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Merge pull request #397 from jlac/activeDev
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 fixed bug tracking FREEC 2nd pass output
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@jlac
jlac committed Jan 17, 2019
2 parents 00d2f3c + 138c52f commit ae68b5f
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Showing 2 changed files with 4 additions and 4 deletions.
4 changes: 2 additions & 2 deletions Rules/freec_exome_somatic_pass1.rl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ if config['project']['annotation'] == "hg19":
freectargets=config['project']['workpath']+"/freec_targets.bed",
output: cnvs="freec_out/pass1/{x}.recal.bam_CNVs",
params: dir=config['project']['workpath'],fasta=config['references'][pfamily]['FREECFASTA'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],lengths=config['references'][pfamily]['FREECLENGTHS'],chroms=config['references'][pfamily]['FREECCHROMS'],pile=config['references'][pfamily]['FREECPILEUP'],snps=config['references'][pfamily]['FREECSNPS'],rname="pl:freec"
shell: "module load samtools/1.9; mkdir -p freec_out; mkdir -p freec_out/pass1; mkdir -p freec_out/pass1/{params.tumorsample}; samtools view -H {input.normal} | sed -e 's/SN:1/SN:chr1/' | sed -e 's/SN:2/SN:chr2/' | sed -e 's/SN:3/SN:chr3/' | sed -e 's/SN:4/SN:chr4/' | sed -e 's/SN:5/SN:chr5/' | sed -e 's/SN:6/SN:chr6/' | sed -e 's/SN:7/SN:chr7/' | sed -e 's/SN:8/SN:chr8/' | sed -e 's/SN:9/SN:chr9/' | sed -e 's/SN:10/SN:chr10/' | sed -e 's/SN:11/SN:chr11/' | sed -e 's/SN:12/SN:chr12/' | sed -e 's/SN:13/SN:chr13/' | sed -e 's/SN:14/SN:chr14/' | sed -e 's/SN:15/SN:chr15/' | sed -e 's/SN:16/SN:chr16/' | sed -e 's/SN:17/SN:chr17/' | sed -e 's/SN:18/SN:chr18/' | sed -e 's/SN:19/SN:chr19/' | sed -e 's/SN:20/SN:chr20/' | sed -e 's/SN:21/SN:chr21/' | sed -e 's/SN:22/SN:chr22/' | sed -e 's/SN:X/SN:chrX/' | sed -e 's/SN:Y/SN:chrY/' | sed -e 's/SN:MT/SN:chrM/' | samtools reheader - {input.normal} > freec_out/{input.normal}; samtools view -H {input.tumor} | sed -e 's/SN:1/SN:chr1/' | sed -e 's/SN:2/SN:chr2/' | sed -e 's/SN:3/SN:chr3/' | sed -e 's/SN:4/SN:chr4/' | sed -e 's/SN:5/SN:chr5/' | sed -e 's/SN:6/SN:chr6/' | sed -e 's/SN:7/SN:chr7/' | sed -e 's/SN:8/SN:chr8/' | sed -e 's/SN:9/SN:chr9/' | sed -e 's/SN:10/SN:chr10/' | sed -e 's/SN:11/SN:chr11/' | sed -e 's/SN:12/SN:chr12/' | sed -e 's/SN:13/SN:chr13/' | sed -e 's/SN:14/SN:chr14/' | sed -e 's/SN:15/SN:chr15/' | sed -e 's/SN:16/SN:chr16/' | sed -e 's/SN:17/SN:chr17/' | sed -e 's/SN:18/SN:chr18/' | sed -e 's/SN:19/SN:chr19/' | sed -e 's/SN:20/SN:chr20/' | sed -e 's/SN:21/SN:chr21/' | sed -e 's/SN:22/SN:chr22/' | sed -e 's/SN:X/SN:chrX/' | sed -e 's/SN:Y/SN:chrY/' | sed -e 's/SN:MT/SN:chrM/' | samtools reheader - {input.tumor} > freec_out/{input.tumor}; perl Scripts/make_freec_pass1_exome_tn_config.pl {params.dir}/freec_out/pass1/{params.tumorsample} {params.lengths} {params.chroms} {params.dir}/freec_out/{input.tumor} {params.dir}/freec_out/{input.normal} {params.pile} {params.fasta} {params.snps} {input.freectargets}; module load freec/11.5; module load bedtools/2.27.1; freec -conf {params.dir}/freec_out/pass1/{params.tumorsample}/freec_exome_config.txt; mv {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass1/{output.cnvs}"
