diff --git a/assets/useful_scripts/deepcsa_maf2samplevcfs.py b/assets/useful_scripts/deepcsa_maf2samplevcfs.py
old mode 100644
new mode 100755
diff --git a/bin/deepcsa_maf2samplevcfs.py b/bin/deepcsa_maf2samplevcfs.py
new file mode 100755
index 00000000..7c5637c4
--- /dev/null
+++ b/bin/deepcsa_maf2samplevcfs.py
@@ -0,0 +1,221 @@
+#!/usr/bin/env python
+
+#######
+# This script converts a mutations file (TSV format) to one or multiple VCF-formatted files.
+#######
+
+#######
+# Usage: 
+#######
+## If your sample names are NOT in a column called SAMPLE_ID,
+## you can use the --sample-name-column option to specify it.
+
+# if the maf is from deepCSA, use this one
+# usage: python deepcsa_maf2samplevcfs.py --mutations-file all_samples.somatic.mutations.tsv --output-dir ./test/ --maf-from-deepcsa
+
+# if the maf file is not from deepCSA, use this one
+# usage: python deepcsa_maf2samplevcfs.py --mutations-file all_samples.somatic.mutations.tsv --output-dir ./test/
+
+
+
+#######
+# Mandatory columns in input mutations: 
+#######
+
+# if the maf is from deepCSA, it must contain the following columns, as they were originally generated
+# ['CHROM', 'POS', 'REF', 'ALT', 'FILTER', 'INFO', 'FORMAT', 'SAMPLE']
+
+# if the maf file is not from deepCSA, then it MUST contain the following columns
+# ['CHROM', 'POS', 'REF', 'ALT', 'DEPTH', 'ALT_DEPTH']
+# where:
+#     DEPTH indicates the total number of duplex reads sequenced at the position where the mutation occurs
+#     ALT_DEPTH indicates the total number of duplex reads supporting the variant at the same position
+
+
+
+
+import click
+import pandas as pd
+
+
+def build_vcf_like_dataframe(mutations_dataframe, samplee):
+    """
+    Build a VCF-like dataframe from the mutations dataframe.
+    input needs to have:
+        ['CHROM', 'POS', 'REF', 'ALT', 'DEPTH', 'ALT_DEPTH']
+    output needs to have:
+        ['CHROM', 'POS', 'REF', 'ALT', 'FILTER', 'INFO', 'FORMAT', 'SAMPLE']
+    """
+    for col in ['CHROM', 'POS', 'REF', 'ALT', 'DEPTH', 'ALT_DEPTH']:
+        if col not in mutations_dataframe.columns:
+            raise ValueError(f"Column {col} is missing from the mutations dataframe.")
+    
+    # fill FILTER and INFO columns with default values
+    if "FILTER" not in mutations_dataframe.columns:
+        print("WARNING: FILTER column is missing from the mutations dataframe. Setting it to 'PASS' for all mutations")
+        mutations_dataframe["FILTER"] = "PASS"
+    if "INFO" not in mutations_dataframe.columns:
+        print(f"WARNING: INFO column is missing from the mutations dataframe. Setting it to 'SAMPLE={samplee};'")
+        mutations_dataframe["INFO"] = f"SAMPLE={samplee};"
+
+    # Create a new dataframe with the required columns
+    vcf_like_df = mutations_dataframe[['CHROM', 'POS', 'REF', 'ALT', 'FILTER', 'INFO', 'DEPTH', 'ALT_DEPTH']].copy()
+    vcf_like_df["FORMAT"] = "GT:DP:VD:AD:AF:RD:ALD:CDP:CAD:NDP:CDPAM:CADAM:NDPAM"
+    vcf_like_df["SAMPLE"] = vcf_like_df[['DEPTH', 'ALT_DEPTH']].apply(
+        lambda x: "{GT}:{DP}:{VD}:{AD}:{AF}:{RD}:{ALD}:{CDP}:{CAD}:{NDP}:{CDPAM}:{CADAM}:{NDPAM}".format(
+            GT="0/1",
+            DP=x['DEPTH'],
+            VD=x['ALT_DEPTH'],
+            AD=f"{x['DEPTH'] - x['ALT_DEPTH']},{x['ALT_DEPTH']}",
+            AF=round(x['ALT_DEPTH'] / x['DEPTH'] , 5),
+            RD=f"{(x['DEPTH'] - x['ALT_DEPTH'])//2},{(x['DEPTH'] - x['ALT_DEPTH'])//2 if (x['DEPTH'] - x['ALT_DEPTH']) % 2 == 0 else (x['DEPTH'] - x['ALT_DEPTH'])//2 + 1}",
+            ALD=f"{x['ALT_DEPTH']//2},{x['ALT_DEPTH']//2 if x['ALT_DEPTH'] % 2 == 0 else x['ALT_DEPTH']//2 + 1}",
+            CDP=x['DEPTH'],
+            CAD=f"{x['DEPTH'] - x['ALT_DEPTH']},{x['ALT_DEPTH']}",
+            NDP="0",
+            CDPAM=x['DEPTH'],
+            CADAM=f"{x['DEPTH'] - x['ALT_DEPTH']},{x['ALT_DEPTH']}",
+            NDPAM="0" 
+        ),
+        axis=1
+    )
+    return vcf_like_df
+
+filters_to_remove = ["not_in_exons", "not_covered"]
+def remove_deepcsa_filters(old_filt, filters_to_removee):
+    """
+    Remove deepCSA filters from the FILTER field of the VCF file.
+    """    
+    filter_result = sorted([ x for x in old_filt.split(";") if x not in filters_to_removee ])
+    return ";".join(filter_result) if filter_result != [] else "PASS"
+
+
