From 1abc356d6630611a9a57392e0d6d62ae25614aee Mon Sep 17 00:00:00 2001
From: Dave Roe <roex0050@umn.edu>
Date: Mon, 14 Aug 2023 14:11:40 -0500
Subject: [PATCH] Update annotate.nf

Backed out previous revision. It was a work in progress.
---
 annotate.nf | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

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.