From 725dff4e34a89194298e8fb7ba775480c7bb98ca Mon Sep 17 00:00:00 2001
From: slsevilla <slsevilla@gmail.com>
Date: Wed, 14 Feb 2024 17:47:29 -0500
Subject: [PATCH] style: fix commas, spaces

---
 workflow/rules/annotations.smk               |  1 +
 workflow/scripts/_diff_markdown_wrapper.R    |  6 +++---
 workflow/scripts/_generate_spikein_wrapper.R |  8 +++-----
 workflow/scripts/_go_enrichment_wrapper.R    | 14 +++++++++-----
 4 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/workflow/rules/annotations.smk b/workflow/rules/annotations.smk
index 46a3b10..aea50fe 100644
--- 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 "$clean_sample_list" \\
diff --git a/workflow/scripts/_diff_markdown_wrapper.R b/workflow/scripts/_diff_markdown_wrapper.R
index ec56c7a..2cf1493 100644
--- a/workflow/scripts/_diff_markdown_wrapper.R
+++ b/workflow/scripts/_diff_markdown_wrapper.R
@@ -78,9 +78,9 @@ if (debug){
   tmpdir="/dev/shm"
   gtf="~/../../Volumes/CCBR_Pipeliner/db/PipeDB/Indices/hs1/genes.gtf"
 } else {
-  carlisle_functions=args$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
index a5e1511..9f3c650 100644
--- 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
index e46e2ce..bfef30a 100644
--- 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