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Run only for 'hg19' or 'hg38'
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Snakemake complains of missing key "FREECFASTA" since it is not defined in mm10.json.

So I'm removing the else statement to prevent this rule from running when the genome is mm10; replacing with 'elif' or a new 'if' statement for the sequenza rule.
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@mtandon09 @skchronicles
mtandon09 authored and skchronicles committed Apr 29, 2020
1 parent ab60840 commit 4142003
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Showing 3 changed files with 13 additions and 12 deletions.
6 changes: 3 additions & 3 deletions Rules/freec_exome_somatic_pass1.rl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ if config['project']['annotation'] == "hg19":
freectargets=config['project']['workpath']+"/freec_targets.bed",
output: cnvs="freec_out/pass1/{x}.recal.bam_CNVs.p.value.txt",
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; module load R; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/assess_significance.R | R --slave --args {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt; mv {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs.p.value.txt {output.cnvs}; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/makeGraph.R | R --slave --args 2 {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_BAF.txt"
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}; module load perl/5.18.4; 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; module load R; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/assess_significance.R | R --slave --args {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt; mv {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs.p.value.txt {output.cnvs}; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/makeGraph.R | R --slave --args 2 {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_BAF.txt"

else:
elif config['project']['annotation'] == "hg38":
rule freec_exome_somatic_pass1:
input: normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
Expand All @@ -18,4 +18,4 @@ else:
freectargets=config['project']['workpath']+"/freec_targets.bed",
output: cnvs="freec_out/pass1/{x}.recal.bam_CNVs.p.value.txt",
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; module load R; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/assess_significance.R | R --slave --args {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt; mv {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs.p.value.txt {output.cnvs}; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/makeGraph.R | R --slave --args 2 {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_BAF.txt"
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; module load R; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/assess_significance.R | R --slave --args {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt; mv {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs.p.value.txt {output.cnvs}; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/makeGraph.R | R --slave --args 2 {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt {params.dir}/freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_BAF.txt"
6 changes: 3 additions & 3 deletions Rules/freec_exome_somatic_pass2.rl
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,9 @@ if config['project']['annotation'] == "hg19":
freectargets=config['project']['workpath']+"/freec_targets.bed",
output: cnvs="freec_out/pass2/{x}.recal.bam_CNVs.p.value.txt",
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; module load R; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/assess_significance.R | R --slave --args {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt; mv {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs.p.value.txt {output.cnvs}; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/makeGraph.R | R --slave --args 2 {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_BAF.txt"
shell: "mkdir -p freec_out/pass2; mkdir -p freec_out/pass2/{params.tumorsample}; module load perl/5.18.4; 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; module load R; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/assess_significance.R | R --slave --args {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt; mv {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs.p.value.txt {output.cnvs}; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/makeGraph.R | R --slave --args 2 {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_BAF.txt"

