gridss2 works #35 #69

GooglingTheCancerGenome · Sep 3, 2021 · fda5268 · fda5268
1 parent d2ad42e
commit fda5268
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Showing 3 changed files with 23 additions and 23 deletions.
diff --git a/snakemake/analysis.yaml b/snakemake/analysis.yaml
@@ -15,7 +15,7 @@ mode: p
 genome: data/fasta/chr22.fasta
 
 # filepath of the exclusion list in BED format
-exclusion_list: data/ENCFF001TDO.bed
+exclusion_list: data/ENCFF001TDO_chr22.bed
 exclude_regions: 1 # use the list (1) or don't (0)
 
 # file extensions used by the workflow

diff --git a/snakemake/data/ENCFF001TDO_chr22.bed b/snakemake/data/ENCFF001TDO_chr22.bed
@@ -0,0 +1,2 @@
+chr22	16847814	16862659	Satellite_repeat	1000	.
+chr22	18876789	18884510	Satellite_repeat	1000	.
diff --git a/snakemake/rules/gridss.smk b/snakemake/rules/gridss.smk
@@ -7,7 +7,7 @@ rule gridss_p:  # paired-samples analysis
         normal_bam = get_bam("{path}/{normal}"),
         normal_bai = get_bai("{path}/{normal}")
     params:
-        excl_opt = "BLACKLIST=" + get_bed() if exclude_regions() else ""
+        excl_opt = get_bed() if exclude_regions() else ""
     output:
         os.path.join("{path}/{tumor}--{normal}", get_outdir("gridss"),
                      "gridss" + get_filext("vcf"))
@@ -43,16 +43,15 @@ rule gridss_p:  # paired-samples analysis
         else
             # clean-up outdir prior to SV calling
             rm -fr ${{OUTDIR}}/*gridss* &&
-            gridss gridss.CallVariants \
-                WORKER_THREADS={threads} \
-                REFERENCE_SEQUENCE="{input.fasta}" \
-                {params.excl_opt} \
-                INPUT="{input.normal_bam}" \
-                INPUT="{input.tumor_bam}" \
-                OUTPUT="${{OUTFILE}}" \
-                ASSEMBLY="${{OUTDIR}}/gridss_assembly.bam" \
-                WORKING_DIR="${{TMP}}" \
-                TMP_DIR="${{TMP}}/gridss.${{RANDOM}}" &&
+            gridss \
+                -t {threads} \
+                -r "{input.fasta}" \
+                -o "${{OUTFILE}}" \
+		-b {params.excl_opt} \
+                -a "${{OUTDIR}}/gridss_assembly.bam" \
+                -w "${{TMP}}" \
+		"{input.tumor_bam}" \
+		"{input.normal_bam}" &&
             # somatic + SV quality filtering
             #   'normal' sample assumes index 0
             bcftools filter \
@@ -70,7 +69,7 @@ rule gridss_s:  # single-sample analysis
         bam = get_bam("{path}/{sample}"),
         bai = get_bai("{path}/{sample}")
     params:
-        excl_opt = "BLACKLIST=" + get_bed() if exclude_regions() else ""
+        excl_opt = get_bed() if exclude_regions() else ""
     output:
         os.path.join("{path}/{sample}", get_outdir("gridss"), "gridss" +
                      get_filext("vcf"))
@@ -106,16 +105,15 @@ rule gridss_s:  # single-sample analysis
         else
             # clean-up outdir prior to SV calling
             rm -fr ${{OUTDIR}}/*gridss* &&
-            gridss gridss.CallVariants \
-                WORKER_THREADS={threads} \
-                REFERENCE_SEQUENCE="{input.fasta}" \
-                {params.excl_opt} \
-                INPUT="{input.bam}" \
-                OUTPUT="${{OUTFILE}}" \
-                ASSEMBLY="${{OUTDIR}}/gridss_assembly.bam" \
-                WORKING_DIR="${{TMP}}" \
-                TMP_DIR="${{TMP}}/gridss.${{RANDOM}}" &&
-            # SV quality filtering
+            gridss \
+                -t {threads} \
+                -r "{input.fasta}" \
+                -o "${{OUTFILE}}" \
+                -b {params.excl_opt} \
+		-a "${{OUTDIR}}/gridss_assembly.bam" \
+                -w "${{TMP}}" \
+                "{input.bam}" &&
+	    # SV quality filtering
             bcftools filter \
                 -O v `# uncompressed VCF format` \
                 -o "{output}" \
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		chr22 16847814 16862659 Satellite_repeat 1000 .
		chr22 18876789 18884510 Satellite_repeat 1000 .