diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
index 4fdd305..fc92743 100644
--- a/.github/workflows/pytest-workflow.yml
+++ b/.github/workflows/pytest-workflow.yml
@@ -18,15 +18,15 @@ jobs:
       # Expose matched filters as job 'modules' output variable
       modules: ${{ steps.filter.outputs.changes }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: dorny/paths-filter@v2
+      - uses: dorny/paths-filter@v3
         id: filter
         with:
           filters: "tests/config/pytest_modules.yml"
 
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     name: ${{ matrix.tags }} ${{ matrix.profile }}
     needs: changes
@@ -39,14 +39,14 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
 
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
@@ -56,7 +56,7 @@ jobs:
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow
 
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           path: /usr/local/bin/nextflow
           key: ${{ runner.os }}
diff --git a/modules/cnr-ibba/estsfs/main.nf b/modules/cnr-ibba/estsfs/main.nf
new file mode 100644
index 0000000..3028430
--- /dev/null
+++ b/modules/cnr-ibba/estsfs/main.nf
@@ -0,0 +1,48 @@
+process ESTSFS {
+    tag "$meta.id"
+    label 'process_single'
+    label 'process_long'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    container "docker.io/bunop/est-sfs:2.0.5"
+
+    input:
+    tuple val(meta), path(e_config), path(data), path(seed)
+
+    output:
+    tuple val(meta), path("${prefix}_sfs.txt")      , emit: sfs_out
+    tuple val(meta), path("${prefix}_pvalues.txt")  , emit: pvalues_out
+    tuple val(meta), path("${prefix}.seed")         , emit: seed
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def VERSION = '2.05' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    cp ${seed} ${prefix}.seed
+    est-sfs ${e_config} ${data} ${prefix}.seed ${prefix}_sfs.txt ${prefix}_pvalues.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        est-sfs: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_sfs.txt
+    touch ${prefix}_pvalues.txt
+    touch ${prefix}.seed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        est-sfs: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/cnr-ibba/estsfs/meta.yml b/modules/cnr-ibba/estsfs/meta.yml
new file mode 100644
index 0000000..cae1988
--- /dev/null
+++ b/modules/cnr-ibba/estsfs/meta.yml
@@ -0,0 +1,53 @@
+---
+name: "estsfs"
+description: estimation of the unfolded site frequency spectrum
+keywords:
+  - site frequency spectrum
+  - ancestral alleles
+  - derived alleles
+tools:
+  - "estsfs":
+      description: "est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities by maximum likelihood (ML)."
+      homepage: "https://sourceforge.net/projects/est-usfs/"
+      documentation: "https://sourceforge.net/projects/est-usfs/"
+      tool_dev_url: "https://sourceforge.net/projects/est-usfs/files/est-sfs-release-2.04.tar.gz"
+      doi: "10.1534/genetics.118.301120"
+      licence: "['Free for Academic Use']"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test']`
+  - e_config:
+      type: file
+      description: config file for est-sfs
+      pattern: "*.txt"
+  - data:
+      type: file
+      description: input data file for est-sfs
+      pattern: "*.txt"
+  - seed:
+      type: file
+      description: text file containing random number seed
+      pattern: "*.txt"
+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"
+  - sfs_out:
+      type: file
+      description: output file consists of the comma-separated estimated uSFS vector
+      pattern: "*.txt"
+  - pvalues_out:
+      type: file
+      description: this file contains the estimated ancestral state probabilities for each site
+      pattern: "*.txt"
+authors:
+  - "@BioInf2305"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index e6431fc..078c934 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -10,6 +10,10 @@ bcftools/concat:
   - modules/nf-core/bcftools/concat/**
   - tests/modules/nf-core/bcftools/concat/**
 
+estsfs:
+  - modules/cnr-ibba/estsfs/**
+  - tests/modules/cnr-ibba/estsfs/**
+
 freebayes/chunk:
   - modules/cnr-ibba/freebayes/chunk/**
   - tests/modules/cnr-ibba/freebayes/chunk/**
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 93347cf..3eba9ab 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -49,6 +49,8 @@ params {
 
                 mmseqs_tar_gz                                  = "${params.test_data_base}/data/genomics/sarscov2/genome/db/mmseqs.tar.gz"
 
+                resfinder_tar_gz                               = "${params.test_data_base}/data/genomics/sarscov2/genome/db/resfinder.tar.gz"
+
                 all_sites_fas                                  = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/all_sites.fas"
                 informative_sites_fas                          = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/informative_sites.fas"
 
@@ -129,6 +131,8 @@ params {
                 test_fastq_gz                                  = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fastq/test.fastq.gz"
 
