diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5babbeb9..790022d5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
 [#66](https://github.com/nf-core/multiplesequencealign/issues/66) - README: add new metromap and available tool list.
 [#54](https://github.com/nf-core/multiplesequencealign/issues/54) - Update modules versions from nf-core tools.
 [#80](https://github.com/nf-core/multiplesequencealign/pull/80) - Update modules versions from nf-core tools with nf-test.
+[#32](https://github.com/nf-core/multiplesequencealign/issues/32) - Update Stats workflow with nf-core modules for merging.
 
 ### `Dependencies`
 
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 163dc6e4..98791456 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,3 +1,2 @@
 id,fasta,reference,structures,template
 seatoxin-ref,test-dataset/setoxin-ref.fa,test-dataset/setoxin.ref,https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz,
-toxin-ref,test-dataset/toxin-ref.fa,test-dataset/toxin.ref,
diff --git a/assets/toolsheet.csv b/assets/toolsheet.csv
index deb788c3..7af6a027 100644
--- a/assets/toolsheet.csv
+++ b/assets/toolsheet.csv
@@ -1,8 +1,4 @@
 tree,args_tree,aligner,args_aligner
 FAMSA,"-gt upgma -parttree",FAMSA,""
 "","",MAFFT,"--anysymbol --quiet --dpparttree"
-"","","KALIGN",""
-CLUSTALO,"--force",3DCOFFEE,"-method TMalign_pair"
-CLUSTALO,"--force",TCOFFEE,"-reg -reg_method famsa_msa -reg_nseq 100"
-"","",FAMSA,""
-FAMSA,"",TCOFFEE,"-reg -reg_method famsa_msa -reg_nseq 100"
+
diff --git a/bin/calc_seqstats.py b/bin/calc_seqstats.py
index 098dc70b..9b06a7de 100755
--- a/bin/calc_seqstats.py
+++ b/bin/calc_seqstats.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 from Bio import SeqIO
 import pandas as pd
-import time
 import sys
 
 fam_name = sys.argv[1]
diff --git a/conf/modules.config b/conf/modules.config
index 22bbd186..e153ba6b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -18,6 +18,31 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    withName: TCOFFEE_SEQREFORMAT_SIM{
+        ext.args = "-output=sim_idscore"
+        publishDir = [
+            path: { "${params.outdir}/stats/${task.process.tokenize(':')[-1].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: PARSE_SIM{
+        publishDir = [
+            path: { "${params.outdir}/stats/${task.process.tokenize(':')[-1].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: "CALCULATE_SEQSTATS"{
+        publishDir = [
+            path: { "${params.outdir}/stats/${task.process.tokenize(':')[-1].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: "FAMSA_GUIDETREE"{
         ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}" }
         ext.args = { "${meta.args_tree}" == "null" ? '' : "${meta.args_tree}" }
@@ -38,6 +63,15 @@ process {
         ]
     }
 
+    withName: "CREATE_TCOFFEETEMPLATE"{
+        ext.prefix = { "${meta.id}" }
+        publishDir = [
+            path: { "${params.outdir}/alignment/templates" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: ".*ALIGN"{
         ext.prefix = { "${meta.id}_${meta.tree}-args-${meta.argstree_clean}_${meta.aligner}-args-${meta.argsaligner_clean}" }
         ext.args = { "${meta.args_aligner}" == "null" ? '' : "${meta.args_aligner}" }
@@ -70,7 +104,9 @@ process {
         ]
     }
 
-    withName: "MERGE_STATS"{
+
+    withName: "CONCAT_SEQSTATS"{
+        ext.prefix = { "summary_seqstats" }
         publishDir = [
             path: { "${params.outdir}/stats/" },
             mode: params.publish_dir_mode,
@@ -78,9 +114,19 @@ process {
         ]
     }
 
-    withName: "TCOFFEE_SEQREFORMAT_SIM|CALCULATE_SEQSTATS"{
+    withName: "CONCAT_SIMSTATS"{
+        ext.prefix = { "summary_simstats" }
         publishDir = [
-            path: { "${params.outdir}/stats/${task.process.tokenize(':')[-1].toLowerCase()}" },
+            path: { "${params.outdir}/stats/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: "MERGE_STATS"{
+        ext.prefix = { "complete_summary_stats" }
+        publishDir = [
+            path: { "${params.outdir}/stats/" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/conf/test.config b/conf/test.config
index 359de16c..0ea9a401 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Stats
-    skip_stats = true
+    skip_stats = false
     skip_eval  = true
 
     // Input data
diff --git a/modules.json b/modules.json
index 32ba2d12..00ce3c5e 100644
--- a/modules.json
+++ b/modules.json
@@ -15,6 +15,16 @@
                         "git_sha": "1f253ec05723293df7757af8769f8389b7a1884e",
                         "installed_by": ["modules"]
                     },
+                    "csvtk/concat": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "csvtk/join": {
+                        "branch": "master",
+                        "git_sha": "b2420a8bbd8af137380aa0a0c2e9a92456e5bb21",
+                        "installed_by": ["modules"]
+                    },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
@@ -65,6 +75,11 @@
                         "git_sha": "c83c78835ca6d7a55b3f200718d887cbc7149d37",
                         "installed_by": ["modules"]
                     },
+                    "tcoffee/seqreformat": {
+                        "branch": "master",
+                        "git_sha": "f759fd45ecabb40c761df1338a4bb3851171a7f7",
+                        "installed_by": ["modules"]
+                    },
                     "untar": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
diff --git a/modules/local/calculate_seqstats.nf b/modules/local/calculate_seqstats.nf
index a47ad69c..511d8432 100644
--- a/modules/local/calculate_seqstats.nf
+++ b/modules/local/calculate_seqstats.nf
@@ -3,7 +3,10 @@ process CALCULATE_SEQSTATS {
     tag "$meta.id"
     label 'process_low'
 