+vardict_vcf_header = '''##fileformat=VCFv4.2
+##source=artificially_generated_vcf_VarDict_v1.8.2-like
+##FILTER=<ID=AMPBIAS,Description="Indicate the variant has amplicon bias.">
+##FILTER=<ID=AM_no_pileup_support,Description="Variant not supported when inspecting the BAM with mpileup. deepUMIcaller.">
+##FILTER=<ID=AM_not_searched_COMPLEX,Description="Complex variant. Recounting of alt depth from mpileup output not done for this type of variants. deepUMIcaller.">
+##FILTER=<ID=AM_not_searched_SV,Description="Structural variant. Recounting of alt depth from mpileup output not done for this type of variants. deepUMIcaller.">
+##FILTER=<ID=Bias,Description="Strand Bias">
+##FILTER=<ID=Cluster0bp,Description="Two variants are within 0 bp">
+##FILTER=<ID=InGap,Description="The variant is in the deletion gap, thus likely false positive">
+##FILTER=<ID=InIns,Description="The variant is adjacent to an insertion variant">
+##FILTER=<ID=LongMSI,Description="The somatic variant is flanked by long A/T (>=14)">
+##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 13 monomer MSI">
+##FILTER=<ID=NM20,Description="Mean mismatches in reads >= 20, thus likely false positive">
+##FILTER=<ID=Q10,Description="Mean Mapping Quality Below 10">
+##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
+##FILTER=<ID=d3,Description="Total Depth < 3">
+##FILTER=<ID=f0.0,Description="Allele frequency < 0.0">
+##FILTER=<ID=low_complex_repetitive,Description="Variant located in a low complexity or repetitive genomic region. deepUMIcaller.">
+##FILTER=<ID=low_mappability,Description="Variant located in a genomic region with low mappability. deepUMIcaller.">
+##FILTER=<ID=n_rich,Description="Variant located in a position with more Ns than expected. Threshold in this sample: 0.491005. deepUMIcaller.">
+##FILTER=<ID=no_pileup_support,Description="Variant not supported when inspecting the BAM with mpileup. deepUMIcaller.">
+##FILTER=<ID=not_searched_COMPLEX,Description="Complex variant. Recounting of alt depth from mpileup output not done for this type of variants. deepUMIcaller.">
+##FILTER=<ID=not_searched_SV,Description="Structural variant. Recounting of alt depth from mpileup output not done for this type of variants. deepUMIcaller.">
+##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
+##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
+##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
+##FILTER=<ID=v2,Description="Var Depth < 2">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">
+##FORMAT=<ID=CAD,Number=2,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed. ONLY ONE ALT allele. Recomputed using mpileup output, this might not sum to CDP. deepUMIcaller.">
+##FORMAT=<ID=CADAM,Number=2,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed. ONLY ONE ALT allele. Recomputed using mpileup output, this might not sum to CDP. deepUMIcaller.">
+##FORMAT=<ID=CDP,Number=1,Type=Integer,Description="Total Depth recomputed using mpileup output. deepUMIcaller.">
+##FORMAT=<ID=CDPAM,Number=1,Type=Integer,Description="Total Depth recomputed using mpileup output. deepUMIcaller.">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=NDP,Number=1,Type=Integer,Description="Total number of Ns computed using mpileup output. deepUMIcaller.">
+##FORMAT=<ID=NDPAM,Number=1,Type=Integer,Description="Total number of Ns computed using mpileup output. deepUMIcaller.">
+##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">
+##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+##INFO=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AMPFLAG,Number=1,Type=Integer,Description="Top variant in amplicons don't match">
+##INFO=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=DUPRATE,Number=1,Type=Float,Description="Duplication rate in fraction">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">
+##INFO=<ID=GDAMP,Number=1,Type=Integer,Description="No. of amplicons supporting variant">
+##INFO=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">
+##INFO=<ID=HICNT,Number=1,Type=Integer,Description="High quality variant reads">
+##INFO=<ID=HICOV,Number=1,Type=Integer,Description="High quality total reads">
+##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">
+##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">
+##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MicroSatellite unit length in bp">
+##INFO=<ID=NCAMP,Number=1,Type=Integer,Description="No. of amplicons don't work">
+##INFO=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">
+##INFO=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">
+##INFO=<ID=PMEAN,Number=1,Type=Float,Description="The mean distance to the nearest 5 or 3 prime read end (whichever is closer) in all reads that support the variant call">
+##INFO=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">
+##INFO=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">
+##INFO=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">
+##INFO=<ID=REFBIAS,Number=1,Type=String,Description="Reference depth by strand">
+##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
+##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
+##INFO=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">
+##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">
+##INFO=<ID=SN,Number=1,Type=Float,Description="Signal to noise">
+##INFO=<ID=SPANPAIR,Number=1,Type=Integer,Description="No. of pairs supporting SV">
+##INFO=<ID=SPLITREAD,Number=1,Type=Integer,Description="No. of split reads supporting SV">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="The length of SV in bp">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type: INV DUP DEL INS FUS">
+##INFO=<ID=TLAMP,Number=1,Type=Integer,Description="Total of amplicons covering variant">
+##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
+##INFO=<ID=VARBIAS,Number=1,Type=String,Description="Variant depth by strand">
+##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
+'''
+
+
+@click.command()
+@click.option('--mutations-file', required=True, type=click.Path(exists=True), help="Path to the mutations file (TSV format).")
+@click.option('--output-dir', required=True, type=click.Path(), help="Directory to save the output VCF files.")
+@click.option('--maf-from-deepcsa', is_flag=True, default=False, help="Flag to indicate if the MAF file is from deepCSA.")
+@click.option('--sample-name-column', default="SAMPLE_ID", type=str, help="Column name for sample names in the mutations file.")
+def main(mutations_file, output_dir, maf_from_deepcsa, sample_name_column):
+    """
+    Convert a mutations file to one or multiple VCF-formatted files.
+    """
+
+    mutations = pd.read_table(mutations_file)
+    mutations[sample_name_column] = mutations[sample_name_column].astype(str)
+    for sample in mutations[sample_name_column].unique():
+        
+        # filter the dataframe for the current sample
+        sample_mutations = mutations[mutations[sample_name_column] == sample]
+
+        if maf_from_deepcsa:
+            vcf_info_sample = sample_mutations[['CHROM', 'POS', 'REF', 'ALT', 'FILTER', 'INFO', 'FORMAT', 'SAMPLE']].copy()
+        else:
+            vcf_info_sample = build_vcf_like_dataframe(sample_mutations, sample)
+            # mandatory columns should be: [['CHROM', 'POS', 'REF', 'ALT', 'FILTER', 'DEPTH', 'ALT_DEPTH']]
+            # Ns can be assumed 0 and AM can be assumed to be the same as duplex
+
+        # clean FILTER field of all deepCSA annotations
+        if len(filters_to_remove) > 0:
+            vcf_info_sample["FILTER"] = vcf_info_sample["FILTER"].apply(remove_deepcsa_filters, filters_to_removee = filters_to_remove)
+        
+        # add other necessary columns
+        vcf_info_sample["ID"] = '.'
+        vcf_info_sample["QUAL"] = 100
+
+        # rename sample column
+        vcf_info_sample.rename(columns={"SAMPLE": sample}, inplace=True)
+        
+        cols = ["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO", "FORMAT", sample]
+        
+        sample_file = f"{output_dir}/{sample}.vcf"
+        
+        with open(sample_file, "w") as f:
+            f.write(vardict_vcf_header)
+            f.write("#" + "\t".join(cols) + "\n")
+            
+            # write the data
+            vcf_info_sample.to_csv(f, sep="\t", columns=cols, index=False, header=False)
+            
+        print(f"VCF file for {sample} : {sample_file}")
+
+if __name__ == "__main__":
+    main()
diff --git a/conf/modules.config b/conf/modules.config
index ea420932..e68e4409 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -139,9 +139,23 @@ process {
     // }
 
