diff --git a/annotate.nf b/annotate.nf index 2a66aa2..7b0c6a6 100755 --- a/annotate.nf +++ b/annotate.nf @@ -1,6 +1,5 @@ #! /usr/bin/env nextflow -nextflow.enable.dsl=2 -// todo hangs on KP420444.fasta + /* * Annotates strings in fasta files. * @@ -37,10 +36,8 @@ if(params.sbt == null) { raw = "${params.raw}/*{fasta,fa,fasta.gz,fa.gz}" reads = Channel.fromPath(raw).ifEmpty { error "cannot find any reads matching ${raw}" }.map { path -> tuple(sample(path), path) } -annotateReads = Channel.fromPath(annotateFile) -//readTap = reads.tap(annotateReads).filter{ it[1] != params.sbt } -//readTap = reads.tap(annotateReads) -readTap = annotateReads +annotateReads = Channel.create() +readTap = reads.tap(annotateReads).filter{ it[1] != params.sbt } /* * Use the capture probes to orient the input sequences.