diff --git a/CHANGELOG.md b/CHANGELOG.md
index a5743a60..56cf4020 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -58,6 +58,7 @@ Code contributions to the hotfix:
 - [Jaime Ozaez](https://github.com/jaimeozaez)
 - [Sara Monzón](https://github.com/saramonzon)
 - [Sarai Varona](https://github.com/svarona)
+- [Daniel Valle](https://github.com/Daniel-VM)
 
 
 ### Template fixes and updates
@@ -67,6 +68,7 @@ Code contributions to the hotfix:
 - Small changes to `buisciii_tools/bu_isciii/templates/viralrecon/RESULTS/viralrecon_results` for blast and new excel_generator.py
 - Introduced better error handling in excel_generator.py. Now it can also be used for single files
 - Brought back `PASS_ONLY` to exometrio's `exomiser_configfile.yml`
+- [#187](https://github.com/BU-ISCIII/buisciii-tools/pull/187) - Added new template for bacterial assembly. Allowing for short, long and hybrid assembly.
 
 ### Modules
 
diff --git a/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog b/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog
index 9503c3f9..bd8f8549 100644
--- a/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog
+++ b/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog
@@ -1,31 +1,97 @@
-echo "Do you want to save trimmed reads in outdir?"
+# Function to print colored text
+print_color() {
+    case "$2" in
+        "red")
+            echo -e "\e[1;31m$1\e[0m"
+            ;;
+        "green")
+            echo -e "\e[1;32m$1\e[0m"
+            ;;
+        "blue")
+            echo -e "\e[1;34m$1\e[0m"
+            ;;
+        *)
+            echo "$1"
+            ;;
+    esac
+}
 
-read -p 'Write y or n: ' trimmed
+# Function to prompt with color
+prompt_with_color() {
+    read -p "$(print_color $1 'blue') $2" response
+}
 
-TRIMMED=$(echo "${trimmed}" | tr '[:upper:]' '[:lower:]')
+# Select assembly mode
+assembly_options=("short" "long" "hybrid")
+print_color "Indicate the preferred assembly mode:" 'blue'
+select ASSEMBLY_MODE in "${assembly_options[@]}"; do
+    if [ -n "$ASSEMBLY_MODE" ]; then
+        if [ $ASSEMBLY_MODE == "short" ]; then 
+            ASSEMBLER="unicycler"
+        elif [ "$ASSEMBLY_MODE" == "long" ] || [ "$ASSEMBLY_MODE" == "hybrid" ]; then
+            ASSEMBLER="dragonflye"
+        fi
+        break
+    else
+        print_color "Invalid input. Please select a valid option." 'red'
+    fi
+done
+print_color "Selected assembly mode: $ASSEMBLY_MODE" 'green'
 
-if [ "$TRIMMED" == "yes" ] || [ "$TRIMMED" == "y" ]
-then SAVETRIMMED="True"
-else SAVETRIMMED="False"
-fi
+# Select whether to save trimmed reads
+trim_options=("Yes" "No")
+print_color "Do you want to save trimmed reads in outdir?" 'blue'
+select TRIMMED in "${trim_options[@]}"; do
+    if [ -n "$TRIMMED" ]; then
+        # rename trimmed
+        if [ "$TRIMMED" == "Yes" ] || [ "$TRIMMED" == "y" ]; then
+            SAVETRIMMED="true"
+        else 
+            SAVETRIMMED="false"
+        fi
 
-echo "Is gram positive or negative?"
+        break
+    else
+        print_color "Invalid input. Please select a valid option." 'red'
+    fi
+done
+print_color "Selected trimmed file option: $TRIMMED save trimmed" 'green'
 
-read -p 'Write + or -: ' grammtype
+# Select Prokka gram type
+gram_options=("+" "-" "skip")
 
-if [ "$grammtype" != "-" ] && [ "$grammtype" != "+" ]
-then
-    echo "The given param: $grammtype does not match any of the accepted params ('+' or '-')"
-    exit 1
-fi
+print_color "Is gram positive or negative?" 'blue'
+select GRAMTYPE in "${gram_options[@]}"; do
+    if [ -n "$GRAMTYPE" ]; then
+        if [ "$GRAMTYPE" != "skip" ]; then
+            PROKKA_ARGS="--prokka_args '--gram ${GRAMTYPE}'"
+        fi
+        break
+    else
+        print_color "Invalid input. Please select a valid option." 'red'
+    fi
+done
 
+print_color "Selected Prokka gram type: $GRAMTYPE" 'green'
+
+
+# SETUP INTPUT SAMPLE SHEET
 ln -s ../00-reads .
 ln -s ../samples_id.txt .
 
