 's/^chr//g' ${output_dir}/conpair/${name}.normal.gatk.mpileup
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python3 /dataseq/jmdna/software/Conpair-master/scripts/verify_concordance.py \
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-H \
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-T ${output_dir}/conpair/${name}.tumor.gatk.mpileup \
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-N ${output_dir}/conpair/${name}.normal.gatk.mpileup \
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-O ${output_dir}/conpair/${name}_concordance.txt
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python3 /dataseq/jmdna/software/Conpair-master/scripts/estimate_tumor_normal_contamination.py \
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-T ${output_dir}/conpair/${name}.tumor.gatk.mpileup \
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-N ${output_dir}/conpair/${name}.normal.gatk.mpileup \
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-O ${output_dir}/conpair/${name}_contamination.txt
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>>>
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output {
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String concordance = "${output_dir}/conpair/${name}_concordance.txt"
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String contamination = "${output_dir}/conpair/${name}_contamination.txt"
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}
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}
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task mmr {
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String codesDir
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String name
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String output_dir
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String germline_filtered
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command <<<
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if [ ! -d ${output_dir}/MMR ];then
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mkdir -p ${output_dir}/MMR
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fi
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perl ${codesDir}/mmr_controlsample.pl ${output_dir} ${name}
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>>>
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output {
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String mmr = "${output_dir}/MMR/${name}_mmr.txt"
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}
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}
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task hrr {
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String codesDir
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String name
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String output_dir
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String germline_filtered
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command <<<
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if [ ! -d ${output_dir}/HRR ];then
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mkdir -p ${output_dir}/HRR
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fi
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perl ${codesDir}/hrr_controlsample_tissue.pl ${output_dir} ${name}
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>>>
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output {
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String hrr = "${output_dir}/HRR/${name}_hrr.txt"
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}
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}
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task hotspot {
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String name
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String output_dir
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String ref
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String rmdupBam
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String codesDir
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command <<<
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if [ ! -d ${output_dir}/mutation/hotspot/ ];then
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mkdir -p ${output_dir}/mutation/hotspot/
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fi
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samtools mpileup -Bq 20 -Q 20 \
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-f ${ref} \
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-l ${codesDir}/hotspot.bed \
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-o ${output_dir}/mutation/hotspot/${name}.hotspot.pileup \
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${rmdupBam}
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java -jar $VARSCAN mpileup2cns \
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${output_dir}/mutation/hotspot/${name}.hotspot.pileup \
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--min-var-freq 0.005 \
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--min-avg-qual 20 \
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--output-vcf 1 \
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--variants 1 \
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--p-value 0.99 \
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--min-reads2 2 \
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--strand-filter 0 \
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> ${output_dir}/mutation/hotspot/${name}.hotspot.L.snp.indel.vcf
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java -jar $VARSCAN mpileup2cns \
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${output_dir}/mutation/hotspot/${name}.hotspot.pileup \
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--min-var-freq 0.01 \
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--min-avg-qual 20 \
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--output-vcf 1 \
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--variants 1 \
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--p-value 0.05 \
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--min-reads2 3 \
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--strand-filter 1 \
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> ${output_dir}/mutation/hotspot/${name}.hotspot.H.snp.indel.vcf
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perl ${codesDir}/hotspot.hvl.pl ${output_dir} ${name}
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if [ -e "${output_dir}/mutation/hotspot/${name}.hotspot.snp.indel.vcf" ]; then
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table_annovar.pl \
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${output_dir}/mutation/hotspot/${name}.hotspot.snp.indel.vcf \
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/dataseq/jmdna/software/annovar/humandb/ \
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-buildver hg19 -nastring . -vcfinput -remove -otherinfo \
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-protocol refGene \
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-argument '-hgvs' \
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-operation g \
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--outfile ${output_dir}/mutation/hotspot/${name}.hotspot.snp.indel.anno
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perl ${codesDir}/hotspot.filter.pl ${output_dir} ${name}
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fi
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>>>
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output {
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String hotspot = "${output_dir}/mutation/hotspot/${name}.hotspot.H.snp.indel.vcf"
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}
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}
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task auto_report {
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String cancer
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String codesDir
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String output_dir
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|
|
String normal
|
|
String tumor
|
|
|
|
String cnv_cns
|
|
String cnv_png
|
|
|
|
String fusion_pos
|
|
String snvindel_filtered
|
|
|
|
String tmb
|
|
String mmr
|
|
String hrr
|
|
String hereditary_pre
|
|
|
|
command <<<
|
|
|
|
if [ ! -d ${output_dir}/report ];then
|
|
mkdir -p ${output_dir}/report
|
|
fi
|
|
|
|
perl /home/jm001/test_duantao/database_update/codes/682/indication.pl ${output_dir} ${cancer}
|
|
python3 ${codesDir}/drug_dedup.py ${output_dir} ${tumor}
|
|
perl ${codesDir}/file_format_change.pl ${output_dir} ${tumor}
|
|
python3 ${codesDir}/report_template/682gene_tissue_control_report.py ${output_dir} ${tumor} ${normal} ${cancer}
|
|
|
|
ln -s ${cnv_cns} ${output_dir}/report/
|
|
ln -s ${cnv_png} ${output_dir}/report/
|
|
|
|
ln -s ${fusion_pos} ${output_dir}/report/
|
|
ln -s ${snvindel_filtered} ${output_dir}/report/
|
|
|
|
ln -s ${tmb} ${output_dir}/report/
|
|
|
|
ln -s ${mmr} ${output_dir}/report/
|
|
|
|
ln -s ${hrr} ${output_dir}/report/
|
|
|
|
ln -s ${hereditary_pre} ${output_dir}/report/
|
|
|
|
>>>
|
|
} |