From bf2950de67f085c99ac011aee006d93d4dfbb704 Mon Sep 17 00:00:00 2001 From: jlac Date: Thu, 20 Sep 2018 22:30:35 -0400 Subject: [PATCH] repaired starfusion bug and hg38 exome somatic only bug --- Rules/all-rnafusion.rl | 6 +++--- Rules/all-wgslow.rl | 34 ++++++++++++++++++++++++++++++++-- Rules/fusioninsp_starfus.rl | 2 +- Rules/qualimap.rl | 2 +- Rules/qualimap_wgs.rl | 2 +- Rules/starfusion.rl | 2 +- hg38.json | 5 +++-- rules.json | 15 ++++++++------- 8 files changed, 50 insertions(+), 18 deletions(-) diff --git a/Rules/all-rnafusion.rl b/Rules/all-rnafusion.rl index 0de497f..c510a46 100644 --- a/Rules/all-rnafusion.rl +++ b/Rules/all-rnafusion.rl @@ -21,7 +21,7 @@ if config['project']['annotation'] == "hg19": expand("fusioncatcher/{x}/final-list_candidate-fusion-genes.txt",x=samples), expand("starfusion/fusioninspector/{x}/{x}.fusion_predictions.final",x=samples), expand("fusioncatcher/fusioninspector/{x}/{x}.fusion_predictions.final",x=samples), - expand("starfusion/{x}/star-fusion.fusion_candidates.final",x=samples), + expand("starfusion/{x}/star-fusion.fusion_predictions.tsv",x=samples), expand("{name}.RnaSeqMetrics.txt",name=samples), # "expression/RawCountFile_genes_filtered.txt", # "expression/RawCountFile_junctions_filtered.txt", @@ -62,7 +62,7 @@ elif config['project']['annotation'] == "hg38": expand("fusioncatcher/{x}/final-list_candidate-fusion-genes.txt",x=samples), expand("starfusion/fusioninspector/{x}/{x}.fusion_predictions.final",x=samples), expand("fusioncatcher/fusioninspector/{x}/{x}.fusion_predictions.final",x=samples), - expand("starfusion/{x}/star-fusion.fusion_candidates.final",x=samples), + expand("starfusion/{x}/star-fusion.fusion_predictions.tsv",x=samples), expand("{name}.RnaSeqMetrics.txt",name=samples), # "expression/RawCountFile_genes_filtered.txt", # "expression/RawCountFile_junctions_filtered.txt", @@ -99,7 +99,7 @@ elif config['project']['annotation'] == "mm10": expand("fusioncatcher/{x}/final-list_candidate-fusion-genes.txt",x=samples), expand("starfusion/fusioninspector/{x}/{x}.fusion_predictions.final",x=samples), expand("fusioncatcher/fusioninspector/{x}/{x}.fusion_predictions.final",x=samples), - expand("starfusion/{x}/star-fusion.fusion_candidates.final",x=samples), + expand("starfusion/{x}/star-fusion.fusion_predictions.tsv",x=samples), expand("{name}.RnaSeqMetrics.txt",name=samples), # "expression/RawCountFile_genes_filtered.txt", # "expression/RawCountFile_junctions_filtered.txt", diff --git a/Rules/all-wgslow.rl b/Rules/all-wgslow.rl index 11585b5..6909058 100755 --- a/Rules/all-wgslow.rl +++ b/Rules/all-wgslow.rl @@ -16,6 +16,16 @@ if config['project']['annotation'] == "hg19": expand("{s}"+".g.vcf",s=samples), expand("canvas_out/{s}/CNV.vcf.gz", s=samples), "admixture_out/admixture_table.tsv", + expand("{s}.recal.bam",s=samples), + expand("QC/{s}.R1_fastqc.html",s=samples), +# expand("QC/{s}.R1."+config['project']['filetype']+"_filtered",s=samples), +# expand("{s}.R1.trimmed.fastq.bz2",s=samples), +# expand("QC/{s}.qualimapReport",s=samples), + expand("QC/{s}.{r}.trimmed_fastqc.html",s=samples,r=['R1','R1']), + expand("QC/{s}.{r}.trimmed_screen.txt",s=samples,r=['R1','R1']), + expand("QC/{s}.{r}.trimmed_screen.png",s=samples,r=['R1','R1']), + expand("QC/{s}_run_trimmomatic.err",s=samples), + expand("QC/{s}.qualimapReport/genome_results.txt",s=samples), output: params: rname="final" @@ -41,7 +51,17 @@ elif config['project']['annotation'] == "hg38": config['project']['workpath']+"/svaba_out/svaba.log", expand("{s}"+".g.vcf",s=samples), expand("canvas_out/{s}/CNV.vcf.gz", s=samples), - "admixture_out/admixture_table.tsv" + "admixture_out/admixture_table.tsv", + expand("{s}.recal.bam",s=samples), + expand("QC/{s}.R1_fastqc.html",s=samples), +# expand("QC/{s}.R1."+config['project']['filetype']+"_filtered",s=samples), +# expand("{s}.R1.trimmed.fastq.bz2",s=samples), +# expand("QC/{s}.qualimapReport",s=samples), + expand("QC/{s}.{r}.trimmed_fastqc.html",s=samples,r=['R1','R1']), + expand("QC/{s}.{r}.trimmed_screen.txt",s=samples,r=['R1','R1']), + expand("QC/{s}.