diff --git a/CHANGELOG.md b/CHANGELOG.md
index d706f7ca..2fd6cb6e 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,11 +4,11 @@ All notable changes to this project will be documented in this file.
 
 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).
 
-## [2.1.0dev] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.X
+## [2.2.Xdev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.X
 
 ### Credits
 
-Code contributions to the hotfix:
+Code contributions to the new version:
 
 ### Template fixes and updates
 
@@ -44,6 +44,50 @@ Code contributions to the hotfix:
 
 ### Requirements
 
+## [2.1.0] - 2024-04-19 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.0
+
+### Credits
+
+Code contributions to the new version:
+- [Sarai Varona](https://github.com/svarona)
+- [Pablo Mata](https://github.com/Shettland)
+- [Daniel Valle](https://github.com/Daniel-VM)
+
+### Template fixes and updates
+
+- Added blast_nt template to services.json [#208](https://github.com/BU-ISCIII/buisciii-tools/pull/208) 
+- Included new user to sftp_user.json
+- Included a missing sed inside IRMA's 04-irma/lablog [#213](https://github.com/BU-ISCIII/buisciii-tools/pull/213) 
+- Changed singularity mount options in Viralrecon template to fix errors with Nextflow v23.10.0
+- excel_generator.py reverted to last state, now lineage tables are merged when argument -l is given
+- Adapted viralrecon_results lablog to new excel_generator.py argument
+- IRMA/RESULTS now creates a summary of the different types of flu found in irma_stats.txt
+- Updated IRMA to v1.1.4 date 02-2024 and reduced threads to 16
+- IRMA 04-irma/lablog now creates B and C dirs only if those flu-types are present
+- Fixed characterization template [#220](https://github.com/BU-ISCIII/buisciii-tools/pull/220)
+- Created Chewbbaca template [#230](https://github.com/BU-ISCIII/buisciii-tools/pull/230)
+
+### Modules
+
+#### Added enhancements
+
+- [#207](https://github.com/BU-ISCIII/buisciii-tools/pull/207) - Bioinfo-doc updates: email password can be given in buisciii_config.yml and delivery notes in a text file
+
+#### Fixes
+
+- Added missing url for service assembly_annotation in module list
+- Autoclean-sftp refined folder name parsing with regex label adjustment 
+- Autoclean_sftp does not crash anymore. New argument from 'utils.prompt_yn_question()' in v2.0.0 was missing: 'dflt'
+- Bioinfo-doc now sends email correctly to multiple CCs
+
+#### Changed
+
+#### Removed
+
+- Removed empty strings from services.json
+
+### Requirements
+
 ## [2.0.0] - 2024-03-01 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.0.0
 
 ### Credits
diff --git a/README.md b/README.md
index 96310623..9d597a7c 100644
--- a/README.md
+++ b/README.md
@@ -110,7 +110,7 @@ Output:
 ┏━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
 ┃           Service name ┃ Description                               ┃ Github                                     ┃
 ┡━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
-│    assembly_annotation │ Nextflow assembly pipeline to assemble    │                                            │
+│    assembly_annotation │ Nextflow assembly pipeline to assemble    │ https://github.com/Daniel-VM/bacass/...    │
 │                        │ bacterial genomes                         │                                            │
 │        mtbseq_assembly │ Mycobacterium tuberculosis mapping,       │ https://github.com/ngs-fzb/MTBseq_source   │
 │                        │ variant calling and detection of          │                                            │
diff --git a/bu_isciii/__main__.py b/bu_isciii/__main__.py
old mode 100644
new mode 100755
index 9dcbbb25..50be620b
--- a/bu_isciii/__main__.py
+++ b/bu_isciii/__main__.py
@@ -55,7 +55,7 @@ def run_bu_isciii():
     )
 
     # stderr.print("[green]                                          `._,._,'\n", highlight=False)
-    __version__ = "1.0.1"
+    __version__ = "2.0.0"
     stderr.print(
         "[grey39]    BU-ISCIII-tools version {}".format(__version__), highlight=False
     )
@@ -507,6 +507,7 @@ def bioinfo_doc(
     """
     Create the folder documentation structure in bioinfo_doc server
     """
+    email_pass = email_psswd if email_psswd else ctx.obj.get("email_password")
     new_doc = bu_isciii.bioinfo_doc.BioinfoDoc(
         type,
         resolution,
@@ -517,7 +518,7 @@ def bioinfo_doc(
         results_md,
         ctx.obj["api_user"],
         ctx.obj["api_password"],
-        email_psswd,
+        email_pass,
     )
     new_doc.create_documentation()
 
