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main2.nf
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nextflow.enable.dsl=2
/*
* pipeline input parameters
*/
params.reference_16s = "/home/bhargavam/Documents/rnamods-nf/references/k12_16s.fa"
params.reference_23s = "/home/bhargavam/Documents/rnamods-nf/references/k12_23s.fa"
params.nativereads = "$baseDir/native/*.fastq"
params.ivtreads = "$baseDir/ivt/*.fastq"
params.nativefast5s = "/home/bhargavam/Documents/data/k12_native_fast5_all"
params.ivtfast5s = "/home/bhargavam/Documents/data/k12_ivt_fast5_all"
params.outdir = "results"
include { multitosingle as multitosingle_n_1_16s; multitosingle as multitosingle_n_2_16s; multitosingle as multitosingle_n_3_16s; multitosingle as multitosingle_n_1_23s; multitosingle as multitosingle_n_2_23s; multitosingle as multitosingle_n_3_23s } from '/home/bhargavam/Documents/nextflowmodules/multitosingle'
include { multitosingle as multitosingle_i_1_16s; multitosingle as multitosingle_i_2_16s; multitosingle as multitosingle_i_3_16s; multitosingle as multitosingle_i_1_23s; multitosingle as multitosingle_i_2_23s; multitosingle as multitosingle_i_3_23s } from '/home/bhargavam/Documents/nextflowmodules/multitosingle'
include { tomboresquiggle as tomboresquiggle_n_1_16s; tomboresquiggle as tomboresquiggle_n_2_16s; tomboresquiggle as tomboresquiggle_n_3_16s; tomboresquiggle as tomboresquiggle_n_1_23s; tomboresquiggle as tomboresquiggle_n_2_23s; tomboresquiggle as tomboresquiggle_n_3_23s } from '/home/bhargavam/Documents/nextflowmodules/tomboresquiggle'
include { tomboresquiggle as tomboresquiggle_i_1_16s; tomboresquiggle as tomboresquiggle_i_2_16s; tomboresquiggle as tomboresquiggle_i_3_16s; tomboresquiggle as tomboresquiggle_i_1_23s; tomboresquiggle as tomboresquiggle_i_2_23s; tomboresquiggle as tomboresquiggle_i_3_23s } from '/home/bhargavam/Documents/nextflowmodules/tomboresquiggle'
include { f5cindex as f5cindex1_n_16s; f5cindex as f5cindex1_n_23s ; f5cindex as f5cindex1_i_16s; f5cindex as f5cindex1_i_23s } from '/home/bhargavam/Documents/nextflowmodules/f5cindex'
include { f5cindex as f5cindex2_n_16s; f5cindex as f5cindex2_n_23s ; f5cindex as f5cindex2_i_16s; f5cindex as f5cindex2_i_23s} from '/home/bhargavam/Documents/nextflowmodules/f5cindex'
include { f5cindex as f5cindex3_n_16s; f5cindex as f5cindex3_n_23s ; f5cindex as f5cindex3_i_16s; f5cindex as f5cindex3_i_23s} from '/home/bhargavam/Documents/nextflowmodules/f5cindex'
include { f5ceventalign as f5ceventalign1_n_16s; f5ceventalign as f5ceventalign1_n_23s ; f5ceventalign as f5ceventalign1_i_16s; f5ceventalign as f5ceventalign1_i_23s} from '/home/bhargavam/Documents/nextflowmodules/f5ceventalign'
include { f5ceventalign as f5ceventalign2_n_16s; f5ceventalign as f5ceventalign2_n_23s ; f5ceventalign as f5ceventalign2_i_16s; f5ceventalign as f5ceventalign2_i_23s} from '/home/bhargavam/Documents/nextflowmodules/f5ceventalign'
include { f5ceventalign as f5ceventalign3_n_16s; f5ceventalign as f5ceventalign3_n_23s ; f5ceventalign as f5ceventalign3_i_16s; f5ceventalign as f5ceventalign3_i_23s} from '/home/bhargavam/Documents/nextflowmodules/f5ceventalign'
include { tombocompare as tombocompare_1_16s; tombocompare as tombocompare_2_16s; tombocompare as tombocompare_3_16s; tombocompare as tombocompare_1_23s; tombocompare as tombocompare_2_23s; tombocompare as tombocompare_3_23s } from '/home/bhargavam/Documents/nextflowmodules/tombocompare'
include { tomboextract_16s as tomboextract_16s_1 ; tomboextract_16s as tomboextract_16s_2 ; tomboextract_16s as tomboextract_16s_3 } from '/home/bhargavam/Documents/nextflowmodules/tomboextract_16s'
include { tomboextract_23s as tomboextract_23s_1 ; tomboextract_23s as tomboextract_23s_2 ; tomboextract_23s as tomboextract_23s_3 } from '/home/bhargavam/Documents/nextflowmodules/tomboextract_23s'
/*
* WORKFLOW
*/
workflow {
Channel
.value(file(params.reference_16s))
.set {reference_16s_ch}
Channel
.value(file(params.reference_23s))
.set {reference_23s_ch}
Channel
.fromPath(params.nativereads)
.set {nativefastqs_ch}
Channel
.fromPath(params.ivtreads)
.set {ivtfastqs_ch}
Channel
.value(file(params.nativefast5s))
.set {nativefast5s_ch}
Channel
.value(file(params.ivtfast5s))
.set {ivtfast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_native_1_16s")
.set {native_1_16s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_native_2_16s")
.set {native_2_16s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_native_3_16s")
.set {native_3_16s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_native_1_23s")
.set {native_1_23s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_native_2_23s")
.set {native_2_23s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_native_3_23s")
.set {native_3_23s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_ivt_1_16s")
.set {ivt_1_16s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_ivt_2_16s")
.set {ivt_2_16s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_ivt_3_16s")
.set {ivt_3_16s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_ivt_1_23s")
.set {ivt_1_23s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_ivt_2_23s")
.set {ivt_2_23s_fast5s_ch}
Channel
.fromPath("$baseDir/results/fast5s_ivt_3_23s")
.set {ivt_3_23s_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_native_1_16s_single"))
.set {native_1_16s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_native_2_16s_single"))
.set {native_2_16s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_native_3_16s_single"))
.set {native_3_16s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_native_1_23s_single"))
.set {native_1_23s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_native_2_23s_single"))
.set {native_2_23s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_native_3_23s_single"))
.set {native_3_23s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_ivt_1_16s_single"))
.set {ivt_1_16s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_ivt_2_16s_single"))
.set {ivt_2_16s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_ivt_3_16s_single"))
.set {ivt_3_16s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_ivt_1_23s_single"))
.set {ivt_1_23s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_ivt_2_23s_single"))
.set {ivt_2_23s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/fast5s_ivt_3_23s_single"))
.set {ivt_3_23s_single_fast5s_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_16s_native/native_1_16s.fastq"))
.set {native_16s_1_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_16s_native/native_2_16s.fastq"))
.set {native_16s_2_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_16s_native/native_3_16s.fastq"))
.set {native_16s_3_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_16s_ivt/ivt_1_16s.fastq"))
.set {ivt_16s_1_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_16s_ivt/ivt_2_16s.fastq"))
.set {ivt_16s_2_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_16s_ivt/ivt_3_16s.fastq"))
.set {ivt_16s_3_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_23s_native/native_1_23s.fastq"))
.set {native_23s_1_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_23s_native/native_2_23s.fastq"))
.set {native_23s_2_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_23s_native/native_3_23s.fastq"))
.set {native_23s_3_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_23s_ivt/ivt_1_23s.fastq"))
.set {ivt_23s_1_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_23s_ivt/ivt_2_23s.fastq"))
.set {ivt_23s_2_fastqs_ch}
Channel
.value(file("$baseDir/results/mappedfastqs_23s_ivt/ivt_3_23s.fastq"))
.set {ivt_23s_3_fastqs_ch}
fastqinput1 = [
("$baseDir/results/mappedfastqs_16s_native/native_1_16s.fastq"),
("$baseDir/results/mappedfastqs_16s_native/native_1_16s.fastq.index"),
