adding alignment stats to report

biocorecrg · Sep 12, 2024 · cf1d1e0 · cf1d1e0
1 parent da7a838
commit cf1d1e0
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/mop_preprocess/mop_preprocess.nf b/mop_preprocess/mop_preprocess.nf
@@ -99,6 +99,9 @@ switch(params.demultiplexing) {
     case "deeplexicon":
         demux_models = "${projectDir}/deeplexicon_models/"
     break;
+    case "seqtagger":
+        demux_models = "${projectDir}/seqtagger_models/"
+    break;
 }
 
 dorado_models = "${projectDir}/dorado_models/"
@@ -160,7 +163,7 @@ barcodes_to_include = get_barcode_list(params.barcodes)
 def guppy_basecall_pars = guppypars + " " + progPars["basecalling--guppy"]
 
 def basecaller_pars = ["guppy" : guppy_basecall_pars, "dorado" : progPars["basecalling--dorado"] ]
-def demux_pars = ["guppy" : progPars["demultiplexing--guppy"] + " " + guppy_basecall_pars, "deeplexicon": progPars["demultiplexing--deeplexicon"] ]
+def demux_pars = ["guppy" : progPars["demultiplexing--guppy"] + " " + guppy_basecall_pars, "seqtagger":  progPars["demultiplexing--seqtagger"], "deeplexicon": progPars["demultiplexing--deeplexicon"] ]
 
 
 // INCLUDE WORKFLOWS
@@ -407,6 +410,7 @@ workflow {
         else { // BASECALL AND DEMULTIPLEX
             switch(params.demultiplexing) {
                 case "deeplexicon":
+                case "seqtagger":
                 outbc = BASECALL(fast5_4_analysis)
                 demux = DEMULTIPLEX(fast5_4_analysis, outbc.basecalled_fastq)
                 demufq = demux.demultiplexed_fastq
@@ -507,7 +511,7 @@ workflow {
 
     // Perform fastqc QC on fastq
     fastqc_files = FASTQC(fastq_files)
-    multiqc_data = multiqc_data.mix(fastqc_files.map{it[1]})
+    multiqc_data = multiqc_data.mix(stats_aln).mix(fastqc_files.map{it[1]})
 
 
     stats_counts = COUNTING(sorted_alns, aln_indexes).stats_counts