Fix conditional and path joining. GooglingTheCancerGenome#76

Author: Arnold Kuzniar

workflow/Snakefile

@@ -7,7 +7,7 @@
 from helper_functions import *
 
 __author__ = "Arnold Kuzniar"
-__version__ = "1.2.0"
+__version__ = "1.2.1"
 __license__ = "Apache License, Version 2.0"
 
 

workflow/rules/delly.smk

@@ -10,7 +10,8 @@ rule delly_p:  # paired-samples analysis
         excl_opt='-x "%s"' % get_bed() if exclude_regions() else "",
     output:
         os.path.join(
-            "{path}/{tumor}--{normal}",
+            "{path}",
+            "{tumor}--{normal}",
             get_outdir("delly"),
             "delly-{}{}".format("{sv_type}", config.file_exts.bcf),
         ),
@@ -80,7 +81,8 @@ rule delly_s:  # single-sample analysis
         excl_opt='-x "%s"' % get_bed() if exclude_regions() else "",
     output:
         os.path.join(
-            "{path}/{sample}",
+            "{path}",
+            "{sample}",
             get_outdir("delly"),
             "delly-{}{}".format("{sv_type}", config.file_exts.bcf),
         ),
@@ -130,30 +132,34 @@ rule delly_merge:  # used by both modes
     input:
         [
             os.path.join(
-                "{path}/{tumor}--{normal}",
+                "{path}",
+                "{tumor}--{normal}",
                 get_outdir("delly"),
                 "delly-{}{}".format(sv, config.file_exts.bcf),
             )
             for sv in config.callers.delly.sv_types
         ]
-        if config.mode.PAIRED_SAMPLE is True
+        if config.mode is config.mode.PAIRED_SAMPLE
         else [
             os.path.join(
-                "{path}/{sample}",
+                "{path}",
+                "{sample}",
                 get_outdir("delly"),
                 "delly-{}{}".format(sv, config.file_exts.bcf),
             )
             for sv in config.callers.delly.sv_types
         ],
     output:
         os.path.join(
-            "{path}/{tumor}--{normal}",
+            "{path}",
+            "{tumor}--{normal}",
             get_outdir("delly"),
             "delly{}".format(config.file_exts.vcf),
         )
-        if config.mode.PAIRED_SAMPLE is True
+        if config.mode is config.mode.PAIRED_SAMPLE
         else os.path.join(
-            "{path}/{sample}",
+            "{path}",
+            "{sample}",
             get_outdir("delly"),
             "delly{}".format(config.file_exts.vcf),
         ),

workflow/rules/gridss.smk

@@ -10,7 +10,8 @@ rule gridss_p:  # paired-samples analysis
         excl_opt="BLACKLIST={}".format(get_bed()) if exclude_regions() else "",
     output:
         os.path.join(
-            "{path}/{tumor}--{normal}",
+            "{path}",
+            "{tumor}--{normal}",
             get_outdir("gridss"),
             "gridss{}".format(config.file_exts.vcf),
         ),
@@ -76,7 +77,8 @@ rule gridss_s:  # single-sample analysis
         excl_opt="BLACKLIST={}".format(get_bed()) if exclude_regions() else "",
     output:
         os.path.join(
-            "{path}/{sample}",
+            "{path}",
+            "{sample}",
             get_outdir("gridss"),
             "gridss{}".format(config.file_exts.vcf),
         ),

workflow/rules/lumpy.smk

@@ -10,7 +10,8 @@ rule lumpy_p:  # paired-samples analysis
         excl_opt='-x "%s"' % get_bed() if exclude_regions() else "",
     output:
         os.path.join(
-            "{path}/{tumor}--{normal}",
+            "{path}",
+            "{tumor}--{normal}",
             get_outdir("lumpy"),
             "lumpy{}".format(config.file_exts.vcf),
         ),
@@ -64,7 +65,8 @@ rule lumpy_s:  # single-sample analysis
         excl_opt='-x "%s"' % get_bed() if exclude_regions() else "",
     output:
         os.path.join(
-            "{path}/{sample}",
+            "{path}",
+            "{sample}",
             get_outdir("lumpy"),
             "lumpy{}".format(config.file_exts.vcf),
         ),

workflow/rules/manta.smk

@@ -11,7 +11,8 @@ rule manta_p:  # paired-samples analysis
         outfile="results/variants/somaticSV.vcf.gz",
     output:
         os.path.join(
-            "{path}/{tumor}--{normal}",
+            "{path}",
+            "{tumor}--{normal}",
             get_outdir("manta"),
             "manta{}".format(config.file_exts.vcf),
         ),
@@ -66,7 +67,8 @@ rule manta_s:  # single-sample analysis: germline or tumor-only
         else "results/variants/diploidSV.vcf.gz",
     output:
         os.path.join(
-            "{path}/{sample}",
+            "{path}",
+            "{sample}",
             get_outdir("manta"),
             "manta{}".format(config.file_exts.vcf),
         ),

workflow/rules/survivor.smk

@@ -7,7 +7,7 @@ rule survivor_filter:  # used by both modes
             "viola",
             "{}{}".format("{prefix}", config.file_exts.vcf),
         )
-        if config.mode.PAIRED_SAMPLE is True
+        if config.mode is config.mode.PAIRED_SAMPLE
         else os.path.join(
             "{path}",
             "{sample}",
@@ -23,7 +23,7 @@ rule survivor_filter:  # used by both modes
             get_outdir("survivor"),
             "{}{}".format("{prefix}", config.file_exts.vcf),
         )
-        if config.mode.PAIRED_SAMPLE is True
+        if config.mode is config.mode.PAIRED_SAMPLE
         else os.path.join(
             "{path}",
             "{sample}",
@@ -69,7 +69,7 @@ rule survivor_merge:  # used by both modes
             )
             for c in config.enable_callers
         ]
-        if config.mode.PAIRED_SAMPLE is True
+        if config.mode is config.mode.PAIRED_SAMPLE
         else [
             os.path.join(
                 "{path}",
@@ -87,7 +87,7 @@ rule survivor_merge:  # used by both modes
             os.path.join("{path}", "{tumor}--{normal}", survivor_args("merge")[0]),
             os.path.join("{path}", "{tumor}--{normal}", survivor_args("merge")[-1]),
         ]
-        if config.mode.PAIRED_SAMPLE is True
+        if config.mode is config.mode.PAIRED_SAMPLE
         else [
             os.path.join("{path}", "{sample}", survivor_args("merge")[0]),
             os.path.join("{path}", "{sample}", survivor_args("merge")[-1]),

workflow/rules/viola.smk

@@ -6,7 +6,7 @@ rule viola:  # used by both modes
             "{outdir}",
             "{}{}".format("{prefix}", config.file_exts.vcf),
         )
-        if config.mode.PAIRED_SAMPLE is True
+        if config.mode is config.mode.PAIRED_SAMPLE
         else os.path.join(
             "{path}",
             "{sample}",
@@ -21,7 +21,7 @@ rule viola:  # used by both modes
             "viola",
             "{}{}".format("{prefix}", config.file_exts.vcf),
         )
-        if config.mode.PAIRED_SAMPLE is True
+        if config.mode is config.mode.PAIRED_SAMPLE
         else os.path.join(
             "{path}",
             "{sample}",