feat(grohmm): Add Native MultiQC support

nf-core · Sep 27, 2024 · e8a0e46 · e8a0e46
1 parent bba68b5
commit e8a0e46
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Showing 4 changed files with 8 additions and 5 deletions.
diff --git a/bin/transcriptcalling_grohmm.R b/bin/transcriptcalling_grohmm.R
@@ -181,19 +181,21 @@ b_plus <- breakTranscriptsOnGenes(tx_hmm, kg_consensus, strand = "+")
 b_minus <- breakTranscriptsOnGenes(tx_hmm, kg_consensus, strand = "-")
 tx_broken <- c(b_plus, b_minus)
 tx_final <- combineTranscripts(tx_broken, kg_consensus)
-td_final <- getTxDensity(tx_final, con_expressed, mc.cores = args$cores)
 export(
   tx_final,
   con = paste(args$outprefix, ".final.transcripts.bed", sep = "")
 )
-capture.output(td_final, file = paste0(args$outprefix, ".tdFinal.txt"))
 # 1. Output plot
 jpeg(file = paste0(args$outprefix, ".tdplot_mqc.jpg"))
-# 2. Create the plot
+# 2. Create the plot and capture data
 td_final <- getTxDensity(tx_final, con_expressed, mc.cores = args$cores)
 # 3. Close the file
 dev.off()
+capture.output(td_final, file = paste0(args$outprefix, ".tdFinal.txt"))
 
+# Write the data used in the plot to a CSV file
+data_to_write <- data.frame(x = td_final$x, profile = td_final$profile)
+write.csv(data_to_write, file = paste0(args$outprefix, ".tdFinal_mqc.csv"), row.names = FALSE)
 
 ########################
 ## CITE PACKAGES USED ##

diff --git a/modules/local/grohmm/parametertuning/environment.yml b/modules/local/grohmm/parametertuning/environment.yml
@@ -11,4 +11,4 @@ dependencies:
   # NOTE Can't use the official package because of
   # https://github.com/dankoc/groHMM/issues/2
   # - bioconda::bioconductor-grohmm=1.28.0
-  - bioinfoorphanage-grohmm=1.36.1
+  - bioinfoorphanage-grohmm=1.37.0
diff --git a/modules/local/grohmm/transcriptcalling/environment.yml b/modules/local/grohmm/transcriptcalling/environment.yml
@@ -11,4 +11,4 @@ dependencies:
   # NOTE Can't use the official package because of
   # https://github.com/dankoc/groHMM/issues/2
   # - bioconda::bioconductor-grohmm=1.28.0
-  - bioinfoorphanage-grohmm=1.36.1
+  - bioinfoorphanage-grohmm=1.37.0
diff --git a/modules/local/grohmm/transcriptcalling/main.nf b/modules/local/grohmm/transcriptcalling/main.nf
@@ -18,6 +18,7 @@ process GROHMM_TRANSCRIPTCALLING {
     tuple val(meta), path("*.transcripts.bed"), emit: transcripts_bed
     tuple val(meta), path("*.tdFinal.txt")    , emit: td
     tuple val(meta), path("*.tdplot_mqc.jpg") , emit: td_plot
+    tuple val(meta), path("*.tdFinal_mqc.csv") , emit: mqc_csv
     path  "versions.yml"     , emit: versions
 
     when: