Fixing STAR fusion perl issue

This is a separate perl error complaining about mismatched binary sizes of some modules, which can be fixed by explicitly loading the default Perl module (i.e. not the version Pipeliner normally uses).
CCBR · Apr 29, 2020 · 693d84a · 693d84a
1 parent ead71c0
commit 693d84a
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Showing 4 changed files with 13 additions and 6 deletions.
diff --git a/Rules/fusioninsp.rl b/Rules/fusioninsp.rl
@@ -1,5 +1,5 @@
-rule rule fusioninsp:
+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/2.7.0f; 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 STAR/2.7.0f; mkdir -p fusioninspector/{params.sample}; module load perl; 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/2.7.0f; 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 STAR/2.7.0f; mkdir -p fusioncatcher/fusioninspector/{params.sample}; module load perl; 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
@@ -1,5 +1,12 @@
-rule rule fusioninsp_starfus:
+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/2.7.0f; 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: """
+numfusions=$(grep -v ^# {input.fusions} | wc -l)
+if (( $numfusions > 0 )); then
+     module load fusioninspector/1.1.0; module load STAR/2.7.0f; mkdir -p starfusion/fusioninspector/{params.sample}; module load perl; 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
+else
+     touch {output};
+fi
+"""
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/1.6.0; module load STAR/2.7.0f; 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 16"
+     shell: "module load STAR-Fusion/1.6.0; module load STAR/2.7.0f; module load perl; 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 16"