Expand dba rules (#44)

* feat: add cftoolkit v0.6.0 w rmarkdown

* fix: inherit from docker v0.5.0

* feat: move to static images for diff bind and uropa rules

* fix: rework diff bind and uropa scripts for modularity and new rules

* fix: fix hooks, split diff bind and uropa into multiple rule hierarchical rules

* chore: remove planned new docker version

* fix: full path for config

* fix: set cwd at rule instead of script

* fix: cd to output dir in diff bind rule

* fix: make sif cache aware of env

* fix: review changes

* fix: syntax error with rmarkdown::render

* fix: images not image

* fix: remove references to container sif files

* fix: pathing in rmarkdown and syntax in prep_diffbind

bin/DiffBind_v2_ChIPseq.Rmd

@@ -16,34 +16,44 @@ params:
 ---
 
 <style type="text/css">
-  body{
-  font-size: 12pt;
-}
+   body {
+      font-size: 12pt;
+   }
 </style>
 
 ```{r, include=FALSE, warning=FALSE, message=FALSE}
-## grab args
-dateandtime<-format(Sys.time(), "%a %b %d %Y - %X")
-
+# inputs
+dateandtime <- format(Sys.time(), "%a %b %d %Y - %X")
 csvfile <- params$csvfile
+outbase <- dirname(csvfile)
 contrasts <- params$contrasts
 peakcaller <- params$peakcaller
-```
 
-**Groups being compared:**
-    *`r contrasts`*  
-**Peak sources:**
-    *`r peakcaller`*  
-**Report generated:** 
-    *`r dateandtime`*  
+# file output suffixes
+cp_bed <- "_Diffbind_consensusPeaks.bed"
+edger_txt <- "_Diffbind_EdgeR.txt"
+deseq2_txt <- "_Diffbind_Deseq2.txt"
+edger_bed <- "_Diffbind_EdgeR.bed"
+deseq2_bed <- "_Diffbind_Deseq2.bed"
+deseq2_bed_fullist <- "_Diffbind_Deseq2_fullList.txt"
+edger_bed_fullist <- "_Diffbind_EdgeR_fullList.txt"
 
-```{r setup, echo=FALSE, warning=FALSE,message=FALSE}
+# knitr options
 knitr::opts_chunk$set(echo = FALSE, include=TRUE, message=FALSE, warning=FALSE, error=FALSE)
+
+# libraries
 suppressMessages(library(DT))
 suppressMessages(library(DiffBind))
 suppressMessages(library(parallel))
 ```
 
+**Groups being compared:**
+    *`r contrasts`*  
+**Peak sources:**
+    *`r peakcaller`*  
+**Report generated:** 
+    *`r dateandtime`* 
+
 # Peak Data
 Read in sample sheet information and peak information
 ```{r samples} 
@@ -88,13 +98,13 @@ if ( grepl("narrow",samples$samples$Peaks[1]) ) {
    print ("Narrow peak calling tool.")
    print ("Differential peaks are 250bp upstream and downstream of the summits.")
 } else if ( grepl("broad",samples$samples$Peaks[1]) ) {
-  summits <- FALSE
-  print ("Broad peak calling tool.")
-  print ("Differential peaks are consensus peaks.")
+   summits <- FALSE
+   print ("Broad peak calling tool.")
+   print ("Differential peaks are consensus peaks.")
 } else {
-  summits <- FALSE
-  print ("Indeterminate peak calling tool.")
-  print ("Differential peaks are consensus peaks.")
+   summits <- FALSE
+   print ("Indeterminate peak calling tool.")
+   print ("Differential peaks are consensus peaks.")
 }
 ```
 