     withName: 'VCF2MAF' {
-        ext.args            = "--level ${params.confidence_level}"
+        ext.args    = "--level ${params.confidence_level}"
     }
 
+    withName: 'MAF2VCF' {
+        ext.args    = "--output-dir . --maf-from-deepcsa --sample-name-column SAMPLE_ID"
+        publishDir       = [
+            [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/signatures/sigprofilermatrixgenerator/vcfs" },
+                pattern: "**{vcf}"
+            ]
+        ]
+    }
+
+            
+
+
     withName: 'POSTPROCESSVEPPANEL' {
         ext.canonical_only  = params.panel_with_canonical
         publishDir       = [
@@ -486,6 +500,27 @@ process {
         ]
     }
 
+    withName: 'SIGPROMATRIXGENERATOR' {
+        ext.args      = "--plot \
+                            --tsb_stat \
+                            --seqInfo \
+                            --cushion 100"
+        
+        ext.genome_assembly =
+            params.vep_genome == 'GRCh38' ? 'GRCh38' :
+            params.vep_genome == 'GRCh37' ? 'GRCh37' :
+            params.vep_genome == 'GRCm38' ? 'mm10' :
+            params.vep_genome == 'GRCm39' ? 'mm39' :
+            null
+
+        publishDir       = [
+            [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/signatures/sigprofilermatrixgenerator" },
+                pattern: "**{txt,pdf,all}"
+            ]
+        ]
+    }
 
     withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
         publishDir = [
diff --git a/modules/local/maf2vcf/main.nf b/modules/local/maf2vcf/main.nf
new file mode 100644
index 00000000..fe5dbd3c
--- /dev/null
+++ b/modules/local/maf2vcf/main.nf
@@ -0,0 +1,43 @@
+process MAF_2_VCF {
+
+    tag "${meta.id}"
+    label 'process_low'
+
+    container "docker.io/bbglab/deepcsa-core:0.0.1-alpha"
+
+
+    input:
+    tuple val(meta), path (maf_file)
+
+    output:
+    path "*.vcf"        , emit: vcf_files
+    path "versions.yml" , topic: versions
+
+
+    script:
+    def prefix = task.ext.prefix ?: ''
+    prefix = "${meta.id}${prefix}"
+    def args = task.ext.args ?: ""
+    """
+    deepcsa_maf2samplevcfs.py \\
+                    --mutations-file ${maf_file} \\
+                    ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: ""
+    prefix = "${meta.id}${prefix}"
+    """
+    touch ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/signatures/msighdp/main.nf b/modules/local/signatures/msighdp/main.nf
deleted file mode 100644
index 53e1711a..00000000
--- a/modules/local/signatures/msighdp/main.nf
+++ /dev/null
@@ -1,49 +0,0 @@
-process MSIGHDP {
-    tag "$meta.id"
-    label 'process_medium'
-
-    container 'docker.io/ferriolcalvet/msighdp:latest'
-
-    input:
-    tuple val(meta), path(matrix)
-
-    output:
-    tuple val(meta), path("**.pdf")     , emit: plots
-    tuple val(meta), path("**.csv")     , emit: stats
-    path "versions.yml"                 , topic: versions
-
-
-    script:
-    def prefix = task.ext.prefix ?: ""
-    prefix = "${meta.id}${prefix}"
-    def k_guess = task.ext.k_guess ?: "12"
-    """
-    msighdp_run.R \\
-                123 \\
-                ${matrix} \\
-                output.${prefix} \\
-                ${k_guess} \\
-                ${task.cpus}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        R       : \$(Rscript --version | sed -e 's/.*version //g')
-        Rscript : \$(Rscript --version | sed -e 's/.*version //g')
-        mSigHdp : 2.1.2
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: ""
-    prefix = "${meta.id}${prefix}"
-    """
-    touch ${prefix}.pdf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        R       : \$(Rscript --version | sed -e 's/.*version //g')
-        Rscript : \$(Rscript --version | sed -e 's/.*version //g')
-        mSigHdp : 2.1.2
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/signatures/sigprofiler/matrixgenerator/main.nf b/modules/local/signatures/sigprofiler/matrixgenerator/main.nf
new file mode 100644
index 00000000..5ab951e1
--- /dev/null
+++ b/modules/local/signatures/sigprofiler/matrixgenerator/main.nf
@@ -0,0 +1,47 @@
+process SIGPROFILER_MATRIXGENERATOR {
+    tag "${task.ext.prefix}"
+    label 'process_single'
+
+    container 'docker.io/ferriolcalvet/sigprofilermatrixgenerator:1.3.5'
+
+    input:
+    path (vcf)
+
+    output:
+    path("input_mutations/output/plots/*"), optional : true, emit: output_plots
+    path("input_mutations/output/ID/*")   , optional : true, emit: matrices_ID
+    path("input_mutations/output/DBS/*")  , optional : true, emit: matrices_DBS
+    path("input_mutations/output/SBS/*")  , optional : true, emit: matrices_SBS
+    path("input_mutations/output/TSB/*")  , optional : true, emit: transcription_bias
+    path "versions.yml"                                    , topic: versions
+
+
+    script:
+    def prefix = task.ext.prefix ?: 'samples'
+    def args = task.ext.args ?: ""
+    def genome = task.ext.genome_assembly ?: "GRCh38"
+    """
+    mkdir input_mutations
+    cp *.vcf input_mutations/.
+
+    SigProfilerMatrixGenerator matrix_generator \\
+                ${prefix} \\
+                ${genome} \\
+                input_mutations/ \\
+                ${args}
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        SigProfilerMatrixGenerator: 1.3.5
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        SigProfilerMatrixGenerator: 1.3.5
+    END_VERSIONS
+    """
+}
\ No newline at end of file
diff --git a/subworkflows/local/signatures/main.nf b/subworkflows/local/signatures/main.nf
index 5f483c60..08de6b62 100644
--- a/subworkflows/local/signatures/main.nf
+++ b/subworkflows/local/signatures/main.nf
@@ -1,8 +1,7 @@
-include { MATRIX_CONCAT                        as MATRIXCONCATWGS   } from '../../../modules/local/sig_matrix_concat/main'
+include { MATRIX_CONCAT                 as MATRIXCONCATWGS          } from '../../../modules/local/sig_matrix_concat/main'
 include { SIGPROFILERASSIGNMENT                                     } from '../../../modules/local/signatures/sigprofiler/assignment/main'
-include { SIGNATURES_PROBABILITIES             as SIGPROBS          } from '../../../modules/local/combine_sbs/main'
-// include { MSIGHDP                                                   } from '../../../modules/local/signatures/msighdp/main'
-include { HDP_EXTRACTION                       as HDPEXTRACTION     } from '../signatures_hdp/main'
+include { SIGNATURES_PROBABILITIES      as SIGPROBS                 } from '../../../modules/local/combine_sbs/main'
+include { HDP_EXTRACTION                as HDPEXTRACTION            } from '../signatures_hdp/main'
 
 
 workflow SIGNATURES {
@@ -39,13 +38,8 @@ workflow SIGNATURES {
 
     HDPEXTRACTION(named_matrices_wgs_hdp, reference_signatures)
 