@@ -564,6 +565,7 @@ def bioinfo_doc(
     default=None,
     help="Tsv output path + filename with archive stats and info",
 )
+@click.pass_context
 def archive(
     ctx,
     service_id,
diff --git a/bu_isciii/autoclean_sftp.py b/bu_isciii/autoclean_sftp.py
old mode 100644
new mode 100755
index 274a1515..43d2e76d
--- a/bu_isciii/autoclean_sftp.py
+++ b/bu_isciii/autoclean_sftp.py
@@ -68,7 +68,9 @@ class AutoremoveSftpService:
     def __init__(self, path=None, days=14):
         # Parse input path
         if path is None:
-            use_default = bu_isciii.utils.prompt_yn_question("Use default path?: ")
+            use_default = bu_isciii.utils.prompt_yn_question(
+                "Use default path?: ", dflt=False
+            )
             if use_default:
                 data_path = bu_isciii.config_json.ConfigJson().get_configuration(
                     "global"
@@ -107,7 +109,7 @@ def check_path_exists(self):
     def get_sftp_services(self):
         self.sftp_services = {}  # {sftp-service_path : last_update}
         service_pattern = (
-            r"^[SRV][A-Z]+[0-9]+_\d{8}_[A-Z0-9]+_[a-zA-Z]+(?:\.[a-zA-Z]+)?_[a-zA-Z]$"
+            r"^[SRV][A-Z]+[0-9]+_\d{8}_[A-Z0-9.-]+_[a-zA-Z]+(?:\.[a-zA-Z]+)?_[a-zA-Z]$"
         )
 
         stderr.print("[blue]Scanning " + self.path + "...")
@@ -149,7 +151,9 @@ def remove_oldservice(self):
                 "The following services are going to be deleted from the sftp:\n"
                 + service_elements
             )
-            confirm_sftp_delete = bu_isciii.utils.prompt_yn_question("Are you sure?: ")
+            confirm_sftp_delete = bu_isciii.utils.prompt_yn_question(
+                "Are you sure?: ", dflt=False
+            )
             if confirm_sftp_delete:
                 for service in self.marked_services:
                     try:
diff --git a/bu_isciii/bioinfo_doc.py b/bu_isciii/bioinfo_doc.py
old mode 100644
new mode 100755
index f6385457..52e72dfc
--- a/bu_isciii/bioinfo_doc.py
+++ b/bu_isciii/bioinfo_doc.py
@@ -262,13 +262,34 @@ def create_structure(self):
         return
 
     def post_delivery_info(self):
-        delivery_notes = bu_isciii.utils.ask_for_some_text(
-            msg="Write some delivery notes:"
-        )
+        if bu_isciii.utils.prompt_yn_question(
+            msg="Do you wish to provide a text file for delivery notes?", dflt=False
+        ):
+            for i in range(3, -1, -1):
+                self.provided_txt = bu_isciii.utils.prompt_path(
+                    msg="Write the path to the file with RAW text as delivery notes"
+                )
+                if not os.path.isfile(os.path.expanduser(self.provided_txt)):
+                    stderr.print(f"Provided file doesn't exist. Attempts left: {i}")
+                else:
+                    stderr.print(f"File selected: {self.provided_txt}")
+                    break
+            else:
+                stderr.print("No more attempts. Delivery notes will be given by prompt")
+                self.provided_txt = None
+        else:
+            self.provided_txt = None
 
+        if self.provided_txt:
+            with open(os.path.expanduser(self.provided_txt)) as f:
+                self.delivery_notes = " ".join([x.strip() for x in f.readlines()])
+        else:
+            self.delivery_notes = bu_isciii.utils.ask_for_some_text(
+                msg="Write some delivery notes:"
+            )
         delivery_dict = {
             "resolution_number": self.resolution_id,
-            "delivery_notes": delivery_notes,
+            "delivery_notes": self.delivery_notes,
         }
 
         # How json should be fully formatted:
@@ -568,9 +589,15 @@ def email_creation(self):
         if bu_isciii.utils.prompt_yn_question(
             "Do you want to add some delivery notes to the e-mail?", dflt=False
         ):
-            email_data["email_notes"] = bu_isciii.utils.ask_for_some_text(
-                msg="Write email notes"
-            )
+            if self.provided_txt:
+                if bu_isciii.utils.prompt_yn_question(
+                    f"Do you want to use notes from {self.provided_txt}?", dflt=False
+                ):
+                    email_data["email_notes"] = self.delivery_notes
+            else:
+                email_data["email_notes"] = bu_isciii.utils.ask_for_some_text(
+                    msg="Write email notes"
+                )
 
