Merge pull request #376 from tovahmarkowitz/activeDev

Pipeliner 4.0: ChIP-seq Changes
CCBR · Nov 29, 2018 · 5953199 · 5953199
2 parents 4c6c5fb + 7666d42
commit 5953199
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Showing 13 changed files with 437 additions and 381 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,4 @@
 !.gitignore
 **/*~
 **/*.bak
+**/*.DS_Store
diff --git a/Results-template/.DS_Store b/Results-template/.DS_Store
diff --git a/Results-template/Scripts/.DS_Store b/Results-template/Scripts/.DS_Store
diff --git a/Rules/.DS_Store b/Rules/.DS_Store
diff --git a/Rules/ChIPseq.snakefile b/Rules/ChIPseq.snakefile
@@ -604,7 +604,7 @@ rule MACS2_narrow:
         rname='pl:MACS2_narrow:{group}:{name}',
         gsize=config['project']['gsize'],
         #Must use lambda function here (snakemake does not recogize wildcards.variablename in params section)
-        ctrl =  lambda wildcards :join(bam_dir, config['project']['peaks']['inputs'][wildcards.name], '.sorted.Q5DD.bam'),
+        ctrl =  lambda wildcards :join(bam_dir, str(config['project']['peaks']['inputs'][wildcards.name]) + '.sorted.Q5DD.bam'),
         genome=config['project']['annotation'],
 
     shell:
@@ -628,7 +628,7 @@ rule MACS2_broad:
         rname='pl:MACS2_broad:{group}:{name}',
         gsize=config['project']['gsize'],
         #Must use lambda function here (snakemake does not recogize wildcards.variablename in params section)
-        ctrl =  lambda wildcards :join(bam_dir, config['project']['peaks']['inputs'][wildcards.name], '.sorted.Q5DD.bam'),
+        ctrl =  lambda wildcards :join(bam_dir, str(config['project']['peaks']['inputs'][wildcards.name]) +  '.sorted.Q5DD.bam'),
         genome=config['project']['annotation'],
     shell:
         """
@@ -651,7 +651,7 @@ rule SICER :
         rname = "pl:SICER:{group}:{name}",
         #Must use lambda function here (snakemake does not recogize snakewildcards.variablename in params section)
         inputname = lambda wildcards : config['project']['peaks']['inputs'][wildcards.name],
-        ctrl =  lambda wildcards :join(bam_dir, config['project']['peaks']['inputs'][wildcards.name], '.sorted.Q5DD.bam'),
+        ctrl =  lambda wildcards :join(bam_dir, str(config['project']['peaks']['inputs'][wildcards.name]) + '.sorted.Q5DD.bam'),
         SICERDIR = "/usr/local/apps/sicer/1.1",
         genome = config['project']['annotation'],
     run:
@@ -705,7 +705,7 @@ rule GEM:
         readDist='/usr/local/apps/gem/3.0/Read_Distribution_default.txt',
         genome=config['references']['ChIPseq']['GENOMECHR'],
         #Must use lambda function here (snakemake does not recogize wildcards.variablename in params section)
-        ctrl =  lambda wildcards :join(bam_dir, config['project']['peaks']['inputs'][wildcards.name], '.sorted.Q5DD.bam'),
+        ctrl =  lambda wildcards :join(bam_dir, str(config['project']['peaks']['inputs'][wildcards.name]) + '.sorted.Q5DD.bam'),
     threads: 32
     shell:
         """
@@ -720,3 +720,4 @@ rule GEM:
         """
 
 
+