1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
|
Author: Steffen Moeller
Last-Update: 2020-08-24 16:20:02 +0200
Description: Use --selfContained=FALSE option in runDeseqReport.R
Index: pigx-rnaseq/pigx_rnaseq.py
===================================================================
--- pigx-rnaseq.orig/pigx_rnaseq.py
+++ pigx-rnaseq/pigx_rnaseq.py
@@ -503,4 +503,4 @@ rule report3:
log: os.path.join(LOG_DIR, "{analysis}.report.salmon.genes.log")
output:
os.path.join(OUTPUT_DIR, "report", '{analysis}.salmon.genes.deseq.report.html')
- shell: "{RSCRIPT_EXEC} {params.reportR} --logo={params.logo} --prefix='{wildcards.analysis}.salmon.genes' --reportFile={params.reportRmd} --countDataFile={input.counts} --colDataFile={input.coldata} --gtfFile={GTF_FILE} --caseSampleGroups='{params.case}' --controlSampleGroups='{params.control}' --covariates='{params.covariates}' --workdir={params.outdir} --organism='{ORGANISM}' >> {log} 2>&1"
+ shell: "{RSCRIPT_EXEC} {params.reportR} --logo={params.logo} --prefix='{wildcards.analysis}.salmon.genes' --reportFile={params.reportRmd} --countDataFile={input.counts} --colDataFile={input.coldata} --gtfFile={GTF_FILE} --caseSampleGroups='{params.case}' --controlSampleGroups='{params.control}' --covariates='{params.covariates}' --workdir={params.outdir} --organism='{ORGANISM}' --selfContained=FALSE >> {log} 2>&1"
Index: pigx-rnaseq/scripts/runDeseqReport.R
===================================================================
--- pigx-rnaseq.orig/scripts/runDeseqReport.R
+++ pigx-rnaseq/scripts/runDeseqReport.R
@@ -72,7 +72,7 @@ runReport <- function(reportFile,
organism,
prefix,
logo,
- selfContained = TRUE,
+ selfContained = FALSE,
quiet = FALSE) {
outFile <- paste0(prefix, '.deseq.report.html')
@@ -255,7 +255,8 @@ if(!("workdir" %in% argsDF$V1)) {
}
if(!("selfContained" %in% argsDF$V1)) {
- selfContained <- TRUE
+ warning("selfContained not set as argument - defaulting to FALSE")
+ selfContained <- FALSE
} else {
selfContained <- argsL$selfContained
}
|