shell: "module load samtools/1.9; mkdir -p freec_out; mkdir -p freec_out/pass1; mkdir -p freec_out/pass1/{params.tumorsample}; samtools view -H {input.normal} | sed -e 's/SN:1/SN:chr1/' | sed -e 's/SN:2/SN:chr2/' | sed -e 's/SN:3/SN:chr3/' | sed -e 's/SN:4/SN:chr4/' | sed -e 's/SN:5/SN:chr5/' | sed -e 's/SN:6/SN:chr6/' | sed -e 's/SN:7/SN:chr7/' | sed -e 's/SN:8/SN:chr8/' | sed -e 's/SN:9/SN:chr9/' | sed -e 's/SN:10/SN:chr10/' | sed -e 's/SN:11/SN:chr11/' | sed -e 's/SN:12/SN:chr12/' | sed -e 's/SN:13/SN:chr13/' | sed -e 's/SN:14/SN:chr14/' | sed -e 's/SN:15/SN:chr15/' | sed -e 's/SN:16/SN:chr16/' | sed -e 's/SN:17/SN:chr17/' | sed -e 's/SN:18/SN:chr18/' | sed -e 's/SN:19/SN:chr19/' | sed -e 's/SN:20/SN:chr20/' | sed -e 's/SN:21/SN:chr21/' | sed -e 's/SN:22/SN:chr22/' | sed -e 's/SN:X/SN:chrX/' | sed -e 's/SN:Y/SN:chrY/' | sed -e 's/SN:MT/SN:chrM/' | samtools reheader - {input.normal} > freec_out/{input.normal}; samtools view -H {input.tumor} | sed -e 's/SN:1/SN:chr1/' | sed -e 's/SN:2/SN:chr2/' | sed -e 's/SN:3/SN:chr3/' | sed -e 's/SN:4/SN:chr4/' | sed -e 's/SN:5/SN:chr5/' | sed -e 's/SN:6/SN:chr6/' | sed -e 's/SN:7/SN:chr7/' | sed -e 's/SN:8/SN:chr8/' | sed -e 's/SN:9/SN:chr9/' | sed -e 's/SN:10/SN:chr10/' | sed -e 's/SN:11/SN:chr11/' | sed -e 's/SN:12/SN:chr12/' | sed -e 's/SN:13/SN:chr13/' | sed -e 's/SN:14/SN:chr14/' | sed -e 's/SN:15/SN:chr15/' | sed -e 's/SN:16/SN:chr16/' | sed -e 's/SN:17/SN:chr17/' | sed -e 's/SN:18/SN:chr18/' | sed -e 's/SN:19/SN:chr19/' | sed -e 's/SN:20/SN:chr20/' | sed -e 's/SN:21/SN:chr21/' | sed -e 's/SN:22/SN:chr22/' | sed -e 's/SN:X/SN:chrX/' | sed -e 's/SN:Y/SN:chrY/' | sed -e 's/SN:MT/SN:chrM/' | samtools reheader - {input.tumor} > freec_out/{input.tumor}; perl Scripts/make_freec_pass1_exome_tn_config.pl {params.dir}/freec_out/pass1/{params.tumorsample} {params.lengths} {params.chroms} {params.dir}/freec_out/{input.tumor} {params.dir}/freec_out/{input.normal} {params.pile} {params.fasta} {params.snps} {input.freectargets}; module load freec/11.5; module load bedtools/2.27.1; freec -conf {params.dir}/freec_out/pass1/{params.tumorsample}/freec_exome_config.txt; mv {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {output.cnvs}"

else:
rule freec_exome_somatic_pass1:
Expand All @@ -18,4 +18,4 @@ else:
freectargets=config['project']['workpath']+"/freec_targets.bed",
output: cnvs="freec_out/pass1/{x}.recal.bam_CNVs",
params: dir=config['project']['workpath'],fasta=config['references'][pfamily]['FREECFASTA'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],lengths=config['references'][pfamily]['FREECLENGTHS'],chroms=config['references'][pfamily]['FREECCHROMS'],pile=config['references'][pfamily]['FREECPILEUP'],snps=config['references'][pfamily]['FREECSNPS'],rname="pl:freec"
shell: "mkdir -p freec_out; mkdir -p freec_out/pass1; mkdir -p freec_out/pass1/{params.tumorsample}; perl Scripts/make_freec_pass1_exome_tn_config.pl {params.dir}/freec_out/pass1/{params.tumorsample} {params.lengths} {params.chroms} {params.dir}/{input.tumor} {params.dir}/{input.normal} {params.pile} {params.fasta} {params.snps} {input.freectargets}; module load freec/11.5; module load samtools/1.9; module load bedtools/2.27.1; freec -conf {params.dir}/freec_out/pass1/{params.tumorsample}/freec_exome_config.txt; mv {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass1/{output.cnvs}"
shell: "mkdir -p freec_out; mkdir -p freec_out/pass1; mkdir -p freec_out/pass1/{params.tumorsample}; perl Scripts/make_freec_pass1_exome_tn_config.pl {params.dir}/freec_out/pass1/{params.tumorsample} {params.lengths} {params.chroms} {params.dir}/{input.tumor} {params.dir}/{input.normal} {params.pile} {params.fasta} {params.snps} {input.freectargets}; module load freec/11.5; module load samtools/1.9; module load bedtools/2.27.1; freec -conf {params.dir}/freec_out/pass1/{params.tumorsample}/freec_exome_config.txt; mv {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {output.cnvs}"
4 changes: 2 additions & 2 deletions Rules/freec_exome_somatic_pass2.rl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ if config['project']['annotation'] == "hg19":
