From cf1d1e096f936740dd17d32c5ca21d561288bc36 Mon Sep 17 00:00:00 2001 From: Luca Cozzuto Date: Thu, 12 Sep 2024 11:38:09 +0200 Subject: [PATCH] adding alignment stats to report --- mop_preprocess/mop_preprocess.nf | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/mop_preprocess/mop_preprocess.nf b/mop_preprocess/mop_preprocess.nf index 1f72a2d..597cf05 100644 --- 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