         email_data["user_data"] = self.resolution_info["service_user_id"]
         email_data["service_id"] = self.service_name.split("_", 5)[0]
@@ -604,7 +631,7 @@ def send_email(self, html_text, results_pdf_file):
             server.login(user=email_host_user, password=email_host_password)
         except Exception as e:
             stderr.print("[red] Unable to send e-mail" + e)
-
+        default_cc = "bioinformatica@isciii.es"
         msg = MIMEMultipart("alternative")
         msg["To"] = self.resolution_info["service_user_id"]["email"]
         msg["From"] = email_host_user
@@ -617,18 +644,21 @@ def send_email(self, html_text, results_pdf_file):
             + self.service_name.split("_", 5)[2]
         )
         if bu_isciii.utils.prompt_yn_question(
-            "Do you want to add any other sender? appart from "
-            + self.resolution_info["service_user_id"]["email"],
+            "Do you want to add any other sender? apart from %s. Note: %s is the default CC."
+            % (self.resolution_info["service_user_id"]["email"], default_cc),
             dflt=False,
         ):
             stderr.print(
-                "[red] Write emails to be added in semicolon separated format: bioinformatica@isciii.es;icuesta@isciii.es"
+                "[red] Write emails to be added in semicolon separated format: icuesta@isciii.es;user2@isciii.es"
             )
-            msg["CC"] = bu_isciii.utils.ask_for_some_text(msg="E-mails:")
-            rcpt = msg["CC"].split(";") + [msg["To"]]
+            cc_address = bu_isciii.utils.ask_for_some_text(msg="E-mails:")
         else:
-            rcpt = self.resolution_info["service_user_id"]["email"]
-
+            cc_address = str()
+        if cc_address:
+            msg["CC"] = str(default_cc + ";" + str(cc_address))
+        else:
+            msg["CC"] = default_cc
+        rcpt = msg["CC"].split(";") + [msg["To"]]
         html = MIMEText(html_text, "html")
         msg.attach(html)
         with open(results_pdf_file, "rb") as f:
@@ -639,7 +669,6 @@ def send_email(self, html_text, results_pdf_file):
             filename=str(os.path.basename(results_pdf_file)),
         )
         msg.attach(attach)
-
         server.sendmail(
             email_host_user,
             rcpt,
diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog
index 540640fe..43af890a 100755
--- a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog
+++ b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog
@@ -5,7 +5,7 @@ mkdir logs
 
 scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
 
-cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 32 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/bi/pipelines/flu-amd/IRMA FLU_AD ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} &"; done > _01_irma.sh
+cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 16 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/bi/pipelines/flu-amd-202402/IRMA FLU_AD ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} &"; done > _01_irma.sh
 
 echo 'bash create_irma_stats.sh' > _02_create_stats.sh
 
@@ -13,9 +13,9 @@ echo "ls */*HA*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | sort -u | cut -d '_' -
 
 echo "cat HA_types.txt | while read in; do mkdir \${in}; done" >> _03_post_processing.sh
 
-echo "mkdir B" >> _03_post_processing.sh
+echo "if grep -qw 'B__' irma_stats.txt; then mkdir B; fi" >> _03_post_processing.sh
 
-echo "mkdir C" >> _03_post_processing.sh
+echo "if grep -qw 'C__' irma_stats.txt; then mkdir C; fi" >> _03_post_processing.sh
 
 echo "ls */*.fasta | cut -d '/' -f2 | cut -d '.' -f1 | cut -d '_' -f1,2 | sort -u | grep 'A_' > A_fragment_list.txt" >> _03_post_processing.sh
 
@@ -29,7 +29,7 @@ echo 'grep -w 'B__' irma_stats.txt | cut -f1 | while read sample; do cat B_fragm
 
 echo 'grep -w 'C__' irma_stats.txt | cut -f1 | while read sample; do cat C_fragment_list.txt | while read fragment; do if test -f ${sample}/${fragment}*.fasta; then cat ${sample}/${fragment}*.fasta | sed "s/^>/\>${sample}_/g" | sed s/_H1//g | sed s/_H3//g | sed s/_N1//g | sed s/_N2//g | sed s@-@/@g | sed s/_C_/_/g ; fi >> C/${fragment}.txt; done; done' >> _03_post_processing.sh
 
-echo 'cat ../samples_id.txt | while read in; do cat ${in}/*.fasta | sed "s/^>/\>${in}_/g" | sed 's/_H1//g' | sed 's/_H3//g' | sed 's/_N1//g' | sed 's/_N2//g' | sed 's@-@/@g' | 's/_A_/_/g' | sed 's/_B_/_/g' | sed 's/_C_/_/g' >> all_samples_completo.txt; done' >> _03_post_processing.sh
+echo 'cat ../samples_id.txt | while read in; do cat ${in}/*.fasta | sed "s/^>/\>${in}_/g" | sed 's/_H1//g' | sed 's/_H3//g' | sed 's/_N1//g' | sed 's/_N2//g' | sed 's@-@/@g' | sed 's/_A_/_/g' | sed 's/_B_/_/g' | sed 's/_C_/_/g' >> all_samples_completo.txt; done' >> _03_post_processing.sh
 
