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added if to ch_assemblies filter
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erinyoung committed Mar 4, 2024
1 parent 21019cd commit 600d77b
Showing 1 changed file with 2 additions and 5 deletions.
7 changes: 2 additions & 5 deletions donut_falls.nf
Original file line number Diff line number Diff line change
@@ -1345,9 +1345,7 @@ process rasusa {
rasusa ${args} \
--input ${fastq} \
--output rasusa/${prefix}_rasusa.fastq
gzip --force rasusa/${prefix}_rasusa.fastq
--output rasusa/${prefix}_rasusa.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@@ -1962,13 +1960,12 @@ workflow DONUT_FALLS {
}
.set { ch_assemblies }

// TODO : test this
ch_assemblies.dragonflye
.join(ch_nanopore_input, by: 0 , remainder: false).join(ch_illumina_input, by: 0, remainder: true)
.mix(ch_assemblies.flye.join(ch_nanopore_input, by: 0 , remainder: false).join(ch_illumina_input, by: 0, remainder: true))
.mix(ch_assemblies.unicycler.join(ch_nanopore_input, by: 0 , remainder: false).join(ch_illumina_input, by: 0, remainder: true))
.mix(ch_assemblies.raven.join(ch_nanopore_input, by: 0 , remainder: false).join(ch_illumina_input, by: 0, remainder: true))
.filter{it[1]}
.filter{ it -> if (it) {it[1]}}
.set{ch_assembly_reads}

circulocov(ch_assembly_reads)

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