-echo "sample,fastq_1,fastq_2" > samplesheet.csv
-cat samples_id.txt | while read in; do echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz"; done >> samplesheet.csv
+echo "ID,R1,R2,LongFastQ,Fast5,GenomeSize" > samplesheet.csv
+cat samples_id.txt | while read in; do
+    if [ "$ASSEMBLY_MODE" == "short" ]; then
+        echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz,NA,NA,NA";
+    elif [ "$ASSEMBLY_MODE" == "long" ]; then
+        echo "${in},NA,NA,00-reads/${in}.fastq.gz,NA,NA";
+    elif [ "$ASSEMBLY_MODE" == "hybrid" ]; then
+        echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz,00-reads/${in}.fastq.gz,NA,NA";
+    else
+        echo "Format not recognized for the sample : ${in}.";
+    fi
+done >> samplesheet.csv
 
-#module load Nextflow/21.10.6 singularity
 scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
 
 cat <<EOF > assembly.sbatch
@@ -38,20 +104,28 @@ cat <<EOF > assembly.sbatch
 #SBATCH --output $(date '+%Y%m%d')_assembly01.log
 #SBATCH --chdir $scratch_dir
 
-export NXF_OPTS="-Xms500M -Xmx4G"
-
-nextflow run /scratch/bi/pipelines/BU_ISCIII-bacterial-assembly/main.nf \\
-          -c ../../DOC/hpc_slurm_assembly.config \\
-          --input samplesheet.csv \\
-          --outdir ./ \\
-          --cut_mean_quality 20 \\
-          --qualified_quality_phred 20 \\
-          --gram ${grammtype} \\
-          --reference_outdir ../../REFERENCES \\
-	  --save_trimmed ${SAVETRIMMED} \\
-          --kmerfinder_bacteria_database '/data/bi/references/kmerfinder/20190108_stable_dirs/bacteria' \\
-          --reference_ncbi_bacteria '/data/bi/references/bacteria/latest_db/assembly_summary_bacteria.txt' \\
-          -resume
+# module load Nextflow/23.10.0 singularity
+export NXF_OPTS="-Xms500M -Xmx8G"
+
+nextflow run /data/bi/pipelines/nf-core-bacass/main.nf \\
+        -c ../../DOC/hpc_slurm_assembly.config \\
+        -profile singularity \\
+        --input samplesheet.csv \\
+        --outdir ./ \\
+        --assembly_type ${ASSEMBLY_MODE} \\
+        --assembler ${ASSEMBLER} \\
+        --skip_polish true \\
+        --save_trimmed ${SAVETRIMMED} \\
+        --fastp_args '--qualified_quality_phred 20 --cut_mean_quality 20' \\
+        --skip_kraken2 true \\
+        --skip_kmerfinder false \\
+        --kmerfinderdb /data/bi/references/kmerfinder/20190108_stable_dirs/bacteria \\
+        --ncbi_assembly_metadata /data/bi/references/bacteria/20191212/assembly_summary_bacteria.txt \\
+        ${PROKKA_ARGS} \\
+        -resume
+
 EOF
 