-echo 'sed -i "s/__//g" irma_stats.txt' >> _03_post_processing.sh
-echo 'sed -i "s/_\t/\t/g" irma_stats.txt' >> _03_post_processing.sh
\ No newline at end of file
+echo 'sed "s/__//g" irma_stats.txt > clean_irma_stats.txt' >> _03_post_processing.sh
+echo 'sed "s/_\t/\t/g" irma_stats.txt > clean_irma_stats.txt' >> _03_post_processing.sh
\ No newline at end of file
diff --git a/bu_isciii/templates/IRMA/RESULTS/irma_results b/bu_isciii/templates/IRMA/RESULTS/irma_results
index a2a5bb33..eee33aa6 100755
--- a/bu_isciii/templates/IRMA/RESULTS/irma_results
+++ b/bu_isciii/templates/IRMA/RESULTS/irma_results
@@ -7,4 +7,5 @@ ln -s ../../ANALYSIS/*_MET/99-stats/multiqc_report.html ./krona_results.html
 ln -s ../../ANALYSIS/*FLU_IRMA/04-irma/all_samples_completo.txt .
 ln -s ../../ANALYSIS/*FLU_IRMA/04-irma/A_H* .
 ln -s ../../ANALYSIS/*FLU_IRMA/04-irma/B .
-ln -s ../../ANALYSIS/*FLU_IRMA/04-irma/C .
\ No newline at end of file
+ln -s ../../ANALYSIS/*FLU_IRMA/04-irma/C .
+tail -n +2 ../../ANALYSIS/*_FLU_IRMA/04-irma/clean_irma_stats.txt | cut -f4 | sort | uniq -c > flu_type_summary.txt
\ No newline at end of file
diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/01-preprocessing/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/01-preprocessing/lablog
index 83679f26..0c86d16d 100644
--- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/01-preprocessing/lablog
+++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/01-preprocessing/lablog
@@ -1,6 +1,6 @@
 # module load fastp 
 # if assembly pipeline was performed first and the trimmed sequences were saved, this should work:
-# cat ../samples_id | xargs -I mkdir @@; cd $_; ln -s ../../*/01-preprocessing/trimmed_sequences/@@*.gz @@; cd -
+# cat ../samples_id.txt | xargs -I @@ mkdir @@; cd @@; ln -s ../../../*/01-processing/fastp/@@_1.fastp.fastq.gz ./@@_R1_filtered.fastq.gz; ln -s ../../../*/01-processing/fastp/@@_2.fastp.fastq.gz ./@@_R2_filtered.fastq.gz ; cd -
 # else: 
 mkdir logs
 scratch_dir=$(echo $(pwd) | sed 's@/data/bi/scratch_tmp/@/scratch/@g')
diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog
index c67caced..b942fba8 100644
--- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog
+++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog
@@ -1,13 +1,16 @@
 # conda activate ariba
-# ARIBA runs local assembli/processing_Data/bioinformatics/services_and_colaborations/CNM/bacteriologia/20190821_QCASSEMBLT_s.gonzalez_T/RAW/fastqc_2/.
 
 mkdir logs
 scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
+downloaded_ref=$(find ../../../../REFERENCES/ -type d -name 'ref_db')
 
 # Cartesian product of the two files to avoid double looping
 join -j 2 ../../samples_id.txt ../databases.txt | sed 's/^ //g' > sample_database.txt
 
 # col 1 (arr[0]): sample
 # col 2 (arr[1]): database
-cat sample_database.txt | while read in; do arr=($in); echo "mkdir -p ${arr[0]}; srun --chdir $scratch_dir --output logs/ARIBA${arr[0]}_${arr[1]}.%j.log --job-name ARIBA_${arr[0]}_${arr[1]} --cpus-per-task 5 --mem 5G --partition short_idx --time 02:00:00 ariba run /data/bi/references/ariba/20211216/${arr[1]}/out.${arr[1]}.prepareref ../../../*ASSEMBLY/01-preprocessing/trimmed_sequences/${arr[0]}_1.trim.fastq.gz ../../../*ASSEMBLY/01-preprocessing/trimmed_sequences/${arr[0]}_2.trim.fastq.gz ${arr[0]}/out_${arr[1]}_${arr[0]}_run &"; done > _01_ariba.sh
-cat sample_database.txt | while read in; do arr=($in); echo "mv ${arr[0]}/out_${arr[1]}_${arr[0]}_run/report.tsv ${arr[0]}/out_${arr[1]}_${arr[0]}_run/${arr[0]}_${arr[1]}_report.tsv"; done > _02_fix_tsvreport.sh
+cat sample_database.txt | grep -v 'pubmlst' | while read in; do arr=($in); echo "mkdir -p ${arr[0]}; srun --chdir $scratch_dir --output logs/ARIBA_${arr[0]}_${arr[1]}.%j.log --job-name ARIBA_${arr[0]}_${arr[1]} --cpus-per-task 5 --mem 5G --partition short_idx --time 02:00:00 ariba run /data/bi/references/ariba/20211216/${arr[1]}/out.${arr[1]}.prepareref ../../01-preprocessing/${arr[0]}/${arr[0]}_R1_filtered.fastq.gz ../../01-preprocessing/${arr[0]}/${arr[0]}_R2_filtered.fastq.gz ${arr[0]}/out_${arr[1]}_${arr[0]}_run &"; done > _01_ariba.sh
+
+cat ../samples_id.txt | while read in; echo "mkdir -p ${arr[0]}; srun --chdir $scratch_dir --output logs/ARIBA_${in}_pubmlst.%j.log --job-name ARIBA_${in}_pubmlst --cpus-per-task 5 --mem 5G --partition short_idx --time 02:00:00 ariba run ${downloaded_ref} ../../01-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../../01-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in}/out_pubmlst_${in}_run &"; done > _01_ariba.sh
+
+cat sample_database.txt | while read in; do arr=($in); echo "mv ${arr[0]}/out_${arr[1]}_${arr[0]}_run/report.tsv ${arr[0]}/out_${arr[1]}_${arr[0]}_run/${arr[0]}_${arr[1]}_report.tsv"; done > _02_fix_tsvreport.sh
\ No newline at end of file
diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog
index 694f2c0a..be959a97 100644
--- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog
+++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog
@@ -8,4 +8,4 @@ scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
 # 1 - Use the ls in parenthesis to find the reports for a certain db, and xargs to make it into a single line
 # 2 - Integrate this into the ariba summary command
 
