diff --git a/BioNextflow b/BioNextflow index 26bb4b9..2d5f69a 160000 --- a/BioNextflow +++ b/BioNextflow @@ -1 +1 @@ -Subproject commit 26bb4b9c27d1274dfcf0e3227e4332259cec140b +Subproject commit 2d5f69a9524d17aa00f7b6166d138c45773434c3 diff --git a/mop_preprocess/mop_preprocess.nf b/mop_preprocess/mop_preprocess.nf index 4673e10..6d511c3 100644 --- a/mop_preprocess/mop_preprocess.nf +++ b/mop_preprocess/mop_preprocess.nf @@ -161,6 +161,8 @@ checkTools(tools, progPars) // Create a channel for excluded ids 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"] ] @@ -425,7 +427,7 @@ workflow { demufq = outbc.demultiplexed_fastqs bc_stats = reshapeSamples(outbc.basecalling_stats) bc_demux_stats = reshapeSamples(outbc.basecalling_stats).groupTuple() - outbc.basecalled_fast5.view() + //outbc.basecalled_fast5.view() break; case "dorado": @@ -452,7 +454,7 @@ workflow { // DEMULTI FAST5 if (demulti_fast5_opt == "ON") { - outbc.basecalled_fast5.view() +// outbc.basecalled_fast5.view() basecalled_fast5 = reshapeSamples(outbc.basecalled_fast5).transpose().groupTuple() if (params.barcodes == "") { DEMULTI_FAST5(bc_demux_stats, basecalled_fast5)