style: fix commas, spaces

CCBR · Feb 14, 2024 · 725dff4 · 725dff4
1 parent 9e46e45
commit 725dff4
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Showing 4 changed files with 16 additions and 13 deletions.
diff --git a/workflow/rules/annotations.smk b/workflow/rules/annotations.smk
@@ -329,6 +329,7 @@ if config["run_contrasts"] == "Y":
                 --rmd {params.rmd} \\
                 --carlisle_functions {params.carlisle_functions} \\
                 --Rlib_dir {params.Rlib_dir} \\
+                --Rpkg_config {params.Rpkg_config} \\
                 --output_dir {params.output_dir} \\
                 --report {output.html} \\
                 --peak_list "$clean_sample_list" \\

diff --git a/workflow/scripts/_diff_markdown_wrapper.R b/workflow/scripts/_diff_markdown_wrapper.R
@@ -78,9 +78,9 @@ if (debug){
   tmpdir="/dev/shm"
   gtf="~/../../Volumes/CCBR_Pipeliner/db/PipeDB/Indices/hs1/genes.gtf"
 } else {
-  carlisle_functions=args$carlisle_functions,
-  Rlib_dir=args$Rlib_dir,
-  Rpkg_config=args$Rpkg_config,
+  carlisle_functions=args$carlisle_functions
+  Rlib_dir=args$Rlib_dir
+  Rpkg_config=args$Rpkg_config
   rawcountsmatrix=args$countsmatrix
   coldata=args$sampleinfo
   dupstatus=args$dupstatus

diff --git a/workflow/scripts/_generate_spikein_wrapper.R b/workflow/scripts/_generate_spikein_wrapper.R
@@ -11,8 +11,6 @@ parser$add_argument("--Rlib_dir", type="character", required=TRUE,
           help="path to R lib directory")
 parser$add_argument("--Rpkg_config", type="character", required=TRUE, 
           help="path to package config")
-parser$add_argument("--sourcefile", type="character", required=TRUE,
-                    help="path to function file")
 parser$add_argument("--report", type="character", required=TRUE,
                     help = "HTML report")
 parser$add_argument("--bam_list", type="character", required=TRUE,
@@ -31,9 +29,9 @@ if (debug){
   bam_list="macs2/peak_output/53_H3K4me3_1_vs_nocontrol.dedup.broad.peaks.bed macs2/peak_output/53_H3K4me3_1_vs_nocontrol.dedup.narrow.peaks.bed macs2/peak_output/53_H3K4me3_2_vs_nocontrol.dedup.broad.peaks.bed macs2/peak_output/53_H3K4me3_2_vs_nocontrol.dedup.narrow.peaks.bed"
   spikein_control="NC_000913.3"
 } else {
-  carlisle_functions=args$carlisle_functions,
-  Rlib_dir=args$Rlib_dir,
-  Rpkg_config=args$Rpkg_config,
+  carlisle_functions=args$carlisle_functions
+  Rlib_dir=args$Rlib_dir
+  Rpkg_config=args$Rpkg_config
   sourcefile=args$sourcefile
   report=args$report
   bam_list=args$bam_list

diff --git a/workflow/scripts/_go_enrichment_wrapper.R b/workflow/scripts/_go_enrichment_wrapper.R
@@ -5,8 +5,12 @@ suppressPackageStartupMessages(library("argparse"))
 parser <- ArgumentParser()
 parser$add_argument("--rmd", type="character", required=TRUE,
                     help="path to rmd")
-parser$add_argument("--sourcefile", type="character", required=TRUE,
-                    help="path to function file")
+parser$add_argument("--carlisle_functions", type="character", required=TRUE, 
+          help="path to carlisle functions file")
+parser$add_argument("--Rlib_dir", type="character", required=TRUE, 
+          help="path to R lib directory")
+parser$add_argument("--Rpkg_config", type="character", required=TRUE, 
+          help="path to package config")
 parser$add_argument("--output_dir", type="character", required=FALSE,
                     help = "output_dir")
 parser$add_argument("--report", type="character", required=TRUE,
@@ -33,9 +37,9 @@ if (debug){
   geneset_id="GOBP"
   dedup_status="dedup"
 } else {
-  carlisle_functions=carlisle_functions,
-  Rlib_dir=Rlib_dir,
-  Rpkg_config=Rpkg_config,
+  carlisle_functions=args$carlisle_functions
+  Rlib_dir=args$Rlib_dir
+  Rpkg_config=args$Rpkg_config
   output_dir=args$output_dir
   report=args$report
   peak_list=args$peak_list