else:
elif config['project']['annotation'] == "hg38":
rule freec_exome_somatic_pass2:
input: normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
Expand All @@ -18,4 +18,4 @@ else:
freectargets=config['project']['workpath']+"/freec_targets.bed",
output: cnvs="freec_out/pass2/{x}.recal.bam_CNVs.p.value.txt",
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.tumorsample}; perl Scripts/make_freec_pass2_exome_tn_config.pl {params.dir}/freec_out/pass2/{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; module load R; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/assess_significance.R | R --slave --args {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt; mv {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs.p.value.txt {output.cnvs}; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/makeGraph.R | R --slave --args 2 {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_BAF.txt"
shell: "mkdir -p freec_out; 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}/{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; module load R; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/assess_significance.R | R --slave --args {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt; mv {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_CNVs.p.value.txt {output.cnvs}; cat /data/CCBR_Pipeliner/db/PipeDB/bin/FREEC/scripts/makeGraph.R | R --slave --args 2 {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_ratio.txt {params.dir}/freec_out/pass2/{params.tumorsample}/{params.tumorsample}.recal.bam_BAF.txt"
13 changes: 7 additions & 6 deletions Rules/sequenza.rl
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
rule sequenza:
input: freeccnvs="freec_out/pass1/{x}.recal.bam_CNVs.p.value.txt",
output: fit="sequenza_out/{x}"+"_alternative_solutions.txt",
params: dir=config['project']['workpath'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],gc=config['references'][pfamily]['SEQUENZAGC'],rname="pl:sequenza"
threads: 8
shell: "mkdir -p sequenza_out; mkdir -p sequenza_out/{params.tumorsample}; module load sequenza-utils/2.2.0; module load samtools/1.9; gzip -c freec_out/pass1/{params.tumorsample}/{params.normalsample}.recal.bam_minipileup.pileup > sequenza_out/{params.tumorsample}/{params.normalsample}.recal.bam_minipileup.pileup.gz; gzip -c freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_minipileup.pileup > sequenza_out/{params.tumorsample}/{params.tumorsample}.recal.bam_minipileup.pileup.gz; sequenza-utils bam2seqz -p -gc {params.gc} -n sequenza_out/{params.tumorsample}/{params.normalsample}.recal.bam_minipileup.pileup.gz -t sequenza_out/{params.tumorsample}/{params.tumorsample}.recal.bam_minipileup.pileup.gz | gzip > sequenza_out/{params.tumorsample}/{params.tumorsample}.seqz.gz; sequenza-utils seqz_binning -w 100 -s sequenza_out/{params.tumorsample}/{params.tumorsample}.seqz.gz | gzip > sequenza_out/{params.tumorsample}/{params.tumorsample}.bin100.seqz.gz; module load R/3.5; Rscript Scripts/run_sequenza.R sequenza_out/{params.tumorsample}/{params.tumorsample}.bin100.seqz.gz {params.dir}/sequenza_out/{params.tumorsample} {threads} {params.normalsample}+{params.tumorsample}; mv {params.dir}/sequenza_out/{params.tumorsample}/{params.normalsample}+{params.tumorsample}_alternative_solutions.txt {output.fit}"
if config['project']['annotation'] == "hg19" or config['project']['annotation'] == "hg38":
rule sequenza:
input: freeccnvs="freec_out/pass1/{x}.recal.bam_CNVs.p.value.txt",
output: fit="sequenza_out/{x}"+"_alternative_solutions.txt",
params: dir=config['project']['workpath'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],gc=config['references'][pfamily]['SEQUENZAGC'],rname="pl:sequenza"
threads: 8
shell: "mkdir -p sequenza_out; mkdir -p sequenza_out/{params.tumorsample}; module load sequenza-utils/2.2.0; module load samtools/1.9; gzip -c freec_out/pass1/{params.tumorsample}/{params.normalsample}.recal.bam_minipileup.pileup > sequenza_out/{params.tumorsample}/{params.normalsample}.recal.bam_minipileup.pileup.gz; gzip -c freec_out/pass1/{params.tumorsample}/{params.tumorsample}.recal.bam_minipileup.pileup > sequenza_out/{params.tumorsample}/{params.tumorsample}.recal.bam_minipileup.pileup.gz; sequenza-utils bam2seqz -p -gc {params.gc} -n sequenza_out/{params.tumorsample}/{params.normalsample}.recal.bam_minipileup.pileup.gz -t sequenza_out/{params.tumorsample}/{params.tumorsample}.recal.bam_minipileup.pileup.gz | gzip > sequenza_out/{params.tumorsample}/{params.tumorsample}.seqz.gz; sequenza-utils seqz_binning -w 100 -s sequenza_out/{params.tumorsample}/{params.tumorsample}.seqz.gz | gzip > sequenza_out/{params.tumorsample}/{params.tumorsample}.bin100.seqz.gz; module load R/3.5; Rscript Scripts/run_sequenza.R sequenza_out/{params.tumorsample}/{params.tumorsample}.bin100.seqz.gz {params.dir}/sequenza_out/{params.tumorsample} {threads} {params.normalsample}+{params.tumorsample}; mv {params.dir}/sequenza_out/{params.tumorsample}/{params.normalsample}+{params.tumorsample}_alternative_solutions.txt {output.fit}"

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