 echo "sbatch assembly.sbatch" > _01_nf_assembly.sh
+
+
diff --git a/bu_isciii/templates/assembly/ANALYSIS/lablog_assembly b/bu_isciii/templates/assembly/ANALYSIS/lablog_assembly
index bcbdefd6..c5e90e0e 100644
--- a/bu_isciii/templates/assembly/ANALYSIS/lablog_assembly
+++ b/bu_isciii/templates/assembly/ANALYSIS/lablog_assembly
@@ -1,4 +1,21 @@
 mkdir -p 00-reads
-cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R1*.fastq.gz %_R1.fastq.gz" | bash; cd -
-cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R2*.fastq.gz %_R2.fastq.gz" | bash; cd -
-mv ANALYSIS01_ASSEMBLY $(date '+%Y%m%d')_ANALYSIS01_ASSEMBLY
+cd 00-reads
+
+# Loop through each file in the directory
+while IFS= read -r sample; do
+    # Extract the file name with&without extension
+    filename_noext=$(basename -s .fastq.gz ../../RAW/${sample}*)
+
+    ### Check if the file is a short read or long read
+    for fileitem in $filename_noext; do
+        if [[ "$fileitem" =~ _R[12] ]]; then
+            ln -s -f ../../RAW/${sample}*_R1*.fastq.gz ${sample}_R1.fastq.gz
+            ln -s -f ../../RAW/${sample}*_R2*.fastq.gz ${sample}_R2.fastq.gz
+        elif [[ ! "$fileitem" =~ _R[12] ]]; then
+            ln -s -f ../../RAW/${sample}.fastq.gz ${sample}.fastq.gz
+        fi
+    done
+done < ../samples_id.txt
+
+cd -
+mv ANALYSIS01_ASSEMBLY "$(date '+%Y%m%d')_ANALYSIS01_ASSEMBLY"
diff --git a/bu_isciii/templates/assembly/DOC/hpc_slurm_assembly.config b/bu_isciii/templates/assembly/DOC/hpc_slurm_assembly.config
index 73bfc79b..04dddf4d 100644
--- a/bu_isciii/templates/assembly/DOC/hpc_slurm_assembly.config
+++ b/bu_isciii/templates/assembly/DOC/hpc_slurm_assembly.config
@@ -1,26 +1,231 @@
-conda   {
-	enabled = true
-	autoMounts = true
-}
+/*
+    HPC XTUTATIS CONFIGURATION
+*/
 
 singularity {
-	enabled = true
-	autoMounts = true
+        enabled                 = true
+        autoMounts              = true
+        singularity.cacheDir    = '/data/bi/pipelines/singularity-images'
 }
 
