Commit dc09e58d authored by Mathias Walzer's avatar Mathias Walzer
Browse files

fixed report details for up(TransitionGroupPicker) and down(Rmd render cwd) stream nextflows

parent 73952d74
......@@ -30,9 +30,9 @@ if (is.null(opt$tric) || is.null(opt$annot) ){
source("/scripts/OpenSWATHtoMSstatsFormat.R")
library(data.table)
library(MSstats)
print ("Loading tric file...")
raw.openMS <- read.csv(opt$tric,
sep= "\t",
......@@ -53,6 +53,7 @@ print("Run MSstats analysis...")
goldstandard.proposed <-dataProcess(input.openms,
normalization=FALSE,
summaryMethod="TMP",
featureSubset="top3",
cutoffCensored="minFeature",
censoredInt="0",
MBimpute=TRUE,
......
......@@ -29,6 +29,7 @@ library(patchwork)
source('/scripts/DIA_downstream_datacarpentry.R')
```
# N.B.: the directory of wherever this rmd is in will be the working directory by default! e.g. /tmp/this.rmd will operate in /tmp/ and _not_ from where the Rcmd is being called from
```{r, echo=FALSE}
#Annotations still needed for plots and tables
annot <- read.csv(params$ann,
......
......@@ -95,8 +95,9 @@ process rdaMSSTATS {
script:
"""
cp /scripts/DIA_downstream_report.rmd /tmp/
Rscript --vanilla -e "rmarkdown::render('/tmp/DIA_downstream_report.rmd', params = list(rda = '${rda_file}', ann = '${annotation}', pxdid = '${params.descriptor}') )"
# N.B.: the directory of wherever this rmd is in will be the working directory by default! e.g. /tmp/this.rmd will operate in /tmp/ and _not_ from where the Rcmd is being called from
cp /scripts/DIA_downstream_report.rmd .
Rscript --vanilla -e "rmarkdown::render('DIA_downstream_report.rmd', params = list(rda = '${rda_file}', ann = '${annotation}', pxdid = '${params.descriptor}') )"
"""
// no direct knit from /script/DIA_downstream_report.rmd - read-only filesystem
// also means all output is being routed to /tmp/
......
......@@ -339,7 +339,10 @@ process mzmlOSW {
-ppm_irtwindow \
-rt_extraction_window $params.openswath.rt_extraction_window \
-Scoring:stop_report_after_feature 5 \
-Scoring:TransitionGroupPicker:compute_peak_quality false
-Scoring:TransitionGroupPicker:compute_peak_quality true \
-Scoring:TransitionGroupPicker:compute_peak_shape_metrics \
-Scoring:TransitionGroupPicker:background_subtraction ${params.openswath.background_subtraction} \
-Scoring:TransitionGroupPicker:min_peak_width ${params.openswath.min_peak_width}
rm -rf ${params.out_dir}/tmp_cache/${mzML_file.baseName}
"""
else
......@@ -366,7 +369,10 @@ process mzmlOSW {
-ppm_irtwindow \
-rt_extraction_window $params.openswath.rt_extraction_window \
-Scoring:stop_report_after_feature 5 \
-Scoring:TransitionGroupPicker:compute_peak_quality false
-Scoring:TransitionGroupPicker:compute_peak_quality true \
-Scoring:TransitionGroupPicker:compute_peak_shape_metrics \
-Scoring:TransitionGroupPicker:background_subtraction ${params.openswath.background_subtraction} \
-Scoring:TransitionGroupPicker:min_peak_width ${params.openswath.min_peak_width}
rm -rf ${params.out_dir}/tmp_cache/${mzML_file.baseName}
"""
// 2.5 only: Unknown option(s) '[x_ -ms1_isotopes, r_ -irt_mz_extraction_window_unit, r_ -mz_extraction_window_ms1_unit, x_ -mz_extraction_window_ms1, x_ -mz_extraction_window_unit]' // x: deleted r: replacement
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment