Merge pull request #344 from maxplanck-ie/ksikora_minor_fixe

Ksikora minor fixe
maxplanck-ie · Nov 27, 2018 · 1c4c344 · 1c4c344
2 parents 040a189 + 6b56c4c
commit 1c4c344
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Showing 4 changed files with 11 additions and 5 deletions.
diff --git a/snakePipes/shared/rscripts/WGBS_stats_report_template.Rmd b/snakePipes/shared/rscripts/WGBS_stats_report_template.Rmd
@@ -61,7 +61,7 @@ knitr::include_graphics(pval_plot)
 ```
 
 Features were filtered using a threshold on minimum absolute difference in mean methylation `r system('grep minAbsDiff ../WGBS.config.yaml',intern=TRUE)` as well as a threshold on maximum false discovery rate `r system('grep FDR ../WGBS.config.yaml',intern=TRUE)` to produce the list of statistically differentially methylated features.
-There were `r get_nrow_topTable(params$outdir,params$stat_category)` features passing these filters.
+There were `r ifelse(is.null(get_nrow_topTable(params$outdir,params$stat_category)),"no",get_nrow_topTable(params$outdir,params$stat_category))` features passing these filters.
 
 A volcano plot was produced to visualize the effect of threshold application onto the test results.
 

diff --git a/snakePipes/shared/rscripts/WGBSstats_functions.R b/snakePipes/shared/rscripts/WGBSstats_functions.R
@@ -29,6 +29,7 @@ get_nrow_filtered<-function(resdir,statscat){
     } else if (statscat %in% "user_intervals"){
         nrf<-unlist(lapply(dir(resdir,pattern="*.aggCpG.RData",full.names=TRUE),function(X){load(X);sprintf("%s (%s)",nrow(CGI.limdat.CC),gsub(".aggCpG.RData","",basename(X)))}))
     }
+    if(is.null(nrf)){nrf<-0}
     return(nrf)
 }
 
@@ -41,6 +42,7 @@ get_nrow_topTable<-function(resdir,statscat){
     } else if (statscat %in% "user_intervals"){
         nrtt<-unlist(lapply(dir(resdir,pattern="*.tT_filt.txt",full.names=TRUE),function(X)sprintf("%s (%s)",length(readLines(X)),gsub(".tT_filt.txt","",basename(X)))))
     }
+    if(is.null(nrtt)){nrtt<-0}
     return(nrtt)
 }
 

diff --git a/snakePipes/shared/rules/WGBS.snakefile b/snakePipes/shared/rules/WGBS.snakefile
@@ -540,7 +540,8 @@ if sampleSheet:
         input: 
             Limdat='{}/limdat.LG.RData'.format(get_outdir("singleCpG_stats_limma"))
         output:
-            RDatAll='{}/singleCpG.RData'.format(get_outdir("singleCpG_stats_limma"))
+            RDatAll='{}/singleCpG.RData'.format(get_outdir("singleCpG_stats_limma")),
+            sinfo='{}/sessionInfo.txt'.format(get_outdir("singleCpG_stats_limma"))
         params:
             statdir=os.path.join(outdir,'{}'.format(get_outdir("singleCpG_stats_limma"))),
             sampleSheet=sampleSheet,
@@ -558,7 +559,7 @@ if sampleSheet:
     rule CpG_report:
         input: 
             Limdat='{}/limdat.LG.RData'.format(get_outdir("singleCpG_stats_limma")),
-            RDatAll='{}/singleCpG.RData'.format(get_outdir("singleCpG_stats_limma"))
+            sinfo='{}/sessionInfo.txt'.format(get_outdir("singleCpG_stats_limma"))
         output:
             html='{}/Stats_report.html'.format(get_outdir("singleCpG_stats_limma"))
         params:
@@ -682,7 +683,8 @@ if intList:
                 sampleSheet=sampleSheet,
                 aux=run_int_aggStats(intList,False)
             output:
-                outFiles=run_int_aggStats(intList,sampleSheet)
+                outFiles=run_int_aggStats(intList,sampleSheet),
+                sinfo='{}/sessionInfo.txt'.format(get_outdir("aggregate_stats_limma"))
             params:
                 auxshell=lambda wildcards,input:';'.join(['Rscript --no-save --no-restore ' + os.path.join(workflow_rscripts,'WGBSpipe.interval_stats.limma.R ') + os.path.join(outdir,'{}'.format(get_outdir("aggregate_stats_limma"))) + ' ' + li +' '+ aui +' ' + os.path.join(outdir,input.Limdat) + ' '  + input.sampleSheet + ' ' + str(minAbsDiff) + ' ' + str(FDR) + ' ' + os.path.join(workflow_rscripts, "WGBSstats_functions.R")  for li,aui in zip(intList,[os.path.join(outdir,"aux_files",re.sub('.fa',re.sub('.bed','.CpGlist.bed',os.path.basename(x)),os.path.basename(refG))) for x in intList])])
             log:
@@ -695,7 +697,7 @@ if intList:
 
         rule intAgg_report:
             input: 
-                outFiles=run_int_aggStats(intList,sampleSheet)
+                outFiles='{}/sessionInfo.txt'.format(get_outdir("aggregate_stats_limma"))
             output:
                 html='{}/Stats_report.html'.format(get_outdir("aggregate_stats_limma"))
             params:

diff --git a/snakePipes/workflows/WGBS/cluster.yaml b/snakePipes/workflows/WGBS/cluster.yaml
@@ -12,6 +12,8 @@ downsample_reads:
     memory: 6G
 conv_rate:
     memory: 6G
+prep_for_stats:
+    memory: 30G
 CpG_stats:
     memory: 30G
 cleanup_metilene: