diff --git a/CHANGELOG.md b/CHANGELOG.md
index ff4ec69..69e8982 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,7 +2,11 @@
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-Naming based on: [Mythical creatures](https://en.wikipedia.org/wiki/List_of_legendary_creatures_by_type).
+Naming based on: [Audiologists](https://en.wikipedia.org/wiki/Category:Audiologists).
+
+## v0.7.0 - Chris Campbell [13/12/2024]
+
+- TODO
 
 ## v0.6.1 - Robert Beiny H1 [08/10/2024]
 
diff --git a/modules.json b/modules.json
index d4e081b..8ca244a 100644
--- a/modules.json
+++ b/modules.json
@@ -7,34 +7,34 @@
                 "nf-core": {
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gfastats": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/gfastats/gfastats.diff"
                     },
                     "merquryfk/merquryfk": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff"
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml
index 17a04ef..9b01c86 100644
--- a/modules/nf-core/cat/cat/environment.yml
+++ b/modules/nf-core/cat/cat/environment.yml
@@ -1,7 +1,5 @@
-name: cat_cat
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::pigz=2.3.4
diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml
index 00a8db0..81778a0 100644
--- a/modules/nf-core/cat/cat/meta.yml
+++ b/modules/nf-core/cat/cat/meta.yml
@@ -9,25 +9,32 @@ tools:
       description: Just concatenation
       documentation: https://man7.org/linux/man-pages/man1/cat.1.html
       licence: ["GPL-3.0-or-later"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - files_in:
-      type: file
-      description: List of compressed / uncompressed files
-      pattern: "*"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - files_in:
+        type: file
+        description: List of compressed / uncompressed files
+        pattern: "*"
 output:
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - file_out:
-      type: file
-      description: Concatenated file. Will be gzipped if file_out ends with ".gz"
-      pattern: "${file_out}"
+      - meta:
+          type: file
+          description: Concatenated file. Will be gzipped if file_out ends with ".gz"
+          pattern: "${file_out}"
+      - ${prefix}:
+          type: file
+          description: Concatenated file. Will be gzipped if file_out ends with ".gz"
+          pattern: "${file_out}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@erikrikarddaniel"
   - "@FriederikeHanssen"
diff --git a/modules/nf-core/gfastats/environment.yml b/modules/nf-core/gfastats/environment.yml
index 1c875ce..b47bbdb 100644
--- a/modules/nf-core/gfastats/environment.yml
+++ b/modules/nf-core/gfastats/environment.yml
@@ -1,7 +1,5 @@
-name: gfastats
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::gfastats=1.3.6
diff --git a/modules/nf-core/gfastats/meta.yml b/modules/nf-core/gfastats/meta.yml
index d0e97a8..a621343 100644
--- a/modules/nf-core/gfastats/meta.yml
+++ b/modules/nf-core/gfastats/meta.yml
@@ -16,56 +16,67 @@ tools:
       documentation: "https://github.com/vgl-hub/gfastats/tree/main/instructions"
       tool_dev_url: "https://github.com/vgl-hub/gfastats"
       doi: "10.1093/bioinformatics/btac460"
-      licence: "['MIT']"
+      licence: ["MIT"]
+      identifier: biotools:gfastats
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - assembly:
-      type: file
-      description: Draft assembly file
-      pattern: "*.{fasta,fastq,gfa}(.gz)?"
-  - out_fmt:
-      type: string
-      description: Output format (fasta, fastq, gfa)
-  - genome_size:
-      type: integer
-      description: estimated genome size (bp) for NG* statistics (optional).
-  - target:
-      type: string
-      description: target specific sequence by header, optionally with coordinates (optional).
-  - agpfile:
-      type: file
-      description: converts input agp to path and replaces existing paths.
-  - include_bed:
-      type: file
-      description: generates output on a subset list of headers or coordinates in 0-based bed format.
-  - exclude_bed:
-      type: file
-      description: opposite of --include-bed. They can be combined (no coordinates).
-  - instructions:
-      type: file
-      description: set of instructions provided as an ordered list.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - assembly:
+        type: file
+        description: Draft assembly file
+        pattern: "*.{fasta,fastq,gfa}(.gz)?"
+  - - out_fmt:
+        type: string
+        description: Output format (fasta, fastq, gfa)
+  - - genome_size:
+        type: integer
+        description: estimated genome size (bp) for NG* statistics (optional).
+  - - target:
+        type: string
+        description: target specific sequence by header, optionally with coordinates
+          (optional).
+  - - agpfile:
+        type: file
+        description: converts input agp to path and replaces existing paths.
+  - - include_bed:
+        type: file
+        description: generates output on a subset list of headers or coordinates in
+          0-based bed format.
+  - - exclude_bed:
+        type: file
+        description: opposite of --include-bed. They can be combined (no coordinates).
+  - - instructions:
+        type: file
+        description: set of instructions provided as an ordered list.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - assembly_summary:
-      type: file
-      description: Assembly summary statistics file
-      pattern: "*.assembly_summary"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.assembly_summary":
+          type: file
+          description: Assembly summary statistics file
+          pattern: "*.assembly_summary"
   - assembly:
-      type: file
-      description: The assembly as modified by gfastats
-      pattern: "*.{fasta,fastq,gfa}.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.${out_fmt}.gz":
+          type: file
+          description: The assembly as modified by gfastats
+          pattern: "*.{fasta,fastq,gfa}.gz"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@mahesh-panchal"
 maintainers:
diff --git a/modules/nf-core/merquryfk/merquryfk/environment.yml b/modules/nf-core/merquryfk/merquryfk/environment.yml
deleted file mode 100644
index 44a5ee9..0000000
--- a/modules/nf-core/merquryfk/merquryfk/environment.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-name: merquryfk_merquryfk
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
diff --git a/modules/nf-core/merquryfk/merquryfk/main.nf b/modules/nf-core/merquryfk/merquryfk/main.nf
index f0e78cc..79c404d 100644
--- a/modules/nf-core/merquryfk/merquryfk/main.nf
+++ b/modules/nf-core/merquryfk/merquryfk/main.nf
@@ -6,26 +6,28 @@ process MERQURYFK_MERQURYFK {
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2'
 