("$baseDir/results/mappedfastqs_16s_native/native_1_16s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_16s_native/native_1_16s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_16s_native/native_1_16s.fastq.index.readdb")
]
fastqinput2 = [
("$baseDir/results/mappedfastqs_16s_native/native_2_16s.fastq"),
("$baseDir/results/mappedfastqs_16s_native/native_2_16s.fastq.index"),
("$baseDir/results/mappedfastqs_16s_native/native_2_16s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_16s_native/native_2_16s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_16s_native/native_2_16s.fastq.index.readdb")
]
fastqinput3 = [
("$baseDir/results/mappedfastqs_16s_native/native_3_16s.fastq"),
("$baseDir/results/mappedfastqs_16s_native/native_3_16s.fastq.index"),
("$baseDir/results/mappedfastqs_16s_native/native_3_16s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_16s_native/native_3_16s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_16s_native/native_3_16s.fastq.index.readdb")
]
fastqinput4 = [
("$baseDir/results/mappedfastqs_16s_ivt/ivt_1_16s.fastq"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_1_16s.fastq.index"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_1_16s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_1_16s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_1_16s.fastq.index.readdb")
]
fastqinput5 = [
("$baseDir/results/mappedfastqs_16s_ivt/ivt_2_16s.fastq"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_2_16s.fastq.index"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_2_16s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_2_16s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_2_16s.fastq.index.readdb")
]
fastqinput6 = [
("$baseDir/results/mappedfastqs_16s_ivt/ivt_3_16s.fastq"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_3_16s.fastq.index"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_3_16s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_3_16s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_16s_ivt/ivt_3_16s.fastq.index.readdb")
]
fastqinput7 = [
("$baseDir/results/mappedfastqs_23s_native/native_1_23s.fastq"),
("$baseDir/results/mappedfastqs_23s_native/native_1_23s.fastq.index"),
("$baseDir/results/mappedfastqs_23s_native/native_1_23s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_23s_native/native_1_23s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_23s_native/native_1_23s.fastq.index.readdb")
]
fastqinput8 = [
("$baseDir/results/mappedfastqs_23s_native/native_2_23s.fastq"),
("$baseDir/results/mappedfastqs_23s_native/native_2_23s.fastq.index"),
("$baseDir/results/mappedfastqs_23s_native/native_2_23s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_23s_native/native_2_23s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_23s_native/native_2_23s.fastq.index.readdb")
]
fastqinput9 = [
("$baseDir/results/mappedfastqs_23s_native/native_3_23s.fastq"),
("$baseDir/results/mappedfastqs_23s_native/native_3_23s.fastq.index"),
("$baseDir/results/mappedfastqs_23s_native/native_3_23s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_23s_native/native_3_23s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_23s_native/native_3_23s.fastq.index.readdb")
]
fastqinput10 = [
("$baseDir/results/mappedfastqs_23s_ivt/ivt_1_23s.fastq"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_1_23s.fastq.index"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_1_23s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_1_23s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_1_23s.fastq.index.readdb")
]
fastqinput11 = [
("$baseDir/results/mappedfastqs_23s_ivt/ivt_2_23s.fastq"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_2_23s.fastq.index"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_2_23s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_2_23s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_2_23s.fastq.index.readdb")