{r}.trimmed_screen.png",s=samples,r=['R1','R1']), + expand("QC/{s}_run_trimmomatic.err",s=samples), + expand("QC/{s}.qualimapReport/genome_results.txt",s=samples), output: params: rname="final" @@ -66,7 +86,17 @@ elif config['project']['annotation'] == "mm10": config['project']['workpath']+"/delly_out/insertions.bcf", config['project']['workpath']+"/svaba_out/svaba.log", expand("canvas_out/{s}/CNV.vcf.gz", s=samples), - "admixture_out/admixture_table.tsv" + "admixture_out/admixture_table.tsv", + expand("{s}.recal.bam",s=samples), + expand("QC/{s}.R1_fastqc.html",s=samples), +# expand("QC/{s}.R1."+config['project']['filetype']+"_filtered",s=samples), +# expand("{s}.R1.trimmed.fastq.bz2",s=samples), +# expand("QC/{s}.qualimapReport",s=samples), + expand("QC/{s}.{r}.trimmed_fastqc.html",s=samples,r=['R1','R1']), + expand("QC/{s}.{r}.trimmed_screen.txt",s=samples,r=['R1','R1']), + expand("QC/{s}.{r}.trimmed_screen.png",s=samples,r=['R1','R1']), + expand("QC/{s}_run_trimmomatic.err",s=samples), + expand("QC/{s}.qualimapReport/genome_results.txt",s=samples), output: params: rname="final" shell: """ diff --git a/Rules/fusioninsp_starfus.rl b/Rules/fusioninsp_starfus.rl index e8d579a..b2d52ab 100644 --- a/Rules/fusioninsp_starfus.rl +++ b/Rules/fusioninsp_starfus.rl @@ -1,5 +1,5 @@ rule rule fusioninsp_starfus: - input: fusions="starfusion/{x}/star-fusion.fusion_candidates.final",file1="{x}.R1.trimmed.fastq.gz",file2="{x}.R2.trimmed.fastq.gz" + input: fusions="starfusion/{x}/star-fusion.fusion_predictions.tsv",file1="{x}.R1.trimmed.fastq.gz",file2="{x}.R2.trimmed.fastq.gz" output: "starfusion/fusioninspector/{x}/{x}.fusion_predictions.final" params: rname='fusioninsp',sample="{x}",starlib=config['references'][pfamily]['STARFUSIONLIB'] shell: "module load fusioninspector/1.1.0; module load python/2.7; mkdir -p starfusion/fusioninspector/{params.sample}; FusionInspector --fusions {input.fusions} --genome_lib {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --out_dir starfusion/fusioninspector/{params.sample} --out_prefix {params.sample} --prep_for_IGV" \ No newline at end of file diff --git a/Rules/qualimap.rl b/Rules/qualimap.rl index 27c8f05..ee1279c 100755 --- a/Rules/qualimap.rl +++ b/Rules/qualimap.rl @@ -1,5 +1,5 @@ rule qualimap: - input: bam="{x}.dedup.bam", + input: bam="{x}.recal.bam", bed=config['project']['workpath']+"/exome_targets.bed" output: dir="QC/{x}.qualimapReport",txt="QC/{x}.qualimapReport/genome_results.txt" threads: 8 diff --git a/Rules/qualimap_wgs.rl b/Rules/qualimap_wgs.rl index 1241953..bb136fb 100755 --- a/Rules/qualimap_wgs.rl +++ b/Rules/qualimap_wgs.rl @@ -1,5 +1,5 @@ rule qualimap_wgs: - input: "{x}.dedup.bam" + input: "{x}.recal.bam" output: "QC/{x}.qualimapReport","QC/{x}.qualimapReport/genome_results.txt" threads: 8 params: qualimap=config['bin'][pfamily]['QUALIMAP'],organism=config['references'][pfamily]['ORGANISM'],rname="pl:wgs_qualimap" diff --git a/Rules/starfusion.rl b/Rules/starfusion.rl index 81a7735..9d14b0d 100644 --- a/Rules/starfusion.rl +++ b/Rules/starfusion.rl @@ -1,5 +1,5 @@ rule starfusion: input: file1="{x}.R1.trimmed.fastq.gz",file2="{x}.R2.trimmed.fastq.gz" - output: "starfusion/{x}/star-fusion.fusion_candidates.final" + output: "starfusion/{x}/star-fusion.fusion_predictions.tsv" params: rname='starfusion',sample="{x}",starlib=config['references'][pfamily]['STARFUSIONLIB'] shell: "module load STAR-Fusion/1.3.2; module load STAR/2.5.4a; mkdir -p starfusion/{params.sample}; STAR-Fusion --genome_lib_dir {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --output_dir starfusion/{params.sample} --CPU 32" \ No newline at end of file diff --git a/hg38.json b/hg38.json index c949411..660e1d6 100755 --- a/hg38.json +++ b/hg38.json @@ -8,7 +8,7 @@ "CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch38.bed", "INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz", # "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_g1k_v37_iupac.nix", -# "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/reformatS04380219_qualimap.bed", + "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/reformatS04380219_qualimap.bed", "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz", "ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt", "ADMIXTUREREFS": "5", @@ -79,7 +79,7 @@ "CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_refFlat.txt", "INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz", # "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_g1k_v37_iupac.nix", -# "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/reformatS04380219_qualimap.bed", + "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/reformatS04380219_qualimap.bed", "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz", "ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt", "ADMIXTUREREFS": "5", @@ -130,6 +130,7 @@ "VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/ExAC_nonTCGA.r0.3.1.sites.vep.GRCh38.vcf.gz", "VEPGENOME": "/fdb/VEP/88/cache/GRCh38.fa", "CANVASGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/WholeGenomeFasta", + "CANVASPLOIDY": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_knownPloidy_hg19.vcf", "CANVASKMER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/kmer.fa", "CANVASFILTER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/filter13.bed", "CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_refFlat.txt", diff --git a/rules.json b/rules.json index 6a59781..d6501b8 100755 --- a/rules.json +++ b/rules.json @@ -1,6 +1,7 @@ { "rules": { "avia": ["wgslow","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","rnaseqvargerm"], + "index_bams": ["wgslow","exomeseq-germline","wgs-somatic-tumoronly","exomeseq-somatic-tumoronly","wgs-somatic","exomeseq-somatic"], "rnaseqforfusions": ["rnaseqfusion"], "rnafusioncleanup": ["none"], "vcf2maf": ["exomeseq-somatic","wgs-somatic"], @@ -31,11 +32,11 @@ "gatk_select_variants_rnaseqvar": ["rnaseqvargerm"], "gatk.merge.chrom": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","rnaseqvargerm"], "ngsqc": ["initialqc","initialqcgenomeseq","rnaseqvargerm"], - "fastqc.fastq": ["initialqc","initialqcgenomeseq"], + "fastqc.fastq": ["initialqc","initialqcgenomeseq","wgslow","exomeseq-germline","wgs-somatic-tumoronly","exomeseq-somatic-tumoronly","wgs-somatic","exomeseq-somatic"], "fastqc.rnaseqvar": ["rnaseqvargerm","rnaseqfusion"], - "bamstats": ["initialqc"], + "bamstats": ["initialqc","exomeseq-germline","exomeseq-somatic-tumoronly","exomeseq-somatic"], "make_target_files": ["initialqc","exomeseq-somatic","exomeseq-somatic-tumoronly","exomeseq-germline"], - "fastq_screen": ["initialqc","initialqcgenomeseq","rnaseqvargerm","rnaseqfusion"], + "fastq_screen": ["initialqc","initialqcgenomeseq","rnaseqvargerm","rnaseqfusion","wgslow","exomeseq-germline","wgs-somatic-tumoronly","exomeseq-somatic-tumoronly","wgs-somatic","exomeseq-somatic"], "multiqc": ["initialqc"], "multiqc_genomeseq": ["initialqcgenomeseq"], "alview": ["exomeseq-somatic"], @@ -62,13 +63,13 @@ "cnvkit_somatic_tumoronly": ["exomeseq-somatic-tumoronly"], "cnvkit_summary_tumoronly": ["exomeseq-somatic-tumoronly"], "delly_somatic": ["exomeseq-somatic","wgs-somatic"], - "fastqc.trimmed": ["initialqc","initialqcgenomeseq","rnaseqvargerm","rnaseqfusion"], - "trimmomatic": ["initialqc","initialqcgenomeseq","rnaseqvargerm","rnaseqfusion"], + "fastqc.trimmed": ["initialqc","initialqcgenomeseq","rnaseqvargerm","rnaseqfusion","wgslow","exomeseq-germline","wgs-somatic-tumoronly","exomeseq-somatic-tumoronly","wgs-somatic","exomeseq-somatic"], + "trimmomatic": ["initialqc","initialqcgenomeseq","rnaseqvargerm","rnaseqfusion","wgslow","exomeseq-germline","wgs-somatic-tumoronly","exomeseq-somatic-tumoronly","wgs-somatic","exomeseq-somatic"], "samtools.flagstats": ["none"], "samtools.flagstats.dedup": ["none"], "qualimap_rnaseqvar": ["rnaseqvargerm"], - "qualimap_wgs": ["initialqcgenomeseq"], - "qualimap": ["initialqc"], + "qualimap_wgs": ["initialqcgenomeseq","wgslow","wgs-somatic-tumoronly","wgs-somatic"], + "qualimap": ["initialqc","exomeseq-germline","exomeseq-somatic-tumoronly","exomeseq-somatic"], "bwa.mem": ["initialqc","initialqcgenomeseq"], "novocraft.novoalign": ["none"], "bwa.index.ref": ["none"],