     input:
-    tuple val(meta), path(fastk_hist), path(fastk_ktab), path(assembly), path(haplotigs)
+    tuple val(meta), path(fastk_hist),path(fastk_ktab),path(assembly),path(haplotigs)
+    path matktab                                                                        //optional
+    path patktab                                                                        //optional
 
     output:
-    tuple val(meta), path("${prefix}.completeness.stats") , emit: stats
-    tuple val(meta), path("${prefix}.*_only.bed")         , emit: bed
-    tuple val(meta), path("${prefix}.*.qv")               , emit: assembly_qv
-    tuple val(meta), path("${prefix}.*.spectra-cn.fl.png"), emit: spectra_cn_fl_png,  optional: true
-    tuple val(meta), path("${prefix}.*.spectra-cn.fl.pdf"), emit: spectra_cn_fl_pdf,  optional: true
-    tuple val(meta), path("${prefix}.*.spectra-cn.ln.png"), emit: spectra_cn_ln_png,  optional: true
-    tuple val(meta), path("${prefix}.*.spectra-cn.ln.pdf"), emit: spectra_cn_ln_pdf,  optional: true
-    tuple val(meta), path("${prefix}.*.spectra-cn.st.png"), emit: spectra_cn_st_png,  optional: true
-    tuple val(meta), path("${prefix}.*.spectra-cn.st.pdf"), emit: spectra_cn_st_pdf,  optional: true
-    tuple val(meta), path("${prefix}.qv")                 , emit: qv
-    tuple val(meta), path("${prefix}.spectra-asm.fl.png") , emit: spectra_asm_fl_png, optional: true
-    tuple val(meta), path("${prefix}.spectra-asm.fl.pdf") , emit: spectra_asm_fl_pdf, optional: true
-    tuple val(meta), path("${prefix}.spectra-asm.ln.png") , emit: spectra_asm_ln_png, optional: true
-    tuple val(meta), path("${prefix}.spectra-asm.ln.pdf") , emit: spectra_asm_ln_pdf, optional: true
-    tuple val(meta), path("${prefix}.spectra-asm.st.png") , emit: spectra_asm_st_png, optional: true
-    tuple val(meta), path("${prefix}.spectra-asm.st.pdf") , emit: spectra_asm_st_pdf, optional: true
-    path "versions.yml"                                   , emit: versions
+    tuple val(meta), path("${prefix}.completeness.stats")         , emit: stats
+    tuple val(meta), path("${prefix}.*_only.bed")                 , emit: bed
+    tuple val(meta), path("${prefix}.*.qv")                       , emit: assembly_qv
+    tuple val(meta), path("${prefix}.*.spectra-cn.fl.{png,pdf}")  , emit: spectra_cn_fl,  optional: true
+    tuple val(meta), path("${prefix}.*.spectra-cn.ln.{png,pdf}")  , emit: spectra_cn_ln,  optional: true
+    tuple val(meta), path("${prefix}.*.spectra-cn.st.{png,pdf}")  , emit: spectra_cn_st,  optional: true
+    tuple val(meta), path("${prefix}.qv")                         , emit: qv
+    tuple val(meta), path("${prefix}.spectra-asm.fl.{png,pdf}")   , emit: spectra_asm_fl, optional: true
+    tuple val(meta), path("${prefix}.spectra-asm.ln.{png,pdf}")   , emit: spectra_asm_ln, optional: true
+    tuple val(meta), path("${prefix}.spectra-asm.st.{png,pdf}")   , emit: spectra_asm_st, optional: true
+    tuple val(meta), path("${prefix}.phased_block.bed")           , emit: phased_block_bed,   optional: true
+    tuple val(meta), path("${prefix}.phased_block.stats")         , emit: phased_block_stats, optional: true
+    tuple val(meta), path("${prefix}.continuity.N.{pdf,png}")     , emit: continuity_N,       optional: true
+    tuple val(meta), path("${prefix}.block.N.{pdf,png}")          , emit: block_N,            optional: true
+    tuple val(meta), path("${prefix}.block.blob.{pdf,png}")       , emit: block_blob,         optional: true
+    tuple val(meta), path("${prefix}.hapmers.blob.{pdf,png}")     , emit: hapmers_blob,       optional: true
+    path "versions.yml"                                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -37,11 +39,10 @@ process MERQURYFK_MERQURYFK {
     }
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
+    def mat_ktab = matktab ? "${matktab.find{ it.toString().endsWith(".ktab") }}" : ''
+    def pat_ktab = patktab ? "${patktab.find{ it.toString().endsWith(".ktab") }}" : ''
     def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     def MERQURY_VERSION = '8ae344092df5dcaf83cfb7f90f662597a9b1fc61' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-
-    // Passing in the link through FASTK works, however passing in through YAML_INPUT results in being unable to find file
-    // seems as though it is because it is in a folder rather directly in the folder merqury is running in.
     """
     cp ${fastk_ktab}/*ktab . && cp ${fastk_ktab}/.*ktab.* .
 