]
fastqinput12 = [
("$baseDir/results/mappedfastqs_23s_ivt/ivt_3_23s.fastq"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_3_23s.fastq.index"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_3_23s.fastq.index.fai"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_3_23s.fastq.index.gzi"),
("$baseDir/results/mappedfastqs_23s_ivt/ivt_3_23s.fastq.index.readdb")
]
baminput1 = [
file("$baseDir/results/mappedbams_16s_native/native_1_16s_sorted.bam"),
file("$baseDir/results/mappedbams_16s_native/native_1_16s_sorted.bam.bai")
]
baminput2 = [
file("$baseDir/results/mappedbams_16s_native/native_2_16s_sorted.bam"),
file("$baseDir/results/mappedbams_16s_native/native_2_16s_sorted.bam.bai")
]
baminput3 = [
file("$baseDir/results/mappedbams_16s_native/native_3_16s_sorted.bam"),
file("$baseDir/results/mappedbams_16s_native/native_3_16s_sorted.bam.bai")
]
baminput4 = [
file("$baseDir/results/mappedbams_16s_ivt/ivt_1_16s_sorted.bam"),
file("$baseDir/results/mappedbams_16s_ivt/ivt_1_16s_sorted.bam.bai")
]
baminput5 = [
file("$baseDir/results/mappedbams_16s_ivt/ivt_2_16s_sorted.bam"),
file("$baseDir/results/mappedbams_16s_ivt/ivt_2_16s_sorted.bam.bai")
]
baminput6 = [
file("$baseDir/results/mappedbams_16s_ivt/ivt_3_16s_sorted.bam"),
file("$baseDir/results/mappedbams_16s_ivt/ivt_3_16s_sorted.bam.bai")
]
baminput7 = [
file("$baseDir/results/mappedbams_23s_native/native_1_23s_sorted.bam"),
file("$baseDir/results/mappedbams_23s_native/native_1_23s_sorted.bam.bai")
]
baminput8 = [
file("$baseDir/results/mappedbams_23s_native/native_2_23s_sorted.bam"),
file("$baseDir/results/mappedbams_23s_native/native_2_23s_sorted.bam.bai")
]
baminput9 = [
file("$baseDir/results/mappedbams_23s_native/native_3_23s_sorted.bam"),
file("$baseDir/results/mappedbams_23s_native/native_3_23s_sorted.bam.bai")
]
baminput10 = [
file("$baseDir/results/mappedbams_23s_ivt/ivt_1_23s_sorted.bam"),
file("$baseDir/results/mappedbams_23s_ivt/ivt_1_23s_sorted.bam.bai")
]
baminput11 = [
file("$baseDir/results/mappedbams_23s_ivt/ivt_2_23s_sorted.bam"),
file("$baseDir/results/mappedbams_23s_ivt/ivt_2_23s_sorted.bam.bai")
]
baminput12 = [
file("$baseDir/results/mappedbams_23s_ivt/ivt_3_23s_sorted.bam"),
file("$baseDir/results/mappedbams_23s_ivt/ivt_3_23s_sorted.bam.bai")
]
multitosingle_n_1_16s (native_1_16s_fast5s_ch)
multitosingle_n_2_16s (native_2_16s_fast5s_ch)
multitosingle_n_3_16s (native_3_16s_fast5s_ch)
multitosingle_n_1_23s (native_1_23s_fast5s_ch)
multitosingle_n_2_23s (native_2_23s_fast5s_ch)
multitosingle_n_3_23s (native_3_23s_fast5s_ch)
multitosingle_i_1_16s (ivt_1_16s_fast5s_ch)
multitosingle_i_2_16s (ivt_2_16s_fast5s_ch)
multitosingle_i_3_16s (ivt_3_16s_fast5s_ch)
multitosingle_i_1_23s (ivt_1_23s_fast5s_ch)
multitosingle_i_2_23s (ivt_2_23s_fast5s_ch)
multitosingle_i_3_23s (ivt_3_23s_fast5s_ch)
tomboresquiggle_n_1_16s (native_1_16s_single_fast5s_ch, reference_16s_ch, multitosingle_n_1_16s.out.multitosingledone)
tomboresquiggle_n_2_16s (native_2_16s_single_fast5s_ch, reference_16s_ch, multitosingle_n_2_16s.out.multitosingledone)
tomboresquiggle_n_3_16s (native_3_16s_single_fast5s_ch, reference_16s_ch, multitosingle_n_3_16s.out.multitosingledone)
tomboresquiggle_n_1_23s (native_1_23s_single_fast5s_ch, reference_23s_ch, multitosingle_n_1_23s.out.multitosingledone)
tomboresquiggle_n_2_23s (native_2_23s_single_fast5s_ch, reference_23s_ch, multitosingle_n_2_23s.out.multitosingledone)
tomboresquiggle_n_3_23s (native_3_23s_single_fast5s_ch, reference_23s_ch, multitosingle_n_3_23s.out.multitosingledone)
tomboresquiggle_i_1_16s (ivt_1_16s_single_fast5s_ch, reference_16s_ch, multitosingle_i_1_16s.out.multitosingledone)
tomboresquiggle_i_2_16s (ivt_2_16s_single_fast5s_ch, reference_16s_ch, multitosingle_i_2_16s.out.multitosingledone)
tomboresquiggle_i_3_16s (ivt_3_16s_single_fast5s_ch, reference_16s_ch, multitosingle_i_3_16s.out.multitosingledone)
