From 686f7d0de408b002d7d8a75c2d078094ec4b9d46 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Thu, 9 Jan 2025 10:33:12 +0000
Subject: [PATCH 1/2] Remove FKprof again

---
 modules/local/fkutils/fkprof/main.nf | 47 ----------------------------
 1 file changed, 47 deletions(-)
 delete mode 100644 modules/local/fkutils/fkprof/main.nf

diff --git a/modules/local/fkutils/fkprof/main.nf b/modules/local/fkutils/fkprof/main.nf
deleted file mode 100644
index 8562e2c8..00000000
--- a/modules/local/fkutils/fkprof/main.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-process FKUTILS_FKPROF {
-    tag "$meta.id"
-    label 'process_medium'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'docker.io/ubuntu:20.04' }"
-
-    input:
-    tuple val( meta ), path( reference )
-    tuple val( meta2 ), path( ktab )
-
-    output:
-    tuple val( meta ), file( "*bed" ),  emit: bed
-    path "versions.yml",                emit: versions
-
-    script:
-    def args    = task.ext.args     ?: ""
-    def prefix  = task.ext.prefix   ?: "${meta.id}"
-    def VERSION = "2f7b2583092fafb0a5abc654b5857642" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-
-    """
-    ${projectDir}/bin/FKprof \\
-        $args \\
-        -t$task.cpus \\
-        ${reference} \\
-        ${ktab}/*ktab
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fkprof:    $VERSION
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix  = task.ext.prefix   ?: "${meta.id}"
-    def kmer    = 31
-    def VERSION = "2f7b2583092fafb0a5abc654b5857642"  // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-    """
-    touch ${prefix}_${kmer}_read.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fkprof:    $VERSION
-    END_VERSIONS
-    """
-}

From 7f2237291b82e9d198b946ec4002e1988d011506 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Thu, 9 Jan 2025 13:05:11 +0000
Subject: [PATCH 2/2] Declare JBROWSE correctly in main.nf

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 4adb4389..2289d95c 100755
--- a/main.nf
+++ b/main.nf
@@ -73,7 +73,7 @@ workflow {
 }
 
 
-workflow {
+workflow JBROWSE {
     SANGERTOL_TREEVAL_JBROWSE ()
 }