@@ -60,4 +61,20 @@ process MERQURYFK_MERQURYFK {
         r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
     END_VERSIONS
     """
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def MERQURY_VERSION = '8ae344092df5dcaf83cfb7f90f662597a9b1fc61' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.completeness.stats
+    touch ${prefix}.qv
+    touch ${prefix}._.qv
+    touch ${prefix}._only.bed
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastk: $FASTK_VERSION
+        merquryfk: $MERQURY_VERSION
+        r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff b/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff
index 751b30b..84c5901 100644
--- a/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff
+++ b/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff
@@ -1,13 +1,9 @@
 Changes in module 'nf-core/merquryfk/merquryfk'
 --- modules/nf-core/merquryfk/merquryfk/main.nf
 +++ modules/nf-core/merquryfk/merquryfk/main.nf
-@@ -39,11 +39,16 @@
-     prefix = task.ext.prefix ?: "${meta.id}"
+@@ -44,12 +44,12 @@
      def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
      def MERQURY_VERSION = '8ae344092df5dcaf83cfb7f90f662597a9b1fc61' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-+
-+    // Passing in the link through FASTK works, however passing in through YAML_INPUT results in being unable to find file
-+    // seems as though it is because it is in a folder rather directly in the folder merqury is running in.
      """
 +    cp ${fastk_ktab}/*ktab . && cp ${fastk_ktab}/.*ktab.* .
 +
@@ -15,6 +11,8 @@ Changes in module 'nf-core/merquryfk/merquryfk'
          $args \\
          -T$task.cpus \\
 -        ${fastk_ktab.find{ it.toString().endsWith(".ktab") }} \\
+-        ${mat_ktab} \\
+-        ${pat_ktab} \\
 +        *.ktab \\
          $assembly \\
          $haplotigs \\
diff --git a/modules/nf-core/merquryfk/merquryfk/meta.yml b/modules/nf-core/merquryfk/merquryfk/meta.yml
index 7d4af79..82bfbec 100644
--- a/modules/nf-core/merquryfk/merquryfk/meta.yml
+++ b/modules/nf-core/merquryfk/merquryfk/meta.yml
@@ -9,104 +9,209 @@ tools:
       description: "FastK based version of Merqury"
       homepage: "https://github.com/thegenemyers/MERQURY.FK"
       tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK"
-      licence: "https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"
+      licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - fastk_hist:
-      type: file
-      description: A histogram files from the program FastK
-      pattern: "*.hist"
-  - fastk_ktab:
-      type: file
-      description: Histogram ktab files from the program FastK (option -t)
-      pattern: "*.ktab*"
-  - assembly:
-      type: file
-      description: Genome (primary) assembly files (fasta format)
-      pattern: ".fasta"
-  - haplotigs:
-      type: file
-      description: Assembly haplotigs (fasta format)
-      pattern: ".fasta"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fastk_hist:
+        type: file
+        description: A histogram files from the program FastK
+        pattern: "*.hist"
+    - fastk_ktab:
+        type: file
+        description: Histogram ktab files from the program FastK (option -t)
+        pattern: "*.ktab*"
+    - assembly:
+        type: file
+        description: Genome (primary) assembly files (fasta format)
+        pattern: ".fasta"
+    - haplotigs:
+        type: file
+        description: Assembly haplotigs (fasta format)
+        pattern: ".fasta"
+  - - matktab:
+        type: file
+        description: trio maternal histogram ktab files from the program FastK (option
+          -t)
+        pattern: "*.ktab*"
+  - - patktab:
+        type: file
+        description: trio paternal histogram ktab files from the program FastK (option
+          -t)
+        pattern: "*.ktab*"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - stats:
-      type: file
-      description: Assembly statistics file
-      pattern: "*.completeness.stats"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.completeness.stats:
+          type: file
+          description: Assembly statistics file
+          pattern: "*.completeness.stats"
   - bed:
-      type: file
-      description: Assembly only kmer positions not supported by reads in bed format
-      pattern: "*_only.bed"
-  - spectra_cn_fl_png:
-      type: file
-      description: "Unstacked copy number spectra filled plot in PNG format"
-      pattern: "*.spectra-cn.fl.png"
-  - spectra_cn_ln_png:
-      type: file
-      description: "Unstacked copy number spectra line plot in PNG format"
-      pattern: "*.spectra-cn.ln.png"
-  - spectra_cn_st_png:
-      type: file
-      description: "Stacked copy number spectra line plot in PNG format"
-      pattern: "*.spectra-cn.st.png"
-  - spectra_asm_fl_png:
-      type: file
-      description: "Unstacked assembly spectra filled plot in PNG format"
-      pattern: "*.spectra-asm.fl.png"
-  - spectra_asm_ln_png:
-      type: file
-      description: "Unstacked assembly spectra line plot in PNG format"
-      pattern: "*.spectra-asm.ln.png"
-  - spectra_asm_st_png:
-      type: file
-      description: "Stacked assembly spectra line plot in PNG format"
-      pattern: "*.spectra-asm.st.png"
-  - spectra_cn_fl_pdf:
-      type: file
-      description: "Unstacked copy number spectra filled plot in PDF format"
-      pattern: "*.spectra-cn.fl.pdf"
-  - spectra_cn_ln_pdf:
-      type: file
-      description: "Unstacked copy number spectra line plot in PDF format"
-      pattern: "*.spectra-cn.ln.pdf"
-  - spectra_cn_st_pdf:
-      type: file
-      description: "Stacked copy number spectra line plot in PDF format"
-      pattern: "*.spectra-cn.st.pdf"
-  - spectra_asm_fl_pdf:
-      type: file
-      description: "Unstacked assembly spectra filled plot in PDF format"
-      pattern: "*.spectra-asm.fl.pdf"
-  - spectra_asm_ln_pdf:
-      type: file
-      description: "Unstacked assembly spectra line plot in PDF format"
-      pattern: "*.spectra-asm.ln.pdf"
-  - spectra_asm_st_pdf:
-      type: file
-      description: "Stacked assembly spectra line plot in PDF format"
-      pattern: "*.spectra-asm.st.pdf"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.*_only.bed:
+          type: file
+          description: Assembly only kmer positions not supported by reads in bed format
+          pattern: "*_only.bed"
   - assembly_qv:
-      type: file
-      description: "error and qv table for each scaffold of the assembly"
-      pattern: "*.qv"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.*.qv:
+          type: file
+          description: "error and qv table for each scaffold of the assembly"
+          pattern: "*.qv"
+  - spectra_cn_fl:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.*.spectra-cn.fl.{png,pdf}:
+          type: file
+          description: "Unstacked copy number spectra filled plot in PNG or PDF format"
+          pattern: "*.spectra-cn.fl.{png,pdf}"
+  - spectra_cn_ln:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.*.spectra-cn.ln.{png,pdf}:
+          type: file
+          description: "Unstacked copy number spectra line plot in PNG or PDF format"
+          pattern: "*.spectra-cn.ln.{png,pdf}"
+  - spectra_cn_st:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.*.spectra-cn.st.{png,pdf}:
+          type: file
+          description: "Stacked copy number spectra line plot in PNG or PDF format"
+          pattern: "*.spectra-cn.st.{png,pdf}"
   - qv:
-      type: file
-      description: "error and qv of each assembly as a whole"
-      pattern: "*.qv"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.qv:
+          type: file
+          description: "error and qv of each assembly as a whole"
+          pattern: "*.qv"
+  - spectra_asm_fl:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.spectra-asm.fl.{png,pdf}:
+          type: file
+          description: "Unstacked assembly spectra filled plot in PNG or PDF format"