@@ -105,9 +115,9 @@ if (summits == TRUE) {
 	DBdataCounts <- dba.count(samples)
 }
 print(DBdataCounts)
-outfile2 <- paste0(contrasts, "-", peakcaller,"_Diffbind_consensusPeaks.bed")
-consensus2 <- dba.peakset(DBdataCounts,bRetrieve=T)
-consensus2$name <- paste0("Peak",1:length(consensus2))
+outfile2 <- paste0(contrasts, "-", peakcaller, cp_bed)
+consensus2 <- dba.peakset(DBdataCounts, bRetrieve=T)
+consensus2$name <- paste0("Peak", 1:length(consensus2))
 #rtracklayer::export(consensus2,outfile2)
 ```
 
@@ -210,11 +220,24 @@ try(dba.plotHeatmap(DBAnalysisEdgeR,contrast=1,method = DBA_EDGER,correlations=F
 ## Top 500 differentially bound peaks {.tabset .tabset-fade}
 ### DeSeq2 {-}
 ```{r Deseq2Report}
-outfile <- paste0(contrasts, "-", peakcaller, "_Diffbind_Deseq2.txt")
-outfile2 <- paste0(contrasts, "-", peakcaller, "_Diffbind_Deseq2.bed")
+outfile <- paste0(contrasts, "-", peakcaller, deseq2_txt)
+outfile2 <- paste0(contrasts, "-", peakcaller, deseq2_bed)
 DBReportDeseq2$name <- paste0("Peak",1:length(DBReportDeseq2))
-try(rtracklayer::export(DBReportDeseq2, outfile2),silent=TRUE)
-write.table(DBReportDeseq2, outfile, quote=F, sep="\t", row.names=F)
+
+tryDeseqExport <- function(DBReportDeseq2, outfile2) {
+   tryCatch(
+      {
+         rtracklayer::export(DBReportDeseq2, outfile2)
+      },
+      error = function(cond) {
+         print("ERROR: Failed to export DeSeq bed file `rtracklayer::export(DBReportDeseq2, outfile2)`, output blank file")
+         write.table(outfile2, file='empty', col.names=FALSE)
+      }
+   )
+}
+
+tryDeseqExport(DBReportDeseq2, file.path(outbase, outfile2))
+write.table(DBReportDeseq2, file.path(outbase, outfile), quote=F, sep="\t", row.names=F)
 D2i <- length(DBReportDeseq2)
 if (D2i == 0) {
    i=1
@@ -226,17 +249,31 @@ if (D2i == 0) {
 try(DT::datatable(data.frame(DBReportDeseq2)[1:i,], rownames=F),silent=TRUE)
 
 report2 <- dba.report(DBAnalysisDeseq2,method = DBA_DESEQ2,th=100,bNormalized=T,bFlip=FALSE,precision=0,bCalled=T)
-outfile3 <- paste0(contrasts, "-", peakcaller, "_Diffbind_Deseq2_fullList.txt")
-write.table(report2, outfile3, quote=F, sep="\t", row.names=F)
+outfile3 <- paste0(contrasts, "-", peakcaller, deseq2_bed_fullist)
+write.table(report2, file.path(outbase, outfile3), quote=F, sep="\t", row.names=F)
 ```
 
 ### EdgeR {-}
 ```{r EdgeRReport}
-outfile <- paste0(contrasts, "-", peakcaller,"_Diffbind_EdgeR.txt")
-outfile2 <- paste0(contrasts, "-", peakcaller,"_Diffbind_EdgeR.bed")
+outfile <- paste0(contrasts, "-", peakcaller, edger_txt)
+outfile2 <- paste0(contrasts, "-", peakcaller, edger_bed)
 DBReportEdgeR$name <- paste0("Peak",1:length(DBReportEdgeR))
-try(rtracklayer::export(DBReportEdgeR, outfile2),silent=TRUE)
-write.table(DBReportEdgeR, outfile, quote=F, sep="\t", row.names=F)
+
+tryEdgeRExport <- function(edger_report, fout) {
+   tryCatch(
+      {
+         rtracklayer::export(edger_report, fout)
+      },
+      error = function(cond) {
+         print("ERROR: Failed to export EdgeR bed file `rtracklayer::export(edger_report, fout))`, output blank file")
+         write.table(fout, file='empty', col.names=FALSE)
+      }
+   )
+}
+
+tryEdgeRExport(DBReportEdgeR, file.path(outbase, outfile2))
+write.table(DBReportEdgeR, file.path(outbase, outfile), quote=F, sep="\t", row.names=F)
+
 Ei <- length(DBReportEdgeR)
 if (Ei == 0) {
    i=1
@@ -248,8 +285,8 @@ if (Ei == 0) {
 try(DT::datatable(data.frame(DBReportEdgeR)[1:i,], rownames=F),silent=TRUE)
 
 report2 <- dba.report(DBAnalysisEdgeR,method = DBA_EDGER,th=100,bNormalized=T,bFlip=FALSE,precision=0,bCalled=T)
-outfile3 <- paste0(contrasts, "-", peakcaller, "_Diffbind_EdgeR_fullList.txt")
-write.table(report2, outfile3, quote=F, sep="\t", row.names=F)
+outfile3 <- paste0(contrasts, "-", peakcaller, edger_bed_fullist)
+write.table(report2, file.path(outbase, outfile3), quote=F, sep="\t", row.names=F)
 ```
 
 ## R tool version information