Print command line in QC pdf

Print command line on new page in QC pdf, and remove fasta and gtf info from cover (info is in command)
IGDRion · Nov 13, 2024 · c887300 · c887300
1 parent 0e4f952
commit c887300
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/bin/qc.R b/bin/qc.R
@@ -38,8 +38,7 @@ theme_set(
 args = commandArgs(trailingOnly=TRUE)
 prefix = args[1]
 ANNEXA_version = args[2]
-genome_ref = basename(args[3])
-gtf_ref = basename(args[4])
+command = args[3]
 
 #############################################################################
 # GENE level
@@ -399,9 +398,6 @@ cover <- textGrob("ANNEXA report",
                             col = "black"))
 
 sub_cover_text <- paste(
-  str_wrap(paste("Reference genome:", genome_ref), width = 40),
-  str_wrap(paste("Reference annotation:", gtf_ref), width = 40),
-  "\n",
   print(Sys.Date()),
   paste("ANNEXA version:", ANNEXA_version),
   sep = "\n")
@@ -412,6 +408,11 @@ sub_cover <- textGrob(sub_cover_text,
 
 grid.arrange(cover, sub_cover)
 
+# Command line
+grid.arrange(textGrob(
+  paste(command)
+))
+
 # Gene
 grid.arrange(textGrob(
   "Gene Characterization",

diff --git a/modules/qc/report.nf b/modules/qc/report.nf
@@ -23,6 +23,6 @@ process REPORT {
     -ref ${ref} \
     -prefix ${prefix} \
     -tx_discovery ${params.tx_discovery}
-  qc.R ${prefix} ${workflow.manifest.version} ${params.fa} ${params.gtf}
+  qc.R ${prefix} ${workflow.manifest.version} ${workflow.getCommandLine}
   """
 }