+          pattern: "*.spectra-asm.fl.{png,pdf}"
+  - spectra_asm_ln:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.spectra-asm.ln.{png,pdf}:
+          type: file
+          description: "Unstacked assembly spectra line plot in PNG or PDF format"
+          pattern: "*.spectra-asm.ln.{png,pdf}"
+  - spectra_asm_st:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.spectra-asm.st.{png,pdf}:
+          type: file
+          description: "Stacked assembly spectra line plot in PNG or PDF format"
+          pattern: "*.spectra-asm.st.{png,pdf}"
+  - phased_block_bed:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.phased_block.bed:
+          type: file
+          description: Assembly kmer positions seperated by block in bed format
+          pattern: "*.phased.block.bed"
+  - phased_block_stats:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.phased_block.stats:
+          type: file
+          description: phased assembly statistics file
+          pattern: "*.phased.block.stats"
+  - continuity_N:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.continuity.N.{pdf,png}:
+          type: file
+          description: "Stacked assembly N continuity plot in PNG or PDF format"
+          pattern: "*.continuity.N.{png,pdf}"
+  - block_N:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.block.N.{pdf,png}:
+          type: file
+          description: "Stacked assembly N continuity by block plot in PNG or PDF format"
+          pattern: "*.block.N.{png,pdf}"
+  - block_blob:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.block.blob.{pdf,png}:
+          type: file
+          description: "Stacked assembly block plot in PNG or PDF format"
+          pattern: "*.block.blob.{png,pdf}"
+  - hapmers_blob:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.hapmers.blob.{pdf,png}:
+          type: file
+          description: "Stacked assembly hapmers block plot in PNG or PDF format"
+          pattern: "*.hapmers.blob.{png,pdf}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@mahesh-panchal"
+  - "@yumisims"
 maintainers:
   - "@mahesh-panchal"
+  - "@yumisims"
diff --git a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test
new file mode 100644
index 0000000..c46843c
--- /dev/null
+++ b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test
@@ -0,0 +1,170 @@
+nextflow_process {
+
+    name "Test Process MERQURYFK"
+    script "../main.nf"
+    process "MERQURYFK_MERQURYFK"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "merquryfk"
+    tag "merquryfk/merquryfk"
+    tag "fastk"
+    tag "fastk/fastk"
+
+    setup {
+            run("FASTK_FASTK") {
+            script "../../../fastk/fastk"
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+            }
+            run("FASTK_FASTK", alias: "FASTK_MAT") {
+            script "../../../fastk/fastk"
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], 
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                ]
+                """
+            }
+            }
+
+        run("FASTK_FASTK", alias: "FASTK_PAT") {
+            script "../../../fastk/fastk"
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                ]
+                """
+            }
+            }
+        }
+
+   test("homo_sapiens - Illumina - png") {
+        config "./nextflow.png.config"
+        when {
+            process {
+                """
+                assembly = [
+                    [ id:'test', single_end:true ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+
+                haplotigs = [
+                    [ id:'test', single_end:true ], []
+                ]
+                input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs))
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - Illumina - pdf") {
+        config "./nextflow.pdf.config"
+        when {
+            process {
+                """
+                assembly = [
+                    [ id:'test', single_end:true ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+
+                haplotigs = [
+                    [ id:'test', single_end:true ], []
+                ]
+                input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs))
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+    
+    test("homo_sapiens - Illumina - trio") {
+        config "./nextflow.trio.config"
+        when {
+            process {
+                """                
+                assembly = [
+                    [ id:'test', single_end:true ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+
+                haplotigs = [
+                    [ id:'test', single_end:true ], []
+                ]
+                input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs))
+                input[1] = FASTK_MAT.out.ktab
+                input[2] = FASTK_PAT.out.ktab
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - Illumina - stub") {
+        options "-stub"
+        config "./nextflow.pdf.config"
+        when {
+            process {
+                """
+                assembly = [
+                    [ id:'test', single_end:true ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+
+                haplotigs = [
+                    [ id:'test', single_end:true ], []
+                ]
+                input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs))
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+
+    
+}
\ No newline at end of file
diff --git a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap
new file mode 100644
index 0000000..f7ce47f
--- /dev/null
+++ b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap
@@ -0,0 +1,454 @@
+{
+    "homo_sapiens - Illumina - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "10": [
+                    
+                ],
+                "11": [
+                    
+                ],
+                "12": [
+                    
+                ],
+                "13": [
+                    
+                ],
+                "14": [
+                    
+                ],
+                "15": [
+                    
+                ],
+                "16": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    
+                ],
+                "8": [
+                    
+                ],
+                "9": [
+                    
+                ],
+                "assembly_qv": [
+                    
+                ],
+                "bed": [
+                    
+                ],
+                "block_N": [
+                    
+                ],
+                "block_blob": [
+                    
+                ],
+                "continuity_N": [
+                    
+                ],
+                "hapmers_blob": [
+                    
+                ],
+                "phased_block_bed": [
+                    
+                ],
+                "phased_block_stats": [
+                    
+                ],
+                "qv": [
+                    
+                ],
+                "spectra_asm_fl": [
+                    
+                ],
+                "spectra_asm_ln": [
+                    
+                ],
+                "spectra_asm_st": [
+                    
+                ],
+                "spectra_cn_fl": [
+                    
+                ],
+                "spectra_cn_ln": [
+                    
+                ],
+                "spectra_cn_st": [
+                    
+                ],
+                "stats": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-15T15:22:52.240373868"
+    },
+    "homo_sapiens - Illumina - pdf": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "10": [
+                    
+                ],
+                "11": [
+                    
+                ],
+                "12": [
+                    
+                ],
+                "13": [
+                    
+                ],
+                "14": [
+                    
+                ],
+                "15": [
+                    
+                ],
+                "16": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    
+                ],
+                "8": [
+                    
+                ],
+                "9": [
+                    
+                ],
+                "assembly_qv": [
+                    
+                ],
+                "bed": [
+                    
+                ],
+                "block_N": [
+                    
+                ],
+                "block_blob": [
+                    
+                ],
+                "continuity_N": [
+                    
+                ],
+                "hapmers_blob": [
+                    
+                ],
+                "phased_block_bed": [
+                    
+                ],
+                "phased_block_stats": [
+                    
+                ],
+                "qv": [
+                    
+                ],
+                "spectra_asm_fl": [
+                    
+                ],
+                "spectra_asm_ln": [
+                    
+                ],
+                "spectra_asm_st": [
+                    
+                ],
+                "spectra_cn_fl": [
+                    
+                ],
+                "spectra_cn_ln": [
+                    
+                ],
+                "spectra_cn_st": [
+                    
+                ],
+                "stats": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-15T15:22:19.530675341"
+    },
+    "homo_sapiens - Illumina - png": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "10": [
+                    
+                ],
+                "11": [
+                    
+                ],
+                "12": [
+                    
+                ],
+                "13": [
+                    
+                ],
+                "14": [
+                    
+                ],
+                "15": [
+                    
+                ],
+                "16": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    
+                ],
+                "8": [
+                    
+                ],
+                "9": [
+                    
+                ],
+                "assembly_qv": [
+                    
+                ],
+                "bed": [
+                    
+                ],
+                "block_N": [
+                    
+                ],
+                "block_blob": [
+                    
+                ],
+                "continuity_N": [
+                    
+                ],
+                "hapmers_blob": [
+                    
+                ],
+                "phased_block_bed": [
+                    
+                ],
+                "phased_block_stats": [
+                    
+                ],
+                "qv": [
+                    
+                ],
+                "spectra_asm_fl": [
+                    
+                ],
+                "spectra_asm_ln": [
+                    
+                ],
+                "spectra_asm_st": [
+                    
+                ],
+                "spectra_cn_fl": [
+                    
+                ],
+                "spectra_cn_ln": [
+                    
+                ],
+                "spectra_cn_st": [
+                    
+                ],
+                "stats": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-15T15:21:57.682723412"
+    },
+    "homo_sapiens - Illumina - trio": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "10": [
+                    
+                ],
+                "11": [
+                    
+                ],
+                "12": [
+                    
+                ],
+                "13": [
+                    
+                ],
+                "14": [
+                    
+                ],
+                "15": [
+                    
+                ],
+                "16": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    
+                ],
+                "8": [
+                    
+                ],
+                "9": [
+                    
+                ],
+                "assembly_qv": [
+                    
+                ],
+                "bed": [
+                    
+                ],
+                "block_N": [
+                    
+                ],
+                "block_blob": [
+                    
+                ],
+                "continuity_N": [
+                    
+                ],
+                "hapmers_blob": [
+                    
+                ],
+                "phased_block_bed": [
+                    
+                ],
+                "phased_block_stats": [
+                    
+                ],
+                "qv": [
+                    
+                ],
+                "spectra_asm_fl": [
+                    
+                ],
+                "spectra_asm_ln": [
+                    
+                ],
+                "spectra_asm_st": [
+                    
+                ],
+                "spectra_cn_fl": [
+                    
+                ],
+                "spectra_cn_ln": [
+                    
+                ],
+                "spectra_cn_st": [
+                    
+                ],
+                "stats": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-08-15T15:22:40.060937299"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.config b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.config
new file mode 100644
index 0000000..ba1eebc
--- /dev/null
+++ b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: 'FASTK_.*' {
+                ext.args   = '-t'
+                publishDir = [ enabled: false ]
+    }
+}
diff --git a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.pdf.config b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.pdf.config
new file mode 100644
index 0000000..52beeaa
--- /dev/null
+++ b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.pdf.config
@@ -0,0 +1,9 @@
+process {
+    withName: 'FASTK_.*' {
+                ext.args   = '-t'
+                publishDir = [ enabled: false ]
+    }
+    withName: 'MERQURYFK_MERQURYFK' {
+        ext.args   = '-lfs -pdf'
+    }
+}
diff --git a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.png.config b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.png.config
new file mode 100644
index 0000000..47c3d63
--- /dev/null
+++ b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.png.config
@@ -0,0 +1,9 @@
+process {
+    withName: 'FASTK_.*' {
+                ext.args   = '-t'
+                publishDir = [ enabled: false ]
+    }
+    withName: 'MERQURYFK_MERQURYFK' {
+        ext.args   = '-lfs'
+    }
+}
diff --git a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.trio.config b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.trio.config
new file mode 100644
index 0000000..47c3d63
--- /dev/null
+++ b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.trio.config
@@ -0,0 +1,9 @@
+process {
+    withName: 'FASTK_.*' {
+                ext.args   = '-t'
+                publishDir = [ enabled: false ]
+    }
+    withName: 'MERQURYFK_MERQURYFK' {
+        ext.args   = '-lfs'
+    }
+}
diff --git a/modules/nf-core/merquryfk/merquryfk/tests/tags.yml b/modules/nf-core/merquryfk/merquryfk/tests/tags.yml
new file mode 100644
index 0000000..7dcac99
--- /dev/null
+++ b/modules/nf-core/merquryfk/merquryfk/tests/tags.yml
@@ -0,0 +1,2 @@
+merquryfk/merquryfk:
+  - "modules/nf-core/merquryfk/merquryfk/**"
diff --git a/modules/nf-core/minimap2/align/environment.yml b/modules/nf-core/minimap2/align/environment.yml
index 41e8fe9..dc6476b 100644
--- a/modules/nf-core/minimap2/align/environment.yml
+++ b/modules/nf-core/minimap2/align/environment.yml
@@ -1,9 +1,6 @@
-name: minimap2_align
-
 channels:
   - conda-forge
   - bioconda
-  - defaults
 