-    container 'luisas/structural_regression:20'
+    conda "conda-forge::python=3.11.0   conda-forge::biopython=1.80 conda-forge::pandas=1.5.2"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-27978155697a3671f3ef9aead4b5c823a02cc0b7:548df772fe13c0232a7eab1bc1deb98b495a05ab-0' :
+        'biocontainers/mulled-v2-27978155697a3671f3ef9aead4b5c823a02cc0b7:548df772fe13c0232a7eab1bc1deb98b495a05ab-0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/merge_stats.nf b/modules/local/merge_stats.nf
deleted file mode 100644
index bc9c4b70..00000000
--- a/modules/local/merge_stats.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-
-
-process MERGE_STATS {
-    label 'process_low'
-
-    input:
-    path(tcoffee_seqreformat_simtot)
-    path(seqstats_summary)
-
-    output:
-    path '*.csv'       , emit: csv
-    path "versions.yml", emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    """
-    merge_stats.py \
-        "stats_summary_report.csv" \
-        ${tcoffee_seqreformat_simtot} \
-        ${seqstats_summary}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/parse_sim.nf b/modules/local/parse_sim.nf
new file mode 100644
index 00000000..01d5c4c5
--- /dev/null
+++ b/modules/local/parse_sim.nf
@@ -0,0 +1,30 @@
+process PARSE_SIM {
+    tag "$meta.id"
+    label 'process_low'
+
+    input:
+    tuple val(meta), path(infile)
+
+    output:
+    tuple val (meta), path("${prefix}.sim_tot"), emit: sim_tot
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "$prefix" > tmp
+    grep ^TOT $infile | cut -f4 >> tmp
+
+    echo "id,perc_sim" > ${prefix}.sim_tot
+    cat tmp | tr '\\n' ',' | awk 'gsub(/,\$/,x)' >>  ${prefix}.sim_tot
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.sim_tot
+    """
+}
diff --git a/modules/local/tcoffee_seqreformat_sim.nf b/modules/local/tcoffee_seqreformat_sim.nf
deleted file mode 100644
index b1e6c382..00000000
--- a/modules/local/tcoffee_seqreformat_sim.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-
-
-process TCOFFEE_SEQREFORMAT_SIM {
-    tag "$meta.id"
-    label 'process_low'
-
-    conda "bioconda::t-coffee=13.45.0.4846264"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/t-coffee:13.45.0.4846264--hc57179f_5':
-        'biocontainers/t-coffee:13.45.0.4846264--hc57179f_5' }"
-    input:
-    tuple val(meta), path(fasta)
-
-    output:
-    tuple val(meta), path("*.sim"), emit: perc_sim
-    tuple val(meta), path("*.sim_tot"), emit: perc_sim_tot
-    path "versions.yml" , emit: versions
-
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    t_coffee -other_pg seq_reformat -in ${fasta} -output=sim_idscore > "${prefix}.sim"
-
-    echo "$prefix" > tmp
-    grep ^TOT ${prefix}.sim | cut -f4 >> tmp
-
-    echo "id,perc_sim" > ${prefix}.sim_tot
-    cat tmp | tr '\\n' ',' | awk 'gsub(/,\$/,x)' >>  ${prefix}.sim_tot
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        t_coffee: \$( t_coffee -version | sed 's/.*(Version_\\(.*\\)).*/\\1/' )
-    END_VERSIONS
-    """
-}
-
-
diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf
new file mode 100644
index 00000000..ad209ce7
--- /dev/null
+++ b/modules/nf-core/csvtk/concat/main.nf
@@ -0,0 +1,43 @@
+process CSVTK_CONCAT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::csvtk=0.23.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' :
+        'biocontainers/csvtk:0.23.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(csv)
+    val in_format
+    val out_format
+
+    output:
+    tuple val(meta), path("${prefix}.${out_extension}"), emit: csv
+    path "versions.yml"                                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    def delimiter = in_format == "tsv" ? "\t" : (in_format == "csv" ? "," : in_format)
+    def out_delimiter = out_format == "tsv" ? "\t" : (out_format == "csv" ? "," : out_format)
+    out_extension = out_format == "tsv" ? 'tsv' : 'csv'
+    """
+    csvtk \\
+        concat \\
+        $args \\
+        --num-cpus $task.cpus \\
+        --delimiter "${delimiter}" \\
+        --out-delimiter "${out_delimiter}" \\
+        --out-file ${prefix}.${out_extension} \\
+        $csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/csvtk/concat/meta.yml b/modules/nf-core/csvtk/concat/meta.yml
new file mode 100644
index 00000000..19e0e3b9
--- /dev/null
+++ b/modules/nf-core/csvtk/concat/meta.yml
@@ -0,0 +1,51 @@
+name: csvtk_concat
+description: Concatenate two or more CSV (or TSV) tables into a single table
+keywords:
+  - concatenate
+  - tsv
+  - csv
+tools:
+  - csvtk:
+      description: A cross-platform, efficient, practical CSV/TSV toolkit
+      homepage: http://bioinf.shenwei.me/csvtk
+      documentation: http://bioinf.shenwei.me/csvtk
+      tool_dev_url: https://github.com/shenwei356/csvtk
+
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - csv:
+      type: file
+      description: CSV/TSV formatted files
+      pattern: "*.{csv,tsv}"
+  - in_format:
+      type: string
+      description: Input format (csv, tab, or a delimiting character)
+      pattern: "*"
+  - out_format:
+      type: string
+      description: Output format (csv, tab, or a delimiting character)
+      pattern: "*"
+
+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: "version.yml"
+  - csv:
+      type: file
+      description: Concatenated CSV/TSV file
+      pattern: "*.{csv,tsv}"
+
+authors:
+  - "@rpetit3"
diff --git a/modules/nf-core/csvtk/join/main.nf b/modules/nf-core/csvtk/join/main.nf
new file mode 100644
index 00000000..08833d78
--- /dev/null
+++ b/modules/nf-core/csvtk/join/main.nf
@@ -0,0 +1,50 @@
+process CSVTK_JOIN {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "bioconda::csvtk=0.26.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/csvtk:0.26.0--h9ee0642_0':
+        'biocontainers/csvtk:0.26.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(csv)
+
+    output:
+    tuple val(meta), path("${prefix}.${out_extension}"), emit: csv
+    path "versions.yml"                                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv"
+    """
+    csvtk \\
+        join \\
+        $args \\
+        --num-cpus $task.cpus \\
+        --out-file ${prefix}.${out_extension} \\
