diff --git a/CHANGELOG.md b/CHANGELOG.md
index a7e358ea..e61cc28a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -51,6 +51,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed bug in nf-core `RRNATRANSCRIPTS` module [#563](https://github.com/nf-core/rnafusion/issues/563)
 - Fixed bug in `GFFREAD` that caused output `gffread_fasta` not being produced [#565](https://github.com/nf-core/rnafusion/issues/565)
 - Fixed bug in `FUSIONCATCHER_DOWNLOAD` that caused an error when running with singularity profile [#573](https://github.com/nf-core/rnafusion/issues/573)
+- Fixed missing script `gtf2bed` which caused local module `GET_RRNA_TRANSCRIPTS` to fail [#602](https://github.com/nf-core/rnafusion/issues/602)
 
 ### Removed
 
diff --git a/bin/gtf2bed b/bin/gtf2bed
new file mode 100755
index 00000000..cfa91cf7
--- /dev/null
+++ b/bin/gtf2bed
@@ -0,0 +1,123 @@
+#!/usr/bin/env perl
+
+# Copyright (c) 2011 Erik Aronesty (erik@q32.com)
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ALSO, IT WOULD BE NICE IF YOU LET ME KNOW YOU USED IT.
+
+use Getopt::Long;
+
+my $extended;
+GetOptions("x"=>\$extended);
+
+$in = shift @ARGV;
+
+my $in_cmd =($in =~ /\.gz$/ ? "gunzip -c $in|" : $in =~ /\.zip$/ ? "unzip -p $in|" : "$in") || die "Can't open $in: $!\n";
+open IN, $in_cmd;
+
+while (<IN>) {
+    $gff = 2 if /^##gff-version 2/;
+    $gff = 3 if /^##gff-version 3/;
+    next if /^#/ && $gff;
+
+    s/\s+$//;
+    # 0-chr 1-src 2-feat 3-beg 4-end 5-scor 6-dir 7-fram 8-attr
+    my @f = split /\t/;
+    if ($gff) {
+        # most ver 2's stick gene names in the id field
+        ($id) = $f[8]=~ /\bID="([^"]+)"/;
+        # most ver 3's stick unquoted names in the name field
+        ($id) = $f[8]=~ /\bName=([^";]+)/ if !$id && $gff == 3;
+    } else {
+        ($id) = $f[8]=~ /transcript_id "([^"]+)"/;
+    }
+
+    next unless $id && $f[0];
+
+    if ($f[2] eq 'exon') {
+        die "no position at exon on line $." if ! $f[3];
+        # gff3 puts :\d in exons sometimes
+        $id =~ s/:\d+$// if $gff == 3;
+        push @{$exons{$id}}, \@f;
+        # save lowest start
+        $trans{$id} = \@f if !$trans{$id};
+    } elsif ($f[2] eq 'start_codon') {
+        #optional, output codon start/stop as "thick" region in bed
+        $sc{$id}->[0] = $f[3];
+    } elsif ($f[2] eq 'stop_codon') {
+        $sc{$id}->[1] = $f[4];
+    } elsif ($f[2] eq 'miRNA' ) {
+        $trans{$id} = \@f if !$trans{$id};
+        push @{$exons{$id}}, \@f;
+    }
+}
+
+for $id (
+    # sort by chr then pos
+    sort {
+        $trans{$a}->[0] eq $trans{$b}->[0] ?
+        $trans{$a}->[3] <=> $trans{$b}->[3] :
+        $trans{$a}->[0] cmp $trans{$b}->[0]
+    } (keys(%trans)) ) {
+        my ($chr, undef, undef, undef, undef, undef, $dir, undef, $attr, undef, $cds, $cde) = @{$trans{$id}};
+        my ($cds, $cde);
+        ($cds, $cde) = @{$sc{$id}} if $sc{$id};
+
+        # sort by pos
+        my @ex = sort {
+            $a->[3] <=> $b->[3]
+        } @{$exons{$id}};
+
+        my $beg = $ex[0][3];
+        my $end = $ex[-1][4];
+
+        if ($dir eq '-') {
+        # swap
+        $tmp=$cds;
+        $cds=$cde;
+        $cde=$tmp;
+        $cds -= 2 if $cds;
+        $cde += 2 if $cde;
+    }
+
+    # not specified, just use exons
+    $cds = $beg if !$cds;
+    $cde = $end if !$cde;
+
+    # adjust start for bed
+    --$beg; --$cds;
+
+    my $exn = @ex;												# exon count
+    my $exst = join ",", map {$_->[3]-$beg-1} @ex;				# exon start
+    my $exsz = join ",", map {$_->[4]-$_->[3]+1} @ex;			# exon size
+
+        my $gene_id;
+        my $extend = "";
+        if ($extended) {
+            ($gene_id) = $attr =~ /gene_name "([^"]+)"/;
+            ($gene_id) = $attr =~ /gene_id "([^"]+)"/ unless $gene_id;
+            $extend="\t$gene_id";
+        }
+    # added an extra comma to make it look exactly like ucsc's beds
+    print "$chr\t$beg\t$end\t$id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,$extend\n";
+}
+
+
+close IN;
diff --git a/modules.json b/modules.json
index b41d5fa5..0c6c5517 100644
--- a/modules.json
+++ b/modules.json
@@ -20,11 +20,6 @@
                         "git_sha": "467c202a876d26af544fa8c4b22a050a535462a7",
                         "installed_by": ["modules"]
                     },
-                    "bedops/convert2bed": {
-                        "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
-                    },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
diff --git a/modules/local/get_rrna_transcript/main.nf b/modules/local/get_rrna_transcript/main.nf
index 5331f534..901c17b4 100644
--- a/modules/local/get_rrna_transcript/main.nf
+++ b/modules/local/get_rrna_transcript/main.nf
@@ -20,7 +20,7 @@ process GET_RRNA_TRANSCRIPTS {
 
     script:
     """
-    $baseDir/bin/get_rrna_transcripts.py --gtf ${gtf} --output rrna.gtf
+    $baseDir/bin/get_rrna_transcripts.py ${gtf} rrna.gtf
 
     $baseDir/bin/gtf2bed rrna.gtf > rrna.bed
 
diff --git a/modules/nf-core/bedops/convert2bed/environment.yml b/modules/nf-core/bedops/convert2bed/environment.yml
deleted file mode 100644
index 3c13066f..00000000
--- a/modules/nf-core/bedops/convert2bed/environment.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - "bioconda::bedops=2.4.41"
diff --git a/modules/nf-core/bedops/convert2bed/main.nf b/modules/nf-core/bedops/convert2bed/main.nf
deleted file mode 100644
index a23efbd5..00000000
--- a/modules/nf-core/bedops/convert2bed/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-process BEDOPS_CONVERT2BED {
-    tag "$meta.id"
-    label 'process_single'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bedops:2.4.41--h4ac6f70_2':
-        'biocontainers/bedops:2.4.41--h4ac6f70_2' }"
-
-    input:
-    tuple val(meta), path(in_file)
-
-    output:
-    tuple val(meta), path("*.bed"), emit: bed
-    path "versions.yml"           , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def format = in_file.getExtension()
-    """
-    convert2bed \\
-        $args \\
-        -i $format \\
-        < $in_file \\
-        > ${prefix}.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bedops/convert2bed: \$(convert2bed --version | grep vers | sed 's/^.*.version:  //')
-    END_VERSIONS
-    """
-
-    stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bedops/convert2bed: \$(convert2bed --version | grep vers | sed 's/^.*.version:  //')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/bedops/convert2bed/meta.yml b/modules/nf-core/bedops/convert2bed/meta.yml
deleted file mode 100644
index 6d84c031..00000000
--- a/modules/nf-core/bedops/convert2bed/meta.yml
+++ /dev/null
@@ -1,45 +0,0 @@
-name: "bedops_convert2bed"
-description: Convert BAM/GFF/GTF/GVF/PSL files to bed
-keywords:
-  - convert
-  - bed
-  - genomics
-tools:
-  - "bedops":
-      description: "High-performance genomic feature operations."
-      homepage: "https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/convert2bed.html#convert2bed"
-      documentation: "https://bedops.readthedocs.io/en/latest/"
-      tool_dev_url: "https://github.com/bedops"
-      doi: "10.1093/bioinformatics/bts277"
-      licence: ["GNU v2"]
-      identifier: biotools:bedops
-
-input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
-    - in_file:
-        type: file
-        description: Input file
-output:
-  - bed:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
-      - "*.bed":
-          type: file
-          description: Sorted BED file
-          pattern: "*.{bed}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
-authors:
-  - "@rannick"
-maintainers:
-  - "@rannick"
diff --git a/modules/nf-core/bedops/convert2bed/tests/main.nf.test b/modules/nf-core/bedops/convert2bed/tests/main.nf.test
deleted file mode 100644
index 3f2b193a..00000000
--- a/modules/nf-core/bedops/convert2bed/tests/main.nf.test
+++ /dev/null
@@ -1,59 +0,0 @@
-// nf-core modules test bedops/convert2bed
-nextflow_process {
-
-    name "Test Process BEDOPS_CONVERT2BED"
-    script "../main.nf"
-    process "BEDOPS_CONVERT2BED"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "bedops"
-    tag "bedops/convert2bed"
-
-    test("sarscov2 - gtf") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
-                    ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - gtf - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
-                    ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/bedops/convert2bed/tests/main.nf.test.snap b/modules/nf-core/bedops/convert2bed/tests/main.nf.test.snap
deleted file mode 100644
index e2482924..00000000
--- a/modules/nf-core/bedops/convert2bed/tests/main.nf.test.snap
+++ /dev/null
@@ -1,68 +0,0 @@
-{
-    "sarscov2 - gtf - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,d3d58dde1d9baba3700ff9fb5a45ce5b"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,d3d58dde1d9baba3700ff9fb5a45ce5b"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-11T12:06:14.755423333"
-    },
-    "sarscov2 - gtf": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,adfdd36e848a62f4b0ea8a694abe9659"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,d3d58dde1d9baba3700ff9fb5a45ce5b"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,adfdd36e848a62f4b0ea8a694abe9659"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,d3d58dde1d9baba3700ff9fb5a45ce5b"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-11T12:06:08.876003152"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/bedops/convert2bed/tests/tags.yml b/modules/nf-core/bedops/convert2bed/tests/tags.yml
deleted file mode 100644
index fd2c2993..00000000
--- a/modules/nf-core/bedops/convert2bed/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-bedops/convert2bed:
-  - "modules/nf-core/bedops/convert2bed/**"