 dependencies:
   - bioconda::htslib=1.20
diff --git a/modules/nf-core/minimap2/align/meta.yml b/modules/nf-core/minimap2/align/meta.yml
index 8996f88..a4cfc89 100644
--- a/modules/nf-core/minimap2/align/meta.yml
+++ b/modules/nf-core/minimap2/align/meta.yml
@@ -14,62 +14,77 @@ tools:
       homepage: https://github.com/lh3/minimap2
       documentation: https://github.com/lh3/minimap2#uguide
       licence: ["MIT"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FASTA or FASTQ files of size 1 and 2 for single-end
-        and paired-end data, respectively.
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'test_ref']
-  - reference:
-      type: file
-      description: |
-        Reference database in FASTA format.
-  - bam_format:
-      type: boolean
-      description: Specify that output should be in BAM format
-  - bam_index_extension:
-      type: string
-      description: BAM alignment index extension (e.g. "bai")
-  - cigar_paf_format:
-      type: boolean
-      description: Specify that output CIGAR should be in PAF format
-  - cigar_bam:
-      type: boolean
-      description: |
-        Write CIGAR with >65535 ops at the CG tag. This is recommended when
-        doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FASTA or FASTQ files of size 1 and 2 for single-end
+          and paired-end data, respectively.
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test_ref']
+    - reference:
+        type: file
+        description: |
+          Reference database in FASTA format.
+  - - bam_format:
+        type: boolean
+        description: Specify that output should be in BAM format
+  - - bam_index_extension:
+        type: string
+        description: BAM alignment index extension (e.g. "bai")
+  - - cigar_paf_format:
+        type: boolean
+        description: Specify that output CIGAR should be in PAF format
+  - - cigar_bam:
+        type: boolean
+        description: |
+          Write CIGAR with >65535 ops at the CG tag. This is recommended when
+          doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - paf:
-      type: file
-      description: Alignment in PAF format
-      pattern: "*.paf"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.paf":
+          type: file
+          description: Alignment in PAF format
+          pattern: "*.paf"
   - bam:
-      type: file
-      description: Alignment in BAM format
-      pattern: "*.bam"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam":
+          type: file
+          description: Alignment in BAM format
+          pattern: "*.bam"
   - index:
-      type: file
-      description: BAM alignment index
-      pattern: "*.bam.*"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam.${bam_index_extension}":
+          type: file
+          description: BAM alignment index
+          pattern: "*.bam.*"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@heuermh"
   - "@sofstam"
diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml
index cd366d6..62054fc 100644
--- a/modules/nf-core/samtools/merge/environment.yml
+++ b/modules/nf-core/samtools/merge/environment.yml
@@ -1,8 +1,8 @@
-name: samtools_merge
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf
index 693b1d8..34da4c7 100644
--- a/modules/nf-core/samtools/merge/main.nf
+++ b/modules/nf-core/samtools/merge/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_MERGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input_files, stageAs: "?/*")
diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml
index 2e8f3db..235aa21 100644
--- a/modules/nf-core/samtools/merge/meta.yml
+++ b/modules/nf-core/samtools/merge/meta.yml
@@ -15,60 +15,81 @@ tools:
       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 sample information
-        e.g. [ id:'test', single_end:false ]
-  - input_files:
-      type: file
-      description: BAM/CRAM file
-      pattern: "*.{bam,cram,sam}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fasta:
-      type: file
-      description: Reference file the CRAM was created with (optional)
-      pattern: "*.{fasta,fa}"
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fai:
-      type: file
-      description: Index of the reference file the CRAM was created with (optional)
-      pattern: "*.fai"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input_files:
+        type: file
+        description: BAM/CRAM file
+        pattern: "*.{bam,cram,sam}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: Reference file the CRAM was created with (optional)
+        pattern: "*.{fasta,fa}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fai:
+        type: file
+        description: Index of the reference file the CRAM was created with (optional)
+        pattern: "*.fai"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - bam:
-      type: file
-      description: BAM file
-      pattern: "*.{bam}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.bam:
+          type: file
+          description: BAM file
+          pattern: "*.{bam}"
   - cram:
-      type: file
-      description: CRAM file
-      pattern: "*.{cram}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.cram:
+          type: file
+          description: CRAM file
+          pattern: "*.{cram}"
   - csi:
-      type: file
-      description: BAM index file (optional)
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: BAM index file (optional)
+          pattern: "*.csi"
   - crai:
-      type: file
-      description: CRAM index file (optional)
-      pattern: "*.crai"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.crai":
+          type: file
+          description: CRAM index file (optional)
+          pattern: "*.crai"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@yuukiiwa "
diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap
index 17bc846..0a41e01 100644
--- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap
@@ -80,14 +80,14 @@
     "bam_versions": {
         "content": [
             [
-                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
+                "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:46:35.851936597"
+        "timestamp": "2024-09-16T09:16:30.476887194"
     },
     "bams_csi": {
         "content": [
@@ -124,14 +124,14 @@
     "bams_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
+                "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:46:41.405707643"
+        "timestamp": "2024-09-16T09:16:52.203823961"
     },
     "bam_cram": {
         "content": [
@@ -158,14 +158,14 @@
     "bams_versions": {
         "content": [
             [
-                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
+                "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:45:51.695689923"
+        "timestamp": "2024-09-16T08:29:57.524363148"
     },
     "crams_bam": {
         "content": [
@@ -182,14 +182,14 @@
     "crams_versions": {
         "content": [
             [
-                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
+                "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:46:30.185392319"
+        "timestamp": "2024-09-16T09:16:06.977096207"
     },
     "bam_csi": {
         "content": [
diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml
index 36a12ea..62054fc 100644
--- a/modules/nf-core/samtools/sort/environment.yml
+++ b/modules/nf-core/samtools/sort/environment.yml
@@ -1,8 +1,8 @@
-name: samtools_sort
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 8e01909..caf3c61 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -4,19 +4,19 @@ process SAMTOOLS_SORT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta) , path(bam)
     tuple val(meta2), path(fasta)
 