-cat ../databases.txt | while read in; do echo "srun --chdir $scratch_dir --output logs/ARIBA_SUMMARY_${in}.log --job-name ARIBA_${in} --cpus-per-task 5 --mem 5G --partition short_idx --time 00:30:00 ariba summary --cluster_cols ref_seq,match out_summary_${in} $(ls ../run/*/out*_${in}*/*${in}*_report.tsv | xargs)"; done > _01_ariba_summary_prueba.sh
+cat ../databases.txt | while read in; do echo "srun --chdir $scratch_dir --output logs/ARIBA_SUMMARY_${in}.log --job-name ARIBA_${in} --cpus-per-task 5 --mem 5G --partition short_idx --time 00:30:00 ariba summary --cluster_cols ref_seq,match out_summary_${in} $(ls ../run/*/out*_${in}*/*${in}*_report.tsv | xargs) &"; done > _01_ariba_summary_prueba.sh
diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/99-stats/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/99-stats/lablog
index 29bc7b29..9ab99ce9 100644
--- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/99-stats/lablog
+++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/99-stats/lablog
@@ -2,3 +2,5 @@
 python3 /data/bi/pipelines/bacterial_qc/parse_ariba.py --path ../02-ariba/summary/out_summary_card.csv --database card --output_bn ariba_card.bn --output_csv ariba_card.csv
 python3 /data/bi/pipelines/bacterial_qc/parse_ariba.py --path ../02-ariba/summary/out_summary_plasmidfinder.csv --database plasmidfinder --output_bn ariba_plasmidfinder.bn --output_csv ariba_plasmidfinder.csv
 python3 /data/bi/pipelines/bacterial_qc/parse_ariba.py --path ../02-ariba/summary/out_summary_vfdb_full.csv --database vfdb_full --output_bn ariba_vfdb_full.bn --output_csv ariba_vfdb_full.csv
+
+paste <(echo "sample_id") <(cat ../02-ariba/run/*/out_pubmlst_*_run/mlst_report.tsv | head -n1) > ariba_mlst_full.tsv; cat ../samples_id.txt | while read in; do paste <(echo ${in}) <(tail -n1 ../02-ariba/run/${in}/out_pubmlst_${in}_run/mlst_report.tsv); done >> ariba_mlst_full.tsv
\ No newline at end of file
diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/lablog
index dc6d483c..97055cdf 100644
--- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/lablog
+++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/lablog
@@ -1,6 +1,2 @@
 ln -s ../samples_id.txt .
 ln -s ../00-reads .
-mkdir 01-preprocessing
-mkdir 02-srst2
-mkdir 03-ariba
-mkdir 99-stats
diff --git a/bu_isciii/templates/characterization/RAW/REFERENCES/README b/bu_isciii/templates/characterization/REFERENCES/README
similarity index 100%
rename from bu_isciii/templates/characterization/RAW/REFERENCES/README
rename to bu_isciii/templates/characterization/REFERENCES/README
diff --git a/bu_isciii/templates/characterization/REFERENCES/lablog b/bu_isciii/templates/characterization/REFERENCES/lablog
new file mode 100644
index 00000000..ad9f4010
--- /dev/null
+++ b/bu_isciii/templates/characterization/REFERENCES/lablog
@@ -0,0 +1,44 @@
+# conda activate ariba
+
+mkdir logs
+
+scratch_dir=$(echo $(pwd) | sed 's@/data/bi/scratch_tmp/@/scratch/@g')
+
+# 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 "$1"
+            ;;
+    esac
+}
+
+# Function to prompt with color
+prompt_with_color() {
+    read -p "$(print_color $1 'blue') $2" response
+}
+
+print_color "This will take some seconds to display, please wait" 'blue'
+
+# Select genome from PMLST
+IFS=$'\n'
+bacterial_options=( $(ariba pubmlstspecies | sed 's/^/"/g' | sed 's/$/"/g') )
+print_color "Indicate the preferred bacterial genome:" 'blue'
+select BACTERIA in "${bacterial_options[@]}"; do
+    if [ -n "$BACTERIA" ]; then
+        print_color "Selected bacteria: $BACTERIA" 'green'
+        echo "srun --chdir ${scratch_dir} --mem 10G --time 1:00:00 --job-name PUBMLSTGET --output logs/PUBMLSTGET.%j.log --partition short_idx --cpus-per-task 5 ariba pubmlstget $BACTERIA $(date '+%Y%m%d') &" > _01_download_pubmlst.sh
+        break
+    else
+        print_color "Invalid input. Please select a valid option." 'red'
+    fi
+done
\ No newline at end of file
diff --git a/bu_isciii/templates/characterization/RESULTS/README b/bu_isciii/templates/characterization/RESULTS/README
deleted file mode 100644
index 37dc4134..00000000
--- a/bu_isciii/templates/characterization/RESULTS/README
+++ /dev/null
@@ -1 +0,0 @@
-##Folder to hold relevant results of the service
diff --git a/bu_isciii/templates/characterization/RESULTS/lablog_characterization_results b/bu_isciii/templates/characterization/RESULTS/lablog_characterization_results
index 323dc0dd..8879a843 100644
--- a/bu_isciii/templates/characterization/RESULTS/lablog_characterization_results
+++ b/bu_isciii/templates/characterization/RESULTS/lablog_characterization_results
@@ -1,11 +1,12 @@
 DELIVERY_FOLDER="$(date '+%Y%m%d')_entrega"
 