freectargets=config['project']['workpath']+"/freec_targets.bed",
output: cnvs="freec_out/pass2/{x}.recal.bam_CNVs",
params: dir=config['project']['workpath'],fasta=config['references'][pfamily]['FREECFASTA'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],lengths=config['references'][pfamily]['FREECLENGTHS'],chroms=config['references'][pfamily]['FREECCHROMS'],pile=config['references'][pfamily]['FREECPILEUP'],snps=config['references'][pfamily]['FREECSNPS'],rname="pl:freec"
shell: "mkdir -p freec_out/pass2; mkdir -p freec_out/pass2/{params.tumorsample}; perl Scripts/make_freec_pass2_exome_tn_config.pl {params.dir}/freec_out/pass2/{params.tumorsample} {params.lengths} {params.chroms} {params.dir}/freec_out/{input.tumor} {params.dir}/freec_out/{input.normal} {params.pile} {params.fasta} {params.snps} {input.freectargets} {input.fit}; module load samtools/1.9; module load freec/11.5; module load bedtools/2.27.1; freec -conf {params.dir}/freec_out/pass2/{params.tumorsample}/freec_exome_config.txt; mv {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass2/{output.cnvs}"
shell: "mkdir -p freec_out/pass2; mkdir -p freec_out/pass2/{params.tumorsample}; perl Scripts/make_freec_pass2_exome_tn_config.pl {params.dir}/freec_out/pass2/{params.tumorsample} {params.lengths} {params.chroms} {params.dir}/freec_out/{input.tumor} {params.dir}/freec_out/{input.normal} {params.pile} {params.fasta} {params.snps} {input.freectargets} {input.fit}; module load samtools/1.9; module load freec/11.5; module load bedtools/2.27.1; freec -conf {params.dir}/freec_out/pass2/{params.tumorsample}/freec_exome_config.txt; mv {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {output.cnvs}"

else:
rule freec_exome_somatic_pass2:
Expand All @@ -18,4 +18,4 @@ else:
freectargets=config['project']['workpath']+"/freec_targets.bed",
output: cnvs="freec_out/pass2/{x}.recal.bam_CNVs",
params: dir=config['project']['workpath'],fasta=config['references'][pfamily]['FREECFASTA'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],lengths=config['references'][pfamily]['FREECLENGTHS'],chroms=config['references'][pfamily]['FREECCHROMS'],pile=config['references'][pfamily]['FREECPILEUP'],snps=config['references'][pfamily]['FREECSNPS'],rname="pl:freec"
shell: "mkdir -p freec_out; mkdir -p freec_out/pass2; mkdir -p freec_out/pass2/{params.normalsample}+{params.tumorsample}; perl Scripts/make_freec_pass2_exome_tn_config.pl {params.dir}/freec_out/pass2/{params.normalsample}+{params.tumorsample} {params.lengths} {params.chroms} {params.dir}/{input.tumor} {params.dir}/{input.normal} {params.pile} {params.fasta} {params.snps} {input.freectargets} {input.fit}; module load freec/11.5; module load samtools/1.9; module load bedtools/2.27.1; freec -conf {params.dir}/freec_out/pass2/{params.tumorsample}/freec_exome_config.txt; mv {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass2/{output.cnvs}"
shell: "mkdir -p freec_out; mkdir -p freec_out/pass2; mkdir -p freec_out/pass2/{params.normalsample}+{params.tumorsample}; perl Scripts/make_freec_pass2_exome_tn_config.pl {params.dir}/freec_out/pass2/{params.normalsample}+{params.tumorsample} {params.lengths} {params.chroms} {params.dir}/{input.tumor} {params.dir}/{input.normal} {params.pile} {params.fasta} {params.snps} {input.freectargets} {input.fit}; module load freec/11.5; module load samtools/1.9; module load bedtools/2.27.1; freec -conf {params.dir}/freec_out/pass2/{params.tumorsample}/freec_exome_config.txt; mv {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {output.cnvs}"

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