     output:
-    tuple val(meta), path("*.bam"),     emit: bam,  optional: true
-    tuple val(meta), path("*.cram"),    emit: cram, optional: true
-    tuple val(meta), path("*.crai"),    emit: crai, optional: true
-    tuple val(meta), path("*.csi"),     emit: csi,  optional: true
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("*.bam"),  emit: bam,  optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.crai"), emit: crai, optional: true
+    tuple val(meta), path("*.csi"),  emit: csi,  optional: true
+    path  "versions.yml",            emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,7 +32,6 @@ process SAMTOOLS_SORT {
 
     """
     samtools cat \\
-        --threads $task.cpus \\
         ${bam} \\
     | \\
     samtools sort \\
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 341a7d0..a9dbec5 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -15,52 +15,73 @@ tools:
       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 sample information
-        e.g. [ id:'test', single_end:false ]
-  - bam:
-      type: file
-      description: BAM/CRAM/SAM file(s)
-      pattern: "*.{bam,cram,sam}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fasta:
-      type: file
-      description: Reference genome FASTA file
-      pattern: "*.{fa,fasta,fna}"
-      optional: true
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM/CRAM/SAM file(s)
+        pattern: "*.{bam,cram,sam}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: Reference genome FASTA file
+        pattern: "*.{fa,fasta,fna}"
+        optional: true
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - bam:
-      type: file
-      description: Sorted BAM file
-      pattern: "*.{bam}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam":
+          type: file
+          description: Sorted BAM file
+          pattern: "*.{bam}"
   - cram:
-      type: file
-      description: Sorted CRAM file
-      pattern: "*.{cram}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.cram":
+          type: file
+          description: Sorted CRAM file
+          pattern: "*.{cram}"
   - crai:
-      type: file
-      description: CRAM index file (optional)
-      pattern: "*.crai"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.crai":
+          type: file
+          description: CRAM index file (optional)
+          pattern: "*.crai"
   - csi:
-      type: file
-      description: BAM index file (optional)
-      pattern: "*.csi"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: BAM index file (optional)
+          pattern: "*.csi"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@ewels"
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test
index c2ea9c7..b05e669 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test
@@ -39,6 +39,40 @@ nextflow_process {
         }
     }
 