-mkdir $DELIVERY_FOLDER
+mkdir -p $DELIVERY_FOLDER
 mkdir "${DELIVERY_FOLDER}/characterization"
 
 # ARIBA characterization service
 cd $DELIVERY_FOLDER/characterization
-ln -s ../../../ANALYSIS/*CHARACTERIZATION/99-stats/*.csv .
-ln -s ../../../ANALYSIS/*CHARACTERIZATION/02-ariba/summary/*summary*.csv .
-rm *phandango*
+ln -s ../../../ANALYSIS/*CHARACTERIZATION/99-stats/ariba_*.tsv .
+ln -s ../../../ANALYSIS/*CHARACTERIZATION/99-stats/ariba_*.csv .
+find . -xtype l -delete
+
 cd -
diff --git a/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog b/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog
new file mode 100644
index 00000000..d74a4f22
--- /dev/null
+++ b/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog
@@ -0,0 +1,60 @@
+scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+
+# module load singularity
+
+mkdir logs
+
+# 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 "$1"
+            ;;
+    esac
+}
+
+# Function to prompt with color
+prompt_with_color() {
+    read -p "$(print_color $1 'blue') $2" response
+}
+
+while true; do
+    read -p "Is your schema already prepared for ChewBBACA? (yes/no)" yesno
+    case $yesno in
+        [Yy]* ) 
+            print_color "Indicate the path to the schema:" 'blue'
+            read -e schema_path
+            print_color "Using schema from path: $schema_path" 'green'
+            
+            echo "srun --chdir $scratch_dir --output logs/CHEWBBACA-CALLING.%j.log --job-name CHEWBBACA-CALLING --cpus-per-task 20 --mem 20G --partition middle_idx --time 05:00:00 singularity exec --bind ${scratch_dir}/../../../ /scratch/bi/singularity-images/chewbbaca:3.3.3--pyhdfd78af_0 chewBBACA.py AlleleCall -i ../00-assemblies/ -g $schema_path -o allele_calling/ --cpu 20 &" > _01_chewbbaca_calling.sh
+            
+            echo "srun --chdir $scratch_dir --output logs/CHEWBBACA-ALLELECALL-EVALUATOR.%j.log --job-name CHEWBBACA-ALLELECALL-EVALUATOR --cpus-per-task 1 --mem 20G --partition middle_idx --time 05:00:00 singularity exec --bind ${scratch_dir}/../../../ /scratch/bi/singularity-images/chewbbaca:3.3.3--pyhdfd78af_0 chewBBACA.py AlleleCallEvaluator -i ./allele_calling/ -g $schema_path -o ./allele_calling_evaluation &" > _02_chewbacca_allelecall_evaluator.sh
+
+            break
+        ;;
+        [Nn]* ) 
+            print_color "Indicate the path to the schema:" 'blue'
+            read -e schema_path
+            print_color "Using schema from path: $schema_path" 'green'
+            echo "srun --chdir $scratch_dir --output logs/CHEWBBACA-PREPARE-SCHEMA.%j.log --job-name CHEWBBACA-PREPARE-SCHEMA --partition middle_idx --time 12:00:00 singularity exec --bind ${scratch_dir}/../../../ /scratch/bi/singularity-images/chewbbaca:3.3.3--pyhdfd78af_0 chewBBACA.py PrepExternalSchema --schema-directory $schema_path --output-directory prep_schema &" > _01_prep_schema.sh
+
+            echo "srun --chdir $scratch_dir --output logs/CHEWBBACA-SCHEMA-EVALUATOR.%j.log --job-name CHEWBBACA-SCHEMA-EVALUATOR --partition middle_idx --time 12:00:00 singularity exec --bind ${scratch_dir}/../../../ /scratch/bi/singularity-images/chewbbaca:3.3.3--pyhdfd78af_0 chewBBACA.py SchemaEvaluator --schema-directory schema_path --output-directory analyze_schema &" > _02_analyze_schema.sh
+
+            echo "srun --chdir $scratch_dir --output logs/CHEWBBACA-ALLELECALL.%j.log --job-name CHEWBBACA-ALLELECALL --cpus-per-task 4 --mem 64G --partition middle_idx --time 12:00:00 singularity exec --bind ${scratch_dir}/../../../ /scratch/bi/singularity-images/chewbbaca:3.3.3--pyhdfd78af_0 chewBBACA.py AlleleCall -i ../00-assemblies/ -g ./prep_schema/ -o ./allele_calling --cpu 4 &" > _03_allele_calling.sh
+
+            echo "srun --chdir $scratch_dir --output logs/CHEWBBACA-ALLELECALL-EVALUATOR.%j.log --job-name CHEWBBACA-ALLELECALL-EVALUATOR --cpus-per-task 1 --mem 20G --partition middle_idx --time 05:00:00 singularity exec --bind ${scratch_dir}/../../../ /scratch/bi/singularity-images/chewbbaca:3.3.3--pyhdfd78af_0 chewBBACA.py AlleleCallEvaluator -i ./allele_calling/ -g ./prep_schema/ -o ./allele_calling_evaluation &" > _04_chewbacca_allelecall_evaluator.sh
+
+            break
+        ;;
+        * ) echo "Answer either yes or no!";;
+    esac
+done
\ No newline at end of file
diff --git a/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/lablog b/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/lablog
new file mode 100644
index 00000000..bf94164a
--- /dev/null
+++ b/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/lablog
@@ -0,0 +1,6 @@
+ln -s ../samples_id.txt .
+ln -s ../00-reads .
+
+mkdir 01-assemblies 03-grapetree
+
+cd 01-assemblies; echo "rsync -rlv ../../*ASSEMBLY*/03-assembly/unicycler/*.fasta.gz ." | bash; gunzip *; cd -
diff --git a/bu_isciii/templates/chewbbaca/ANALYSIS/lablog_chewbbaca b/bu_isciii/templates/chewbbaca/ANALYSIS/lablog_chewbbaca
new file mode 100644
index 00000000..bd209b18
--- /dev/null