 process {
-	executor = 'slurm'
-	queue = 'middle_idx'
-        conda = '/data/bi/pipelines/miniconda3/envs/assembly'
-        errorStrategy = { task.exitStatus in [140,143,137,138,104,134,139] ? 'retry' : 'finish'; task.exitStatus in [1,4,255] ? 'ignore' : 'finish' }
-        maxRetries = 1
+    executor        = 'slurm'
+	queue           = 'middle_idx'
+	jobName         = { "$task.name - $task.hash" }
+    conda           = null
+	
+	errorStrategy = { task.exitStatus in [140,143,137,138,104,134,139] ? 'retry' : 'finish'; task.exitStatus in [1,4,255] ? 'ignore' : 'finish' }
+    maxRetries = 1
+    maxErrors = '-1'
+
+    withName:PROKKA {
+        container = 'https://zenodo.org/records/10496286/files/bioconda_prokka_v1.14.6_signalp_v4.1.sif?download=1'
+        errorStrategy = { task.exitStatus in [2] ? 'retry' : 'finish'}
+        maxRetries = 2
         maxErrors = '-1'
-        withName:KMERFINDER {
-          container = '/scratch/bi/singularity-images/kmerfinder_v3.0.2.sif'
-        }
+    }
 }
+
 params {
 	max_memory = 376.GB
 	max_cpus = 32
 	max_time = '48.h'
 }
+
+/*
+    CUSTOM OUTPUT FOLDER STRUCTURE -- modules.config
+*/
+params { publish_dir_mode = 'copy' }
+process {
+	withName: '.*:.*:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW' {
+		publishDir = [
+			[
+                path: { "${params.outdir}/01-processing/fastqc/raw" },
+                pattern: "*.{json,html}",
+                mode: params.publish_dir_mode
+		    ],
+            [
+			path: { "${params.outdir}/01-processing/fastqc/raw/zips" },
+            pattern: "*.zip",
+            mode: params.publish_dir_mode
+		    ]
+        ]
+	}
+	withName: '.*:.*:FASTQ_TRIM_FASTP_FASTQC:FASTP' {
+		publishDir = [
+			[
+                path: { "${params.outdir}/01-processing/fastp" },
+                mode: params.publish_dir_mode,
+                enabled: params.save_trimmed
+            ],
+            [
+                path: { "${params.outdir}/01-processing/fastp" },
+                mode: params.publish_dir_mode,
+                pattern: "*.{json,html}"
+            ],
+            [
+                path: { "${params.outdir}/01-processing/fastp/logs" },
+                mode: params.publish_dir_mode,
+                pattern: "*.log"
+            ]
+		]
+	}
+	withName: '.*:.*:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM' {
+		publishDir = [
+			[
+                path: { "${params.outdir}/01-processing/fastqc/trim" },
+                pattern: "*.{json,html}",
+                mode: params.publish_dir_mode
+            ],
+            [
+			    path: { "${params.outdir}/01-processing/fastqc/trim/zips" },
+                pattern: "*.zip",
+                mode: params.publish_dir_mode
+            ]
+		]
+	}
+    withName: 'NANOPLOT' {
+        publishDir = [
+            path: { "${params.outdir}/01-processing/nanoplot" },
+            pattern: "*.txt",
+            mode: params.publish_dir_mode
+        ]
+    }
+    withName: 'PYCOQC' {
+        publishDir = [
+            path: { "${params.outdir}/01-processing/pycoqc" },
+            mode: params.publish_dir_mode
+        ]
+    }
+    withName: 'PORECHOP_PORECHOP' {
+        publishDir = [
+            [
+                path: { "${params.outdir}/01-processing/porechop" },
+                pattern: "*.fastq.gz",
+                mode: params.publish_dir_mode,
+                enabled: params.save_trimmed
+            ],
+            [
+                path: { "${params.outdir}/01-processing/porechop/logs" },
+                pattern: "*.log",
+                mode: params.publish_dir_mode,
+            ]
+        ]
+    } 
+    withName: '.*:.*:KMERFINDER_SUBWORKFLOW:FIND_DOWNLOAD_REFERENCE' {
+        publishDir = [
+            path: { "${params.outdir}/../../REFERENCES" },
+            pattern: "*.{fna,gff}.gz",
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename.equals('versions.yml')){
+                    null
+                } else {
+                    "${refmeta.toString().replace(' ', '_')}/${filename}"
+                }
+            }
+        ]
+    }
+	withName: '.*:.*:KMERFINDER_SUBWORKFLOW:KMERFINDER' {
+		publishDir = [
+            path: { "${params.outdir}/02-taxonomy_contamination/kmerfinder/${meta.id}" },
+            mode: params.publish_dir_mode
+        ]
+	}
+    withName: '.*:.*:KMERFINDER_SUBWORKFLOW:KMERFINDER_SUMMARY' {
+        publishDir = [
+            path: { "${params.outdir}/99-stats" },
+            mode: params.publish_dir_mode
+        ]
+    }
+	withName: 'KRAKEN2|KRAKEN2_LONG' {
+        publishDir = [
+            path: { "${params.outdir}/02-taxonomy_contamination/kraken2" },
+            mode: params.publish_dir_mode
+        ]
+    }
+    withName: 'UNICYCLER|CANU|MINIASM|DRAGONFLYE' {
+        publishDir = [
+            path: { "${params.outdir}/03-assembly/${params.assembler}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                        if (filename.endsWith('.scaffolds.fa.gz') || 
+                                filename.endsWith('.contigs.fasta.gz') || 
+                                filename.endsWith('.contigs.fa') || 
+                                filename.endsWith('.fasta.gz')) {
+                            "${meta.id}.fasta.gz"
+                        } else {
+                            null
+                        }
+                    }
+            ]
+    }
+    withName: 'RACON|MEDAKA|NANOPOLISH' {
+        publishDir = [
+            path: { "${params.outdir}/03-assembly/${params.assembler}/${params.polish_method}" },
+            mode: params.publish_dir_mode
+        ]
+    }
+    withName: 'QUAST|QUAST_BYREFSEQID' {
+        publishDir = [
+            path: { "${params.outdir}/03-assembly/quast" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename.equals('versions.yml') || filename.endsWith('.tsv')){
+                    null
+                } else if (filename.startsWith('GCF')){
+                    "per_reference_reports/${filename}"
+                }
+                else if (!filename.startsWith('GCF')) {
+                    "global_${filename}"
+                }
+            }
+        ]
+    }
+    withName: 'PROKKA' {
+        ext.args = {
+            [
+                '--force',
+                params.prokka_args ? "${params.prokka_args}" : ''
+            ].join(' ').trim()
+        }
+        publishDir = [
+            path: { "${params.outdir}/05-annotation/prokka" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'BAKTA_BAKTA' {
+        ext.args = {
+            [
+                '--force',
+                params.bakta_args ? "${params.bakta_args}" : ''
+            ].join(' ').trim()
+        }
+        publishDir = [
+            path: { "${params.outdir}/05-annotation/bakta/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'MULTIQC' {
+        publishDir = [
+            [ 
+                path: { "${params.outdir}/99-stats/multiqc" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> 
+                    if (filename.equals('versions.yml') || filename.endsWith('.csv')) {
+                        null
+                    } else {
+                        filename
+                    }
+                }
+            ],
+            [
+                path: { "${params.outdir}/99-stats" },
+                mode: params.publish_dir_mode,
+                pattern: "*.csv"
+            ]
+        ]
+    }
+}
diff --git a/bu_isciii/templates/assembly/RESULTS/lablog_assembly_results b/bu_isciii/templates/assembly/RESULTS/lablog_assembly_results
index f112c0b5..508d1d55 100644
--- a/bu_isciii/templates/assembly/RESULTS/lablog_assembly_results
+++ b/bu_isciii/templates/assembly/RESULTS/lablog_assembly_results
@@ -1,12 +1,32 @@
 DELIVERY_FOLDER="$(date '+%Y%m%d')_entrega"
 
