fixing demulti_fast5

biocorecrg · Dec 9, 2024 · 9b6223d · 9b6223d
1 parent fdcf061
commit 9b6223d
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/BioNextflow b/BioNextflow
diff --git 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)
+5 −0		docker_files/remora/Dockerfile
+3 −0		scripts/README.md
+6 −5		scripts/get_singularity.py
+125 −14		subworkflows/basecalling/dorado.nf
+82 −0		subworkflows/chem_modification/f5c.nf
+117 −0		subworkflows/chem_modification/m6anet.nf
+79 −0		subworkflows/chem_modification/modkit.nf
+1 −2		subworkflows/demultiplexing/seq_tagger.nf
+56 −0		subworkflows/format_conversion/blue_crab.nf
+89 −0		subworkflows/format_conversion/slow5_tools.nf
+36 −0		subworkflows/misc/bedtools.nf
+12 −3		subworkflows/misc/demulti_fast5.nf
+1 −1		subworkflows/reporting/multiqc.nf
+41 −2		subworkflows/single_cell/spipe.nf
+1 −1		subworkflows/structural_variant/sniffles.nf
+22 −3		workflows/basecaller.nf
+21 −2		workflows/basecaller_demultiplexer.nf