Add prefix for final report file and output report also as tsv

richardstoeckl · Sep 30, 2024 · 1de7ef6 · 1de7ef6
1 parent f912930
commit 1de7ef6
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Showing 3 changed files with 10 additions and 5 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -3,6 +3,7 @@ main:
     logPath: "logs/"
     interimPath: "interim/"
     resultPath: "results/"
+    prefix: "veryImportantSamples" # this prefix will be used to name the final report file
 
 tools:
     checkm2:

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -34,7 +34,7 @@ RESULTPATH = os.path.normpath(config["main"]["resultPath"])
 
 rule all:
     input:
-        os.path.join(RESULTPATH,"final_report.html"),
+        os.path.join(RESULTPATH,config["main"]["prefix"] + "_final_report.html"),
 
 # Get the number of contigs (=num_seqs) , N50, and length of the largest contig (=max_len)
 checkpoint seqkit_stats:
@@ -324,7 +324,8 @@ rule createReport:
         trnascan=expand(rules.trnascan.output, sampleID=SAMPLES),
         decipher=rules.decipher.output,
     output:
-        report=os.path.join(RESULTPATH,"final_report.html"),
+        reportHTML=os.path.join(RESULTPATH,config["main"]["prefix"] + "_final_report.html"),
+        reportTSV=os.path.join(RESULTPATH,config["main"]["prefix"] + "_final_report.tsv"),
     log:
         os.path.join(LOGPATH, "common", "logs", "createReport.log"),
     params:
@@ -337,5 +338,5 @@ rule createReport:
         os.path.join(workflow.basedir, "envs","r-tools.yaml")
     shell:
         """
-        Rscript {params.script} {input.checkm2} {params.seqkit_stats_dir} {params.samtools_coverage_dir} {input.gtdbtk} {input.decipher} {params.tRNAscan_dir} {output} >{log} 2>&1
+        Rscript {params.script} {input.checkm2} {params.seqkit_stats_dir} {params.samtools_coverage_dir} {input.gtdbtk} {input.decipher} {params.tRNAscan_dir} {output.reportHTML} {output.reportTSV} >{log} 2>&1
         """
diff --git a/workflow/scripts/createReport.R b/workflow/scripts/createReport.R
@@ -29,7 +29,8 @@ samtools_coverage_path <- args[3]
 gtdbtk_path <- args[4]
 decipher_path <- args[5]
 tRNAscan_path <- args[6]
-outfileReport <- args[7]
+outfileReportHTML <- args[7]
+outfileReportTSV <- args[8]
 
 # checkm2
 checkm2 <- read_tsv(checkm2_path) %>%
@@ -192,6 +193,8 @@ style_table <- function(combinedDF) {
 tab <- style_table(combinedDF)
 tab
 
-save_tt(tab, outfileReport, overwrite = TRUE)
+save_tt(tab, outfileReportHTML, overwrite = TRUE)
+
+write_tsv(combinedDF, outfileReportTSV)