diff --git a/modules/local/samtools/fastq_longread/main.nf b/modules/local/samtools/fastq_longread/main.nf
deleted file mode 100644
index e2ec25c5..00000000
--- a/modules/local/samtools/fastq_longread/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-process SAMTOOLS_LONGREAD_FASTQ {
-    tag "$meta.id"
-    label 'process_low'
-
-    conda "bioconda::samtools=1.21"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
-        'biocontainers/samtools:1.21--h50ea8bc_0' }"
-
-    input:
-    tuple val(meta), path(input)
-
-    output:
-    tuple val(meta), path("*.fastq.gz")            , emit: fastq
-    tuple val(meta), path("*_other.fastq.gz")      , optional:true, emit: other
-    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 output = "-o ${prefix}.fastq.gz"
-    """
-    samtools \\
-        fastq \\
-        $args \\
-        --threads ${task.cpus-1} \\
-        -0 ${prefix}_other.fastq.gz \\
-        $output \\
-        $input
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
-    """
-}
diff --git a/subworkflows/local/longread_hostremoval.nf b/subworkflows/local/longread_hostremoval.nf
index a8c8bcd5..b4834c59 100644
--- a/subworkflows/local/longread_hostremoval.nf
+++ b/subworkflows/local/longread_hostremoval.nf
@@ -6,7 +6,7 @@
 include { MINIMAP2_INDEX as MINIMAP2_HOST_INDEX                 } from '../../modules/nf-core/minimap2/index/main'
 include { MINIMAP2_ALIGN as MINIMAP2_HOST_ALIGN                 } from '../../modules/nf-core/minimap2/align/main'
 include { SAMTOOLS_VIEW as SAMTOOLS_HOSTREMOVED_VIEW            } from '../../modules/nf-core/samtools/view/main'
-include { SAMTOOLS_LONGREAD_FASTQ as SAMTOOLS_HOSTREMOVED_FASTQ } from '../../modules/local/samtools/fastq_longread/main'
+include { SAMTOOLS_FASTQ as SAMTOOLS_HOSTREMOVED_FASTQ          } from '../../modules/nf-core/samtools/fastq/main'
 include { SAMTOOLS_INDEX as SAMTOOLS_HOSTREMOVED_INDEX          } from '../../modules/nf-core/samtools/index/main'
 include { SAMTOOLS_STATS as SAMTOOLS_HOSTREMOVED_STATS          } from '../../modules/nf-core/samtools/stats/main'
 
@@ -36,7 +36,7 @@ workflow LONGREAD_HOSTREMOVAL {
     SAMTOOLS_HOSTREMOVED_VIEW ( ch_minimap2_mapped , [[],[]], [] )
     ch_versions      = ch_versions.mix( SAMTOOLS_HOSTREMOVED_VIEW.out.versions.first() )
 
-    SAMTOOLS_HOSTREMOVED_FASTQ ( SAMTOOLS_HOSTREMOVED_VIEW.out.bam )
+    SAMTOOLS_HOSTREMOVED_FASTQ ( SAMTOOLS_HOSTREMOVED_VIEW.out.bam, false )
     ch_versions      = ch_versions.mix( SAMTOOLS_HOSTREMOVED_FASTQ.out.versions.first() )
 
     // Indexing whole BAM for host removal statistics