updated STARfusion, fusioncatcher, and FusionInspector versions

CCBR · Aug 28, 2019 · 0d4e545 · 0d4e545
1 parent 525dc93
commit 0d4e545
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Showing 8 changed files with 10 additions and 16 deletions.
diff --git a/Rules/fusioncatcher.rl b/Rules/fusioncatcher.rl
@@ -3,4 +3,4 @@ rule fusioncatcher:
      output: "fusioncatcher/{x}/final-list_candidate-fusion-genes.txt"
      params: data=config['references'][pfamily]['FUSCATCHDAT'],configfile=config['references'][pfamily]['FUSCATCHDAT'],rname='fusioncatcher',sample="{x}"
      threads: 16
-     shell: "module load fusioncatcher/1.00; mkdir -p fusioncatcher/{params.sample}; fusioncatcher -i {input.file1},{input.file2} -o fusioncatcher/{params.sample} -d {params.data} --threads {threads}"
+     shell: "module load fusioncatcher/1.10; mkdir -p fusioncatcher/{params.sample}; fusioncatcher -i {input.file1},{input.file2} -o fusioncatcher/{params.sample} --threads {threads}"
diff --git a/Rules/fusioninsp.rl b/Rules/fusioninsp.rl
@@ -2,4 +2,4 @@ rule rule fusioninsp:
      input:  starfusion="starfusion/{x}/star-fusion.fusion_predictions.tsv",fusioncatcher="fusioncatcher/fusioninspector/{x}/{x}_fusionInspector.input",file1="{x}.R1.trimmed.fastq.gz",file2="{x}.R2.trimmed.fastq.gz"
      output: "fusioninspector/{x}/{x}.fusion_predictions.final"
      params: rname='fusioninsp',sample="{x}",ref=config['project']['annotation'],starlib=config['references'][pfamily]['STARFUSIONLIB']
-     shell: "module load fusioninspector/1.1.0; module load STAR/2.6.1c; module load python/2.7; mkdir -p fusioninspector/{params.sample}; FusionInspector --fusions {input.starfusion},{input.fusioncatcher} --genome_lib {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --out_dir fusioninspector/{params.sample} --out_prefix {params.sample} --prep_for_IGV --CPU 16 --cleanup --annotate --examine_coding_effect"
+     shell: "module load fusioninspector/1.1.0; module load python/2.7; mkdir -p fusioninspector/{params.sample}; FusionInspector --fusions {input.starfusion},{input.fusioncatcher} --genome_lib {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --out_dir fusioninspector/{params.sample} --out_prefix {params.sample} --prep_for_IGV --CPU 16 --cleanup --annotate --examine_coding_effect"
diff --git a/Rules/fusioninsp_fuscatch.rl b/Rules/fusioninsp_fuscatch.rl
@@ -3,4 +3,4 @@ rule fusioninsp_fuscatch:
      output: "fusioncatcher/fusioninspector/{x}/{x}.fusion_predictions.final","fusioncatcher/fusioninspector/{x}/{x}_fusionInspector.input"
      params: rname='fusioninsp',sample="{x}",ref=config['project']['annotation'],starlib=config['references'][pfamily]['STARFUSIONLIB']
      threads: 8
-     shell: "module load fusioninspector/1.1.0; module load STAR/2.6.1c; module load python/2.7; mkdir -p fusioncatcher/fusioninspector/{params.sample}; perl Scripts/make_fusioninspector_input.pl {params.sample} {params.ref}; FusionInspector --fusions fusioncatcher/fusioninspector/{params.sample}/{params.sample}_fusionInspector.input --genome_lib {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --out_dir fusioncatcher/fusioninspector/{params.sample} --out_prefix {params.sample} --prep_for_IGV"
+     shell: "module load fusioninspector/1.1.0; module load python/2.7; mkdir -p fusioncatcher/fusioninspector/{params.sample}; perl Scripts/make_fusioninspector_input.pl {params.sample} {params.ref}; FusionInspector --fusions fusioncatcher/fusioninspector/{params.sample}/{params.sample}_fusionInspector.input --genome_lib {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --out_dir fusioncatcher/fusioninspector/{params.sample} --out_prefix {params.sample} --prep_for_IGV"
diff --git a/Rules/fusioninsp_starfus.rl b/Rules/fusioninsp_starfus.rl
@@ -2,4 +2,4 @@ rule rule fusioninsp_starfus:
      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 STAR/2.6.1c; 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"
+     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"
diff --git a/Rules/oncofuse.rl b/Rules/oncofuse.rl
@@ -1,4 +1,4 @@
-rule rule oncofuse:
+rule oncofuse:
      input:  fusions="fusioninspector/{x}/{x}.fusion_predictions.final"
      output: infile="oncofuse/{x}/{x}.oncofuse.input",outfile="oncofuse/{x}/{x}.oncofuse.output"
      params: rname='oncofuse',sample="{x}",oncofuse=config['bin'][pfamily]['ONCOFUSE'],build=config['references'][pfamily]['ONCOFUSEBUILD']

diff --git a/Rules/starfusion.rl b/Rules/starfusion.rl
@@ -2,4 +2,4 @@ rule starfusion:
      input:  file1="{x}.R1.trimmed.fastq.gz",file2="{x}.R2.trimmed.fastq.gz"
      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"
+     shell: "module load STAR-Fusion/1.6.0; 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"
diff --git a/hg19.json b/hg19.json
@@ -178,17 +178,11 @@
     "ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
     "ADMIXTUREREFS": "5",
     "ORGANISM": "HUMAN",
-#    "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
-#    "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/TruSeq_and_nextera_adapters_new.fa",
     "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
-#    "GTFFILE2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/gencode.v19.annotation.gtf",
     "FUSIONGTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/lib/GENCODE_GRCh37_ref_annot.gtf",
-#    "REFFLAT2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/refFlatHg19.txt",
-#    "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/human_gencode.transcripts.fa",
     "STARREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/Star_refs/hs37d5/genes-",
-#    "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/gencode.v19.annotation.gtf.rRNA.interval_list",
-    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir",
-    "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/1.00/fusioncatcher/data/human_v90",
+    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37_gencode_v19_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir",
+    "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/1.10/fusioncatcher/data/human_v95",
     "FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
     "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
     "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",

diff --git a/hg38.json b/hg38.json
@@ -178,8 +178,8 @@
      "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
      "STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
 #     "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26",
-    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir",
-    "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/1.00/fusioncatcher/data/human_v90",
+    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38_gencode_v31_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir",
+    "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/1.10/fusioncatcher/data/human_v95",
     "FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
     "GENOME": "/fdb/GENCODE/Gencode_human/release_26/GRCh38.primary_assembly.genome.fa",
 #    "INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",