                 test_sequencing_summary                        = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
+                
+                test2_sequencing_summary                        = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test2.sequencing_summary.txt"
             }
             'metagenome' {
                 classified_reads_assignment                    = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt"
@@ -150,10 +154,19 @@ params {
                 rnaseq_matrix                                  = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv"
                 rnaseq_lengths                                 = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv"
                 deseq_results                                  = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv"
+                genome_19_fasta                                = "${params.test_data_base}/data/genomics/mus_musculus/genome/chr19.fa.gz"
+                genome_19_gtf                                  = "${params.test_data_base}/data/genomics/mus_musculus/genome/chr19.filtered.gtf.gz"
             }
             'illumina' {
                 test_1_fastq_gz                                = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz"
                 test_2_fastq_gz                                = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376999.small.fastq.gz"
+                genome_config                                  = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json"
+                multiome_lib_csv                               = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/lib.csv"
+                test_scARC_gex_R1_fastq_gz                     = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R1_001.fastq.gz"
+                test_scARC_gex_R2_fastq_gz                     = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R2_001.fastq.gz"
+                test_scARC_atac_R1_fastq_gz                    = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R1_001.fastq.gz"
+                test_scARC_atac_R2_fastq_gz                    = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R2_001.fastq.gz"
+                test_scARC_atac_I2_fastq_gz                    = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_I2_001.fastq.gz"
             }
             'csv' {
                 count_table                                    = "${params.test_data_base}/data/genomics/mus_musculus/mageck/count_table.csv"
@@ -278,6 +291,7 @@ params {
                 syntheticvcf_short_score                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score"
                 gnomad_r2_1_1_sv_vcf_gz                        = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz"
                 gnomad2_r2_1_1_sv_vcf_gz                       = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz"
+                genmod_compound_vcf_mt                         = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/genmod_compound.vcf"
 
                 hapmap_3_3_hg38_21_vcf_gz                      = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
                 hapmap_3_3_hg38_21_vcf_gz_tbi                  = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi"
@@ -612,6 +626,19 @@ params {
                 genome_aln_nwk                  = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk"
             }
         }
+        'saccharomyces_cerevisiae' {
+            'genome' {
+                samplesheet                     = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv"
+                genome_gfp_gtf                  = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf"
+		        kallisto_results                = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz"
+                salmon_results                  = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz"
+            }
+        }
+        'actinidia_chinensis' {
+            'genome' {
+                genome_21_fasta_gz              = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz"
+            }
+        }
         'generic' {
             'csv' {
                 test_csv                        = "${params.test_data_base}/data/generic/csv/test.csv"
@@ -620,6 +647,8 @@ params {
                 rmarkdown                       = "${params.test_data_base}/data/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
                 ipython_md                      = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.md"
                 ipython_ipynb                   = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.ipynb"
+                quarto_r                        = "${params.test_data_base}/data/generic/notebooks/quarto/quarto_r.qmd"
+                quarto_python                   = "${params.test_data_base}/data/generic/notebooks/quarto/quarto_python.qmd"
             }
             'tar' {
                 tar_gz                          = "${params.test_data_base}/data/generic/tar/hello.tar.gz"
@@ -670,6 +699,7 @@ params {
                 ups_file1                       = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_12.raw"
                 ups_file2                       = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw"
                 profile_spectra                 = "${params.test_data_base}/data/proteomics/msspectra/peakpicker_tutorial_1.mzML"
+                hla2_file                       = "${params.test_data_base}/data/proteomics/msspectra/PXD012083_e005640_II.raw"
             }
             'database' {
                 yeast_ups                       = "${params.test_data_base}/data/proteomics/database/yeast_UPS.fasta"
@@ -705,6 +735,12 @@ params {
                 contigs     = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.contigs.fa"
             }
         }
+        'arabidopsis_thaliana' {
+            'plastid' {
+                hifi_reads = "${params.test_data_base}/data/genomics/eukaryotes/arabidopsis_thaliana/plastid/ddAraThal4.HiFi.reads.fasta"
+            }
+        }
+
         'imaging' {
             'h5' {
                 plant_wga                       = "${params.test_data_base}/data/imaging/h5/plant_wga.h5"
diff --git a/tests/modules/cnr-ibba/estsfs/main.nf b/tests/modules/cnr-ibba/estsfs/main.nf
new file mode 100644
index 0000000..2d8e9c5
--- /dev/null
+++ b/tests/modules/cnr-ibba/estsfs/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ESTSFS } from '../../../../modules/cnr-ibba/estsfs/main.nf'
+
+workflow test_estsfs {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['generic']['estsfs']['config_file'], checkIfExists: true), file(params.test_data['generic']['estsfs']['data_file'], checkIfExists: true), file(params.test_data['generic']['estsfs']['seed_file'], checkIfExists: true)
+    ]
+
+    ESTSFS ( input )
+}
diff --git a/tests/modules/cnr-ibba/estsfs/nextflow.config b/tests/modules/cnr-ibba/estsfs/nextflow.config
new file mode 100644
index 0000000..50f50a7
--- /dev/null
+++ b/tests/modules/cnr-ibba/estsfs/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/cnr-ibba/estsfs/test.yml b/tests/modules/cnr-ibba/estsfs/test.yml
new file mode 100644
index 0000000..e35b601
--- /dev/null
+++ b/tests/modules/cnr-ibba/estsfs/test.yml
@@ -0,0 +1,11 @@
+- name: estsfs test_estsfs
+  command: nextflow run ./tests/modules/cnr-ibba/estsfs -entry test_estsfs -c ./tests/config/nextflow.config
+  tags:
+    - estsfs
+  files:
+    - path: output/estsfs/test_pvalues.txt
+      md5sum: 63f370e9f2d08591b52c0ea05c8b45a0
+    - path: output/estsfs/test_sfs.txt
+      md5sum: 5da246e273d22b177f0683b44fe6d80a
+    - path: output/estsfs/test.seed
+    - path: output/estsfs/versions.yml