+++ b/bu_isciii/templates/chewbbaca/ANALYSIS/lablog_chewbbaca
@@ -0,0 +1,6 @@
+mkdir -p 00-reads
+
+cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R1*.fastq.gz %_R1.fastq.gz" | bash; cd -
+cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R2*.fastq.gz %_R2.fastq.gz" | bash; cd -
+
+mv ANALYSIS01_CHEWBBACA "$(date '+%Y%m%d')_ANALYSIS03_CHEWBBACA"
\ No newline at end of file
diff --git a/bu_isciii/templates/chewbbaca/DOC/README b/bu_isciii/templates/chewbbaca/DOC/README
new file mode 100644
index 00000000..353f2e2c
--- /dev/null
+++ b/bu_isciii/templates/chewbbaca/DOC/README
@@ -0,0 +1 @@
+##Folder to hold DOC folder
diff --git a/bu_isciii/templates/chewbbaca/RAW/README b/bu_isciii/templates/chewbbaca/RAW/README
new file mode 100644
index 00000000..a774e7bb
--- /dev/null
+++ b/bu_isciii/templates/chewbbaca/RAW/README
@@ -0,0 +1 @@
+##Folder to hold raw reads to analyze in the service
diff --git a/bu_isciii/templates/chewbbaca/REFERENCES/README b/bu_isciii/templates/chewbbaca/REFERENCES/README
new file mode 100644
index 00000000..eaa651aa
--- /dev/null
+++ b/bu_isciii/templates/chewbbaca/REFERENCES/README
@@ -0,0 +1 @@
+##Folder to hold REFERENCE folder
diff --git a/bu_isciii/templates/chewbbaca/RESULTS/lablog_mlst_results b/bu_isciii/templates/chewbbaca/RESULTS/lablog_mlst_results
new file mode 100644
index 00000000..650d3d22
--- /dev/null
+++ b/bu_isciii/templates/chewbbaca/RESULTS/lablog_mlst_results
@@ -0,0 +1,13 @@
+DELIVERY_FOLDER="$(date '+%Y%m%d')_entrega"
+
+mkdir -p $DELIVERY_FOLDER
+mkdir $DELIVERY_FOLDER/mlst
+
+# Assembly service
+cd $DELIVERY_FOLDER/mlst
+
+# Links to reports
+ln -s ../../../ANALYSIS/*CHEWBBACA/*-chewbbaca/allele_calling_evaluation/allelecall_report.html .
+ln -s ../../../ANALYSIS/*CHEWBBACA/*-chewbbaca/allele_calling_evaluation/distance_matrix_symmetric.tsv .
+ln -s ../../../ANALYSIS/*CHEWBBACA/*-grapetree/*.nwk
+ln -s ../../../ANALYSIS/*CHEWBBACA/*-grapetree/*.svg
diff --git a/bu_isciii/templates/chewbbaca/TMP/README b/bu_isciii/templates/chewbbaca/TMP/README
new file mode 100644
index 00000000..ba322945
--- /dev/null
+++ b/bu_isciii/templates/chewbbaca/TMP/README
@@ -0,0 +1 @@
+##Folder to hold temporary files
diff --git a/bu_isciii/templates/services.json b/bu_isciii/templates/services.json
index a2007838..46795322 100755
--- a/bu_isciii/templates/services.json
+++ b/bu_isciii/templates/services.json
@@ -2,7 +2,7 @@
     "assembly_annotation": {
         "label": "",
         "template": "assembly",
-        "url": "",
+        "url": "https://github.com/Daniel-VM/bacass/tree/buisciii-develop",
         "order": 1,
         "begin": "",
         "end": "",
@@ -196,7 +196,7 @@
       "url": "https://github.com/GuilleGorines/Seek-Destroy",
       "description": "Simple pipeline for basic quality control, host removal and exploratory analysis of samples.",
       "clean": {
-        "folders":[""],
+        "folders":[],
         "files":[]
       },
       "no_copy": ["RAW", "TMP", "00-reads"],
@@ -212,7 +212,7 @@
       "end": "",
       "description": "",
       "clean": {
-        "folders":[""],
+        "folders":[],
         "files":[]
       },
       "no_copy": ["RAW", "TMP", "00-reads"],
@@ -229,7 +229,7 @@
       "url": "https://github.com/nf-core/mag",
       "description": "Bioinformatics best-practise analysis pipeline for assembly, binning and annotation of metagenomes.",
       "clean": {
-        "folders":[""],
+        "folders":[],
         "files":[]
       },
       "no_copy": ["RAW", "TMP"],
@@ -321,5 +321,22 @@
       "last_folder":"REFERENCES",
       "delivery_md": "",
       "results_md": ""
+    },
+    "blast_nt": {
+      "label": "",
+      "template": "blast_nt",
+      "url": "",
+      "order": 1,
+      "begin": "",
+      "end": "",
+      "description": "",
+      "clean": {
+        "folders":[],
+        "files":[]
+      },
+      "no_copy": ["RAW", "TMP"],
+      "last_folder":"REFERENCES",
+      "delivery_md": "",
+      "results_md": ""
   }
 }
diff --git a/bu_isciii/templates/sftp_user.json b/bu_isciii/templates/sftp_user.json
old mode 100644
new mode 100755
index 05736dba..bdf82822
--- a/bu_isciii/templates/sftp_user.json
+++ b/bu_isciii/templates/sftp_user.json
@@ -48,5 +48,6 @@
     "sresino": ["Labvirushep"],
     "svaldezate": ["Labtaxonomia"],
     "svazquez": ["Labvirusres"],
-    "ycampos": ["LabUfiecMithocondrial"]
+    "ycampos": ["LabUfiecMithocondrial"],
+    "anadonoso": ["Labenterovirus"]
 }
diff --git a/bu_isciii/templates/viralrecon/DOC/viralrecon_sars.config b/bu_isciii/templates/viralrecon/DOC/viralrecon_sars.config
old mode 100644
new mode 100755
index a4936716..1e36576e
--- a/bu_isciii/templates/viralrecon/DOC/viralrecon_sars.config
+++ b/bu_isciii/templates/viralrecon/DOC/viralrecon_sars.config
@@ -1,7 +1,7 @@
 singularity {
 	enabled = true
 	autoMounts = true
-        runOptions = '-B /data/bi/references/'
+        runOptions = '-B /data/bi/references/ -B /data/bi/pipelines/artic-ncov2019/ -B "$HOME"'
 }
 
