diff --git a/modules.json b/modules.json
index 22939a8d..e396008c 100644
--- a/modules.json
+++ b/modules.json
@@ -102,11 +102,6 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
-                    "samtools/faidx": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
-                    },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
deleted file mode 100644
index 4dd0e5b0..00000000
--- a/modules/nf-core/samtools/faidx/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-process SAMTOOLS_FAIDX {
-    tag "$fasta"
-    label 'process_single'
-
-    conda "bioconda::samtools=1.17"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
-
-    input:
-    tuple val(meta), path(fasta)
-
-    output:
-    tuple val(meta), path ("*.fai"), emit: fai
-    tuple val(meta), path ("*.gzi"), emit: gzi, optional: true
-    path "versions.yml"            , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    """
-    samtools \\
-        faidx \\
-        $args \\
-        $fasta
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
-    """
-
-    stub:
-    """
-    touch ${fasta}.fai
-    cat <<-END_VERSIONS > versions.yml
-
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
deleted file mode 100644
index fe2fe9a1..00000000
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ /dev/null
@@ -1,47 +0,0 @@
-name: samtools_faidx
-description: Index FASTA file
-keywords:
-  - index
-  - fasta
-tools:
-  - samtools:
-      description: |
-        SAMtools is a set of utilities for interacting with and post-processing
-        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
-        These files are generated as output by short read aligners like BWA.
-      homepage: http://www.htslib.org/
-      documentation: http://www.htslib.org/doc/samtools.html
-      doi: 10.1093/bioinformatics/btp352
-      licence: ["MIT"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - fasta:
-      type: file
-      description: FASTA file
-      pattern: "*.{fa,fasta}"
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - fai:
-      type: file
-      description: FASTA index file
-      pattern: "*.{fai}"
-  - gzi:
-      type: file
-      description: Optional gzip index file for compressed inputs
-      pattern: "*.gzi"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@drpatelh"
-  - "@ewels"
-  - "@phue"
diff --git a/workflows/crisprseq_targeted.nf b/workflows/crisprseq_targeted.nf
index 53c28942..6556d79d 100644
--- a/workflows/crisprseq_targeted.nf
+++ b/workflows/crisprseq_targeted.nf
@@ -75,7 +75,6 @@ include { MINIMAP2_ALIGN as MINIMAP2_ALIGN_ORIGINAL } from '../modules/nf-core/m
 include { MINIMAP2_ALIGN as MINIMAP2_ALIGN_UMI_1    } from '../modules/nf-core/minimap2/align/main'
 include { MINIMAP2_ALIGN as MINIMAP2_ALIGN_UMI_2    } from '../modules/nf-core/minimap2/align/main'
 include { MINIMAP2_ALIGN as MINIMAP2_ALIGN_TEMPLATE } from '../modules/nf-core/minimap2/align/main'
-include { SAMTOOLS_FAIDX                            } from '../modules/nf-core/samtools/faidx/main'
 include { MINIMAP2_INDEX                            } from '../modules/nf-core/minimap2/index/main'
 include { MEDAKA                                    } from '../modules/nf-core/medaka/main'
 include { CUTADAPT                                  } from '../modules/nf-core/cutadapt/main'