Merge pull request #27 from N-Hoffmann/stringtie

Add reference genome and gtf info on cover page of QC PDF

bin/qc.R

@@ -37,6 +37,8 @@ theme_set(
 args = commandArgs(trailingOnly=TRUE)
 prefix = args[1]
 ANNEXA_version = args[2]
+genome_ref = basename(args[3])
+gtf_ref = basename(args[4])
 
 #############################################################################
 # GENE
@@ -395,7 +397,14 @@ cover <- textGrob("ANNEXA report",
                   gp = gpar(fontsize = 40,
                             col = "black"))
 
-sub_cover_text <- paste(print(Sys.Date()), paste("ANNEXA version:", ANNEXA_version), sep = "\n")
+sub_cover_text <- paste(
+  paste("Reference genome:", genome_ref),
+  paste("Reference annotation:", gtf_ref),
+  "\n",
+  print(Sys.Date()),
+  paste("ANNEXA version:", ANNEXA_version),
+  sep = "\n")
+
 sub_cover <- textGrob(sub_cover_text,
                   gp = gpar(fontsize = 20,
                             col = "black"))

main.nf

@@ -7,8 +7,8 @@ include { paramsHelp } from 'plugin/nf-schema'
 include { helpHeader           } from './modules/header.nf'
 if (params.help) {
   log.info helpHeader()
-    log.info paramsHelp("nextflow run IGDRion/ANNEXA -profile {test,docker,singularity,conda,slurm} --input samples.txt --gtf /path/to/ref.gtf --fa /path/to/ref.fa")
-    exit 0
+  log.info paramsHelp("nextflow run IGDRion/ANNEXA -profile {test,docker,singularity,conda,slurm} --input samples.txt --gtf /path/to/ref.gtf --fa /path/to/ref.fa")
+  exit 0
 }
 
 if (params.input) { input = file(params.input, checkIfExists: true) }

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}
+  qc.R ${prefix} ${workflow.manifest.version} ${params.fa} ${params.gtf}
   """
 }