diff --git a/modules.json b/modules.json
index 6830ce56..32d0ca5c 100644
--- a/modules.json
+++ b/modules.json
@@ -45,11 +45,6 @@
                         "git_sha": "72e277acfd9e61a9f1368eafb4a9e83f5bcaa9f5",
                         "installed_by": ["modules"]
                     },
-                    "samtools/faidx": {
-                        "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
-                    },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
diff --git a/modules/local/blobtk_depth.nf b/modules/local/blobtk_depth.nf
index 1d96340f..721ae1d7 100644
--- a/modules/local/blobtk_depth.nf
+++ b/modules/local/blobtk_depth.nf
@@ -8,7 +8,7 @@ process BLOBTK_DEPTH {
     container "docker.io/genomehubs/blobtk:0.6.5"
 
     input:
-    tuple val(meta), path(cram), path(bai)
+    tuple val(meta), path(bam), path(bai)
 
     output:
     tuple val(meta), path('*.coverage.bedGraph')    , emit: bedgraph
@@ -22,7 +22,7 @@ process BLOBTK_DEPTH {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     blobtk depth \\
-        -c ${cram} \\
+        -b ${bam} \\
         $args \\
         -O ${prefix}.coverage.bedGraph \\
 
diff --git a/modules/local/change_name.nf b/modules/local/change_name.nf
index 2136e2da..a6aba96b 100644
--- a/modules/local/change_name.nf
+++ b/modules/local/change_name.nf
@@ -1,43 +1,26 @@
 process CHANGE_NAME {
     tag "$meta.id"
-    label 'process_single'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+    executor 'local'
 
     input:
     tuple val(meta), path(file)
 
     output:
     tuple val(meta), path("*.${file.extension}"), emit: file
-    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     def prefix = task.ext.prefix ?: "${meta.id}"
     def new_fn = "${prefix}.${file.extension}"
     """
-    ln -s ${file} ${new_fn}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        coreutils: $VERSION
-    END_VERSIONS
+    ln -sf ${file} ${new_fn}
     """
 
     stub:
-    def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${new_fn}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        coreutils: $VERSION
-    END_VERSIONS
     """
 }
 
diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
deleted file mode 100644
index 62054fc9..00000000
--- a/modules/nf-core/samtools/faidx/environment.yml
+++ /dev/null
@@ -1,8 +0,0 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - bioconda::htslib=1.21
-  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
deleted file mode 100644
index 28c0a81c..00000000
--- a/modules/nf-core/samtools/faidx/main.nf
+++ /dev/null
@@ -1,50 +0,0 @@
-process SAMTOOLS_FAIDX {
-    tag "$fasta"
-    label 'process_single'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ 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(fasta)
-    tuple val(meta2), path(fai)
-
-    output:
-    tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true
-    tuple val(meta), path ("*.fai")        , emit: fai, optional: true
-    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 \\
-        $fasta \\
-        $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
-    """
-
-    stub:
-    def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll()
-    def fastacmd = match[0] ? "touch ${match[0][1]}" : ''
-    """
-    ${fastacmd}
-    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 6721b2cb..00000000
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ /dev/null
@@ -1,80 +0,0 @@
-name: samtools_faidx
-description: Index FASTA file
-keywords:
-  - index
-  - fasta
-  - faidx
-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"]
-      identifier: biotools:samtools
-input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing reference information
-          e.g. [ id:'test' ]
-    - fasta:
-        type: file
-        description: FASTA file
-        pattern: "*.{fa,fasta}"
-  - - meta2:
-        type: map
-        description: |
-          Groovy Map containing reference information
-          e.g. [ id:'test' ]
-    - fai:
-        type: file
-        description: FASTA index file
-        pattern: "*.{fai}"
-output:
-  - fa:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.{fa,fasta}":
-          type: file
-          description: FASTA file
-          pattern: "*.{fa}"
-  - fai:
-      - 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:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.gzi":
-          type: file
-          description: Optional gzip index file for compressed inputs
-          pattern: "*.gzi"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
-authors:
-  - "@drpatelh"
-  - "@ewels"
-  - "@phue"
-maintainers:
-  - "@drpatelh"
-  - "@ewels"
-  - "@phue"
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test
deleted file mode 100644
index 17244ef2..00000000
--- a/modules/nf-core/samtools/faidx/tests/main.nf.test
+++ /dev/null
@@ -1,122 +0,0 @@
-nextflow_process {
-
-    name "Test Process SAMTOOLS_FAIDX"
-    script "../main.nf"
-    process "SAMTOOLS_FAIDX"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "samtools"
-    tag "samtools/faidx"
-
-    test("test_samtools_faidx") {
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-
-                input[1] = [[],[]]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_bgzip") {
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)]
-
-                input[1] = [[],[]]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_fasta") {
-
-        config "./nextflow.config"
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-
-                input[1] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_stub_fasta") {
-
-        config "./nextflow2.config"
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-
-                input[1] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_stub_fai") {
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-
-                input[1] = [[],[]]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
deleted file mode 100644
index 1bbb3ec2..00000000
--- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
+++ /dev/null
@@ -1,249 +0,0 @@
-{
-    "test_samtools_faidx": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "gzi": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-16T07:57:47.450887871"
-    },
-    "test_samtools_faidx_bgzip": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
-                    ]
-                ],
-                "3": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "gzi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-16T07:58:04.804905659"
-    },
-    "test_samtools_faidx_fasta": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ],
-                "fa": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
-                    ]
-                ],
-                "fai": [
-                    
-                ],
-                "gzi": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-16T07:58:23.831268154"
-    },
-    "test_samtools_faidx_stub_fasta": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ],
-                "fa": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "fai": [
-                    
-                ],
-                "gzi": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-16T07:58:35.600243706"
-    },
-    "test_samtools_faidx_stub_fai": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "gzi": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-16T07:58:54.705460167"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config
deleted file mode 100644
index f76a3ba0..00000000
--- a/modules/nf-core/samtools/faidx/tests/nextflow.config
+++ /dev/null
@@ -1,7 +0,0 @@
-process {
-
-    withName: SAMTOOLS_FAIDX {
-        ext.args = 'MT192765.1 -o extract.fa'
-    }
-
-}
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config
deleted file mode 100644
index 33ebbd5d..00000000
--- a/modules/nf-core/samtools/faidx/tests/nextflow2.config
+++ /dev/null
@@ -1,6 +0,0 @@
-process {
-
-    withName: SAMTOOLS_FAIDX {
-        ext.args = '-o extract.fa'
-    }
-}
diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml
deleted file mode 100644
index e4a83948..00000000
--- a/modules/nf-core/samtools/faidx/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-samtools/faidx:
-  - modules/nf-core/samtools/faidx/**
diff --git a/subworkflows/local/convert_stats.nf b/subworkflows/local/convert_stats.nf
index 8e7267e7..cc32345d 100644
--- a/subworkflows/local/convert_stats.nf
+++ b/subworkflows/local/convert_stats.nf
@@ -23,7 +23,7 @@ workflow CONVERT_STATS {
     take:
     bam      // channel: [ val(meta), /path/to/bam, /path/to/bai ]
     fasta    // channel: [ val(meta), /path/to/fasta ]
-    ch_header
+    header   // channel: /path/to/header.sam
 
     main:
     ch_versions = Channel.empty()
@@ -46,14 +46,13 @@ workflow CONVERT_STATS {
                 run_crumble: meta.datatype == "hic" || meta.datatype == "illumina" || meta.datatype == "pacbio"
                 no_crumble: true
         }
-        | set { ch_bams }
+        | set { crumble_selector }
 
-        CRUMBLE ( ch_bams.run_crumble, [], [] )
+        CRUMBLE ( crumble_selector.run_crumble, [], [] )
         ch_versions = ch_versions.mix( CRUMBLE.out.versions )
 
-        // Convert BAM to CRAM
         CRUMBLE.out.bam
-        | mix( ch_bams.no_crumble )
+        | mix( crumble_selector.no_crumble )
         | map { meta, bam -> [meta, bam, []] }
         | set { ch_bams_for_conversion }
 
@@ -89,7 +88,6 @@ workflow CONVERT_STATS {
         ch_bams_to_index = ch_bams_for_conversion.map{ it -> [it[0], it[1]]}
         // Change name of BAM files to final name for publishing
         ch_bam = CHANGE_NAME ( ch_bams_to_index ).file
-        ch_versions = ch_versions.mix( CHANGE_NAME.out.versions.first() )
 
         // Reindex BAM
         SAMTOOLS_INDEX ( ch_bam )
@@ -106,8 +104,8 @@ workflow CONVERT_STATS {
 
     // Optionally insert params.header information to bams
     if ( params.header ) {
-        ch_bam = SAMTOOLS_REHEADER_BAM ( ch_bam, ch_header.first() ).bam
-        ch_cram = SAMTOOLS_REHEADER_CRAM ( ch_cram, ch_header.first() ).bam
+        ch_bam = SAMTOOLS_REHEADER_BAM ( ch_bam, header.first() ).bam
+        ch_cram = SAMTOOLS_REHEADER_CRAM ( ch_cram, header.first() ).cram
         ch_versions = ch_versions.mix ( SAMTOOLS_REHEADER_BAM.out.versions )
                                 .mix ( SAMTOOLS_REHEADER_CRAM.out.versions )
     }