-    // matrix.map{ it -> it[1] }.collect().map{ it -> [[ id:"all_samples" ], it]}.set{ all_matrices }
-    // MATRIXCONCAT(all_matrices, samples)
-    // MATRIXCONCAT.out.wgs_tsv.flatten().map{ it -> [ [id : it.name.tokenize('.')[0]] , it]  }.set{ named_matrices }
-    // MSIGHDP(matrix)
 
     emit:
     plots               = SIGPROFILERASSIGNMENT.out.plots       // channel: [ val(meta), file(depths) ]
-    // plots_extraction    = MSIGHDP.out.plots                     // channel: [ val(meta), file(depths) ]
     mutation_probs      = signature_probs_samples
-}
+}
\ No newline at end of file
diff --git a/subworkflows/local/signatures_hdp/main.nf b/subworkflows/local/signatures_hdp/main.nf
index 5ec77fa0..7ba2cf1a 100644
--- a/subworkflows/local/signatures_hdp/main.nf
+++ b/subworkflows/local/signatures_hdp/main.nf
@@ -1,10 +1,7 @@
 include { PREPARE_INPUT                                         } from '../../../modules/local/signatures/hdp/prepareinput/main'
 include { RUN_HDP_CHAIN_SAMPLING                                } from '../../../modules/local/signatures/hdp/chainsampling/main'
-// include { NORMALIZE_SIGNATURES                                  } from '../../../modules/local/signatures/hdp/normalize_sigs/main'
 include { PROCESS_HDP_RESULTS                                   } from '../../../modules/local/signatures/hdp/process_results/main'
-// include { COMPARE_SIGNATURES as COMPARENORMALIZEDSIGNATURES     } from '../../../modules/local/signatures/hdp/compare_sigs/main'
 include { COMPARE_SIGNATURES as COMPARESIGNATURES               } from '../../../modules/local/signatures/hdp/compare_sigs/main'
-// include { COMPARE_SIGNATURES as COMPARECANCERSIGNATURES         } from '../../../modules/local/signatures/hdp/compare_sigs/main'
 
 
 
@@ -23,13 +20,9 @@ workflow HDP_EXTRACTION {
 
     PREPARE_INPUT(samples_matrix)
 
-    // Create a channel with iter values from 1 to 15
     iter_ch = Channel.of(1..15)
-
-    // Combine the input data channel with the iter channel
     combined_input_ch = PREPARE_INPUT.out.input_data.combine(iter_ch)
 
-    // Run the process with the combined input
     RUN_HDP_CHAIN_SAMPLING(combined_input_ch)
 
     // Collect all iteration results
@@ -37,15 +30,8 @@ workflow HDP_EXTRACTION {
 
     PROCESS_HDP_RESULTS(PREPARE_INPUT.out.input_data, all_iterations_ch)
 
-    // if (params.norm_file != "NA") {
-    //     normalized_results_ch = NORMALIZE_SIGNATURES(processed_results_ch)
-    //     compared_normalized_results_ch = COMPARENORMALIZEDSIGNATURES(normalized_results_ch, reference_signatures)
-    // }
-
     COMPARESIGNATURES(PROCESS_HDP_RESULTS.out.processed_results, reference_signatures)
 
-    // final_results_ch = COMPARECANCERSIGNATURES(compared_results_ch, reference_signatures)
-
 