tomboresquiggle_i_1_23s (ivt_1_23s_single_fast5s_ch, reference_23s_ch, multitosingle_i_1_23s.out.multitosingledone)
tomboresquiggle_i_2_23s (ivt_2_23s_single_fast5s_ch, reference_23s_ch, multitosingle_i_2_23s.out.multitosingledone)
tomboresquiggle_i_3_23s (ivt_3_23s_single_fast5s_ch, reference_23s_ch, multitosingle_i_3_23s.out.multitosingledone)
tombocompare_1_16s (native_1_16s_single_fast5s_ch, ivt_1_16s_single_fast5s_ch, tomboresquiggle_n_1_16s.out.resquiggledone_ch, tomboresquiggle_i_1_16s.out.resquiggledone_ch)
tombocompare_2_16s (native_2_16s_single_fast5s_ch, ivt_2_16s_single_fast5s_ch, tomboresquiggle_n_2_16s.out.resquiggledone_ch, tomboresquiggle_i_2_16s.out.resquiggledone_ch)
tombocompare_3_16s (native_3_16s_single_fast5s_ch, ivt_3_16s_single_fast5s_ch, tomboresquiggle_n_3_16s.out.resquiggledone_ch, tomboresquiggle_i_3_16s.out.resquiggledone_ch)
tombocompare_1_23s (native_1_23s_single_fast5s_ch, ivt_1_23s_single_fast5s_ch, tomboresquiggle_n_1_23s.out.resquiggledone_ch, tomboresquiggle_i_1_23s.out.resquiggledone_ch)
tombocompare_2_23s (native_2_23s_single_fast5s_ch, ivt_2_23s_single_fast5s_ch, tomboresquiggle_n_2_23s.out.resquiggledone_ch, tomboresquiggle_i_2_23s.out.resquiggledone_ch)
tombocompare_3_23s (native_3_23s_single_fast5s_ch, ivt_3_23s_single_fast5s_ch, tomboresquiggle_n_3_23s.out.resquiggledone_ch, tomboresquiggle_i_3_23s.out.resquiggledone_ch)
f5cindex1_n_16s (native_1_16s_fast5s_ch, native_16s_1_fastqs_ch)
f5cindex2_n_16s (native_2_16s_fast5s_ch, native_16s_2_fastqs_ch)
f5cindex3_n_16s (native_3_16s_fast5s_ch, native_16s_3_fastqs_ch)
f5cindex1_i_16s (ivt_1_16s_fast5s_ch, ivt_16s_1_fastqs_ch)
f5cindex2_i_16s (ivt_2_16s_fast5s_ch, ivt_16s_2_fastqs_ch)
f5cindex3_i_16s (ivt_3_16s_fast5s_ch, ivt_16s_3_fastqs_ch)
f5cindex1_n_23s (native_1_23s_fast5s_ch, native_23s_1_fastqs_ch)
f5cindex2_n_23s (native_2_23s_fast5s_ch, native_23s_2_fastqs_ch)
f5cindex3_n_23s (native_3_23s_fast5s_ch, native_23s_3_fastqs_ch)
f5cindex1_i_23s (ivt_1_23s_fast5s_ch, ivt_23s_1_fastqs_ch)
f5cindex2_i_23s (ivt_2_23s_fast5s_ch, ivt_23s_2_fastqs_ch)
f5cindex3_i_23s (ivt_3_23s_fast5s_ch, ivt_23s_3_fastqs_ch)
f5ceventalign1_n_16s (fastqinput1, baminput1, reference_16s_ch, f5cindex1_n_16s.out.f5cindexout)
f5ceventalign2_n_16s (fastqinput2, baminput2, reference_16s_ch, f5cindex2_n_16s.out.f5cindexout)
f5ceventalign3_n_16s (fastqinput3, baminput3, reference_16s_ch, f5cindex3_n_16s.out.f5cindexout)
f5ceventalign1_i_16s (fastqinput4, baminput4, reference_16s_ch, f5cindex1_i_16s.out.f5cindexout)
f5ceventalign2_i_16s (fastqinput5, baminput5, reference_16s_ch, f5cindex2_i_16s.out.f5cindexout)
f5ceventalign3_i_16s (fastqinput6, baminput6, reference_16s_ch, f5cindex3_i_16s.out.f5cindexout)
f5ceventalign1_n_23s (fastqinput7, baminput7, reference_23s_ch, f5cindex1_n_23s.out.f5cindexout)
f5ceventalign2_n_23s (fastqinput8, baminput8, reference_23s_ch, f5cindex2_n_23s.out.f5cindexout)
f5ceventalign3_n_23s (fastqinput9, baminput9, reference_23s_ch, f5cindex3_n_23s.out.f5cindexout)
f5ceventalign1_i_23s (fastqinput10, baminput10, reference_23s_ch, f5cindex1_i_23s.out.f5cindexout)
f5ceventalign2_i_23s (fastqinput11, baminput11, reference_23s_ch, f5cindex2_i_23s.out.f5cindexout)
f5ceventalign3_i_23s (fastqinput12, baminput12, reference_23s_ch, f5cindex3_i_23s.out.f5cindexout)
tomboextract_16s_1 (tombocompare_1_16s.out.tombostat_ch, tombocompare_1_16s.out.tombocomparedone)
tomboextract_16s_2 (tombocompare_2_16s.out.tombostat_ch, tombocompare_2_16s.out.tombocomparedone)
tomboextract_16s_3 (tombocompare_3_16s.out.tombostat_ch, tombocompare_3_16s.out.tombocomparedone)
tomboextract_23s_1 (tombocompare_1_23s.out.tombostat_ch, tombocompare_1_23s.out.tombocomparedone)
tomboextract_23s_2 (tombocompare_2_23s.out.tombostat_ch, tombocompare_2_23s.out.tombocomparedone)
tomboextract_23s_3 (tombocompare_3_23s.out.tombostat_ch, tombocompare_3_23s.out.tombocomparedone)
}