+        $csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv"
+    """
+    touch ${prefix}.${out_extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/csvtk/join/meta.yml b/modules/nf-core/csvtk/join/meta.yml
new file mode 100644
index 00000000..e817a3b5
--- /dev/null
+++ b/modules/nf-core/csvtk/join/meta.yml
@@ -0,0 +1,43 @@
+name: csvtk_join
+description: Join two or more CSV (or TSV) tables by selected fields into a single table
+keywords:
+  - join
+  - tsv
+  - csv
+tools:
+  - csvtk:
+      description: A cross-platform, efficient, practical CSV/TSV toolkit
+      homepage: http://bioinf.shenwei.me/csvtk
+      documentation: http://bioinf.shenwei.me/csvtk
+      tool_dev_url: https://github.com/shenwei356/csvtk
+
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - csv:
+      type: file
+      description: CSV/TSV formatted files
+      pattern: "*.{csv,tsv}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "version.yml"
+  - csv:
+      type: file
+      description: Joined CSV/TSV file
+      pattern: "*.{csv,tsv}"
+
+authors:
+  - "@anoronh4"
diff --git a/modules/nf-core/tcoffee/seqreformat/main.nf b/modules/nf-core/tcoffee/seqreformat/main.nf
new file mode 100644
index 00000000..a48d6bb1
--- /dev/null
+++ b/modules/nf-core/tcoffee/seqreformat/main.nf
@@ -0,0 +1,50 @@
+process TCOFFEE_SEQREFORMAT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::t-coffee=13.46.0.919e8c6b"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/t-coffee:13.46.0.919e8c6b--hfc96bf3_0':
+        'biocontainers/t-coffee:13.46.0.919e8c6b--hfc96bf3_0' }"
+
+    input:
+    tuple val(meta), path(infile)
+
+    output:
+    tuple val(meta), path("${prefix}.txt"), emit: formatted_file
+    path "versions.yml" , emit: versions
+
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    export TEMP='./'
+    t_coffee -other_pg seq_reformat \
+        -in ${infile} \
+        $args \
+        > "${prefix}.txt"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch "${prefix}_${seq_reformat_type}.txt"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}')
+    END_VERSIONS
+    """
+}
+
+
diff --git a/modules/nf-core/tcoffee/seqreformat/main.nf.test b/modules/nf-core/tcoffee/seqreformat/main.nf.test
new file mode 100644
index 00000000..3befc69a
--- /dev/null
+++ b/modules/nf-core/tcoffee/seqreformat/main.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process TCOFFEE_SEQREFORMAT"
+    script "modules/nf-core/tcoffee/seqreformat/main.nf"
+    process "TCOFFEE_SEQREFORMAT"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tcoffee"
+    tag "tcoffee_seqreformat"
+
+
+    test("TCOFFEE_SEQREFORMAT seqidscore") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test' ], // meta map
+                                file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/tcoffee/seqreformat/main.nf.test.snap b/modules/nf-core/tcoffee/seqreformat/main.nf.test.snap
new file mode 100644
index 00000000..5a405d49
--- /dev/null
+++ b/modules/nf-core/tcoffee/seqreformat/main.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "TCOFFEE_SEQREFORMAT seqidscore": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt:md5,fcd4691daf120c88ec5def7ac06fb562"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,68fb841e6e44274d430a1382bb0bbd14"
+                ],
+                "formatted_file": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt:md5,fcd4691daf120c88ec5def7ac06fb562"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,68fb841e6e44274d430a1382bb0bbd14"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-23T10:57:25.909083"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/seqreformat/meta.yml b/modules/nf-core/tcoffee/seqreformat/meta.yml
new file mode 100644
index 00000000..7d92631e
--- /dev/null
+++ b/modules/nf-core/tcoffee/seqreformat/meta.yml
@@ -0,0 +1,45 @@
+name: "tcoffee_seqreformat"
+description: Reformats files with t-coffee
+keywords:
+  - reformatting
+  - alignment
+  - genomics
+tools:
+  - "tcoffee":
+      description: "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures."
+      homepage: "http://www.tcoffee.org/Projects/tcoffee/"
+      documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html"
+      tool_dev_url: "https://github.com/cbcrg/tcoffee"
+      doi: "10.1006/jmbi.2000.4042"
+      licence: "['GPL v3']"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test' ]`
+
+  - fasta:
+      type: file
+      description: Input file to be reformatted
+      pattern: "*"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test' ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - formatted_file:
+      type: file
+      description: Formatted file
+      pattern: "*"
+
+authors:
+  - "@luisas"
diff --git a/modules/nf-core/tcoffee/seqreformat/nextflow.config b/modules/nf-core/tcoffee/seqreformat/nextflow.config
new file mode 100644
index 00000000..e185a5cf
--- /dev/null
+++ b/modules/nf-core/tcoffee/seqreformat/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: TIDDIT_COV_WIG {
+        ext.args = '-w'
+    }
+
+}
diff --git a/subworkflows/local/stats.nf b/subworkflows/local/stats.nf
index 88076044..3eb12a1e 100644
--- a/subworkflows/local/stats.nf
+++ b/subworkflows/local/stats.nf
@@ -1,10 +1,12 @@
 //
 // Compute stats about the input sequences
 //
-
-include {   TCOFFEE_SEQREFORMAT_SIM       } from '../../modules/local/tcoffee_seqreformat_sim.nf'
-include {   CALCULATE_SEQSTATS            } from '../../modules/local/calculate_seqstats.nf'
-include {   MERGE_STATS                   } from '../../modules/local/merge_stats.nf'
+include {   CALCULATE_SEQSTATS                             } from '../../modules/local/calculate_seqstats.nf'
+include {   PARSE_SIM                                      } from '../../modules/local/parse_sim.nf'
+include {   TCOFFEE_SEQREFORMAT as TCOFFEE_SEQREFORMAT_SIM } from '../../modules/nf-core/tcoffee/seqreformat/main.nf'
+include {   CSVTK_CONCAT  as CONCAT_SEQSTATS               } from '../../modules/nf-core/csvtk/concat/main.nf'
+include {   CSVTK_CONCAT  as CONCAT_SIMSTATS               } from '../../modules/nf-core/csvtk/concat/main.nf'
+include {   CSVTK_JOIN    as MERGE_STATS                   } from '../../modules/nf-core/csvtk/join/main.nf'
 