+    test("multiple bam") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                        process.out.bam,
+                        process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                        process.out.versions
+                ).match()}
+            )
+        }
+    }
+
     test("cram") {
 
         config "./nextflow_cram.config"
@@ -98,6 +132,36 @@ nextflow_process {
         }
     }
 
+    test("multiple bam - stub") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ])
+                input[1] = Channel.of([
+                    [ id:'fasta' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
     test("cram - stub") {
 
         options "-stub"
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
index da38d5d..469891f 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
@@ -20,14 +20,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                "versions.yml:md5,2659b187d681241451539d4c53500b9f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T17:19:37.196205"
+        "timestamp": "2024-09-16T08:49:58.207549273"
     },
     "bam - stub": {
         "content": [
@@ -57,7 +57,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
                 ],
                 "bam": [
                     [
@@ -84,15 +84,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T15:54:46.580756"
+        "timestamp": "2024-09-16T08:50:08.630951018"
     },
     "cram - stub": {
         "content": [
@@ -122,7 +122,7 @@
                     
                 ],
                 "4": [
-                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
                 ],
                 "bam": [
                     
@@ -149,15 +149,110 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-22T15:57:30.505698"
+        "timestamp": "2024-09-16T08:50:19.061912443"
+    },
+    "multiple bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam.csi"
+                ]
+            ],
+            [
+                "versions.yml:md5,2659b187d681241451539d4c53500b9f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-08T11:59:55.479443"
+    },
+    "multiple bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2659b187d681241451539d4c53500b9f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-08T11:36:13.781404"
     },
     "bam": {
         "content": [
@@ -167,7 +262,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400"
+                    "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc"
                 ]
             ],
             [
@@ -180,13 +275,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062"
+                "versions.yml:md5,2659b187d681241451539d4c53500b9f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-07-22T15:54:25.872954"
+        "timestamp": "2024-10-08T11:59:46.372244"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index c278c76..7436e70 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -224,7 +224,7 @@ manifest {
     description     = """ERGA Assembly Report pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.0'
-    version         = '0.6.1'
+    version         = '0.7.0'
     doi             = 'https://zenodo.org/records/13819520'
 }
 
diff --git a/workflows/ear.nf b/workflows/ear.nf
index 9f1c434..395946d 100644
--- a/workflows/ear.nf
+++ b/workflows/ear.nf
@@ -125,7 +125,9 @@ workflow EAR {
         // MODULE: MERQURYFK PLOTS OF GENOME
         //
         MERQURYFK_MERQURYFK(
-            merquryfk_input
+            merquryfk_input,
+            [],
+            []
         )
         ch_versions = ch_versions.mix( MERQURYFK_MERQURYFK.out.versions )
     }