 mkdir $DELIVERY_FOLDER
-mkdir "${DELIVERY_FOLDER}/assembly"
+mkdir $DELIVERY_FOLDER/assembly
 
 # Assembly service
 cd $DELIVERY_FOLDER/assembly
-ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/MultiQC/multiqc_report.html .
-ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/kmerfinder.csv .
-ln -s ../../../ANALYSIS/*ASSEMBLY/03-assembly/unicycler assemblies
-ln -s ../../../ANALYSIS/*ASSEMBLY/03-assembly/quast_results/latest*/report.html quast_report.html
+
+# Links to reports
+ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/multiqc/multiqc_report.html .
+ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/summary_assembly_metrics_mqc.csv .
+ln -s ../../../ANALYSIS/*ASSEMBLY/99-stats/kmerfinder_summary.csv .
+ln -s ../../../ANALYSIS/*ASSEMBLY/03-assembly/quast/global_report/report.html quast_global_report.html
+
+# Links to per reference reports
+for dir in ../../../ANALYSIS/*ASSEMBLY/03-assembly/quast/per_reference_reports/*; do
+    base=$(basename "$dir")
+    if compgen -G "$dir" > /dev/null; then
+        ln -s "$dir/report.html" "quast_${base}_report.html"
+    fi
+done
+
+# Links to assemblies
+assembly_dirs=(unicycler dragonflye canu miniasm)
+for tool in "${assembly_dirs[@]}"; do
+    path="../../../ANALYSIS/*ASSEMBLY/03-assembly/${tool}"
+    if compgen -G "$path" > /dev/null; then
+        find $path -type d -exec ln -nsf {} assemblies \;
+        break
+    fi
+done
 cd -
diff --git a/bu_isciii/templates/services.json b/bu_isciii/templates/services.json
index 2d8ac4e1..255531b9 100755
--- a/bu_isciii/templates/services.json
+++ b/bu_isciii/templates/services.json
@@ -6,7 +6,7 @@
         "order": 1,
         "begin": "",
         "end": "",
-        "description": "Nextflow assembly pipeline to assemble bacterial genomes",
+        "description": "nf-core/bacass:  Simple bacterial assembly and annotation pipeline",
         "clean": {
           "folders":["01-preprocessing/trimmed_sequences"],
           "files":[]