 
 workflow STATS {
@@ -14,44 +16,57 @@ workflow STATS {
 
     main:
 
+    ch_seqs.view()
     ch_versions = Channel.empty()
+
+    // // -------------------------------------------
+    // //      SEQUENCE SIMILARITY 
+    // // -------------------------------------------
     TCOFFEE_SEQREFORMAT_SIM(ch_seqs)
-    tcoffee_seqreformat_sim = TCOFFEE_SEQREFORMAT_SIM.out.perc_sim
-    tcoffee_seqreformat_simtot = TCOFFEE_SEQREFORMAT_SIM.out.perc_sim_tot
-    ch_versions = ch_versions.mix(TCOFFEE_SEQREFORMAT_SIM.out.versions.first())                    
+    tcoffee_seqreformat_sim = TCOFFEE_SEQREFORMAT_SIM.out.formatted_file
+    ch_versions = ch_versions.mix(TCOFFEE_SEQREFORMAT_SIM.out.versions.first()) 
+    tcoffee_seqreformat_simtot = PARSE_SIM(tcoffee_seqreformat_sim)
+        
+    ch_sim_summary = tcoffee_seqreformat_simtot.map{ 
+                                                meta, csv -> csv
+                                            }.collect().map{
+                                                csv -> [ [id_simstats:"summary_simstats"], csv]
+                                            }
+    CONCAT_SIMSTATS(ch_sim_summary, "csv", "csv")
 
+    // -------------------------------------------
+    //      SEQUENCE GENERAL STATS
+    //      Sequence length, # of sequences, etc 
+    // -------------------------------------------
     CALCULATE_SEQSTATS(ch_seqs)
     seqstats = CALCULATE_SEQSTATS.out.seqstats
     seqstats_summary = CALCULATE_SEQSTATS.out.seqstats_summary
     ch_versions = ch_versions.mix(CALCULATE_SEQSTATS.out.versions.first())
 
+    ch_seqstats_summary = seqstats_summary.map{ 
+                                                meta, csv -> csv
+                                            }.collect().map{
+                                                csv -> [ [id_seqstats:"summary_seqstats"], csv]
+                                            }
+
+    CONCAT_SEQSTATS(ch_seqstats_summary, "csv", "csv")
 
-    // 
-    // Summarize stats into one summary file
-    //  
-    tcoffee_seqreformat_simtot.map{ it ->  "${it[1].text}" }.collectFile( name: 'tcoffee_seqreformat_simtot_summary.csv',
-                                                                          keepHeader : true,
-                                                                          skip:1,                                         
-                                                                          newLine: false)
-                                                            .set { tcoffee_seqreformat_simtot_summary }
 
+    // -------------------------------------------
+    //      MERGE ALL STATS
+    // -------------------------------------------
 
-    seqstats_summary.map{ it ->  "${it[1].text}" }.collectFile( name: 'seqstats.csv',
-                                                                          keepHeader : true,
-                                                                          skip:1,                                         
-                                                                          newLine: false)
-                                                  .set { seqstats_summary }
+    csv_sim      = CONCAT_SIMSTATS.out.csv.map{ meta, csv -> csv }
+    csv_seqstats = CONCAT_SEQSTATS.out.csv.map{ meta, csv -> csv }
 
-    MERGE_STATS( tcoffee_seqreformat_simtot_summary,
-                 seqstats_summary )
-    
+    csvs_stats = csv_sim.mix(csv_seqstats).collect().map{ csvs -> [[id:"summary_stats"], csvs] }
+    csvs_stats.view()
+    MERGE_STATS(csvs_stats)
+    stats_summary = MERGE_STATS.out.csv
     ch_versions = ch_versions.mix(MERGE_STATS.out.versions)                      
 
 
     emit:
-    tcoffee_seqreformat_sim                           
-    tcoffee_seqreformat_simtot 
-    seqstats
-    seqstats_summary                              
+    stats_summary                             
     versions         = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
 }
\ No newline at end of file