     // emit:
     // plots               = SIGPROFILERASSIGNMENT.out.plots       // channel: [ val(meta), file(depths) ]
diff --git a/workflows/deepcsa.nf b/workflows/deepcsa.nf
index a84f4125..8839da08 100644
--- a/workflows/deepcsa.nf
+++ b/workflows/deepcsa.nf
@@ -1,8 +1,4 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    PRINT PARAMS SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+
 
 include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc      } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -11,15 +7,8 @@ include { methodsDescriptionText    } from '../subworkflows/local/utils_nfcore_d
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT LOCAL MODULES/SUBWORKFLOWS
+    IMPORT LOCAL SUBWORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Consisting of a mix of local and nf-core/modules.
 */
 
 // SUBWORKFLOW
@@ -86,26 +75,36 @@ include { TABIX_BGZIPTABIX_QUERY    as DEPTHSNONPROTCONS    } from '../modules/n
 include { TABIX_BGZIPTABIX_QUERY    as DEPTHSINTRONSCONS    } from '../modules/nf-core/tabix/bgziptabixquery/main'
 include { TABIX_BGZIPTABIX_QUERY    as DEPTHSSYNONYMOUSCONS } from '../modules/nf-core/tabix/bgziptabixquery/main'
 
-include { SELECT_MUTDENSITIES       as SYNMUTDENSITY        } from '../modules/local/select_mutdensity/main'
-include { SELECT_MUTDENSITIES       as SYNMUTREADSRATE      } from '../modules/local/select_mutdensity/main'
-
-include { DNA_2_PROTEIN_MAPPING     as DNA2PROTEINMAPPING   } from '../modules/local/dna2protein/main'
-
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT NF-CORE MODULES/SUBWORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Installed directly from nf-core/modules.
 */
 
 // MODULE
 include { MULTIQC                                           } from '../modules/nf-core/multiqc/main'
 include { CUSTOM_DUMPSOFTWAREVERSIONS                       } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT CUSTOM MODULES
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { TABLE_2_GROUP             as TABLE2GROUP          } from '../modules/local/table2groups/main'
 include { ANNOTATE_DEPTHS           as ANNOTATEDEPTHS       } from '../modules/local/annotatedepth/main'
 include { DOWNSAMPLE_DEPTHS         as DOWNSAMPLEDEPTHS     } from '../modules/local/downsample/depths/main'
-include { TABLE_2_GROUP             as TABLE2GROUP          } from '../modules/local/table2groups/main'
+
+include { SELECT_MUTDENSITIES       as SYNMUTDENSITY        } from '../modules/local/select_mutdensity/main'
+include { SELECT_MUTDENSITIES       as SYNMUTREADSRATE      } from '../modules/local/select_mutdensity/main'
+
+include { DNA_2_PROTEIN_MAPPING     as DNA2PROTEINMAPPING   } from '../modules/local/dna2protein/main'
+
+include { MAF_2_VCF                     as MAF2VCF                  } from '../modules/local/maf2vcf/main'
+include { SIGPROFILER_MATRIXGENERATOR   as SIGPROMATRIXGENERATOR    } from '../modules/local/signatures/sigprofiler/matrixgenerator/main'
+
 include { MUTATIONS_2_SIGNATURES    as MUTS2SIGS            } from '../modules/local/mutations2sbs/main'
 
 /*
@@ -491,8 +490,21 @@ workflow DEEPCSA{
     }
 
 
+
+
     if (params.signatures){
 
+        Channel.of([ [ id: "all_samples" ] ])
+        .join( somatic_mutations )
+        .set{ maf2vcf_inputs }
+
+        MAF2VCF(maf2vcf_inputs)
+        vcf_files = MAF2VCF.out.vcf_files.flatten().collect()
+
+        SIGPROMATRIXGENERATOR(
+            vcf_files,
+            )
+
         // Signature Analysis
         if (params.profileall){
             SIGNATURESALL(MUTPROFILEALL.out.wgs_sigprofiler, cosmic_ref, TABLE2GROUP.out.json_samples)
@@ -502,7 +514,6 @@ workflow DEEPCSA{
             .set{mutations_n_sbs}
             MUTS2SIGS(mutations_n_sbs)
 
-
         }
         if (params.profilenonprot){
             SIGNATURESNONPROT(MUTPROFILENONPROT.out.wgs_sigprofiler, cosmic_ref, TABLE2GROUP.out.json_samples)