 process {
diff --git a/bu_isciii/templates/viralrecon/RESULTS/excel_generator.py b/bu_isciii/templates/viralrecon/RESULTS/excel_generator.py
index b33c761c..8467c414 100755
--- a/bu_isciii/templates/viralrecon/RESULTS/excel_generator.py
+++ b/bu_isciii/templates/viralrecon/RESULTS/excel_generator.py
@@ -4,7 +4,7 @@
 from typing import List, Dict
 
 # conda activate viralrecon_report
-"""Standard usage: python excel_generator.py -r ./reference.tmp"""
+"""Standard usage: python excel_generator.py -r ./reference.tmp --merge_lineage_files"""
 """Single csv to excel usage: python excel_generator.py -s csv_file.csv"""
 parser = argparse.ArgumentParser(
     description="Generate excel files from viralrecon results"
@@ -22,6 +22,12 @@
     default="",
     help="Transform a single csv file to excel format. Omit rest of processes",
 )
+parser.add_argument(
+    "-l",
+    "--merge_lineage_files",
+    action="store_true",
+    help="Merge pangolin and nextclade lineage tables",
+)
 args = parser.parse_args()
 
 
@@ -135,7 +141,7 @@ def main(args):
         ref: str("ref_samples/samples_" + ref + ".tmp") for ref in references
     }
 
-    if len(references) > 1:
+    if args.merge_lineage_files:
         # Merge pangolin and nextclade csv files separatedly and create excel files for them
         merge_lineage_tables(reference_folders, samples_ref_files)
         for reference, folder in reference_folders.items():
diff --git a/bu_isciii/templates/viralrecon/RESULTS/viralrecon_results b/bu_isciii/templates/viralrecon/RESULTS/viralrecon_results
old mode 100644
new mode 100755
index 1b9f2275..e71f4294
--- a/bu_isciii/templates/viralrecon/RESULTS/viralrecon_results
+++ b/bu_isciii/templates/viralrecon/RESULTS/viralrecon_results
@@ -26,7 +26,7 @@ ln -s ../../ANALYSIS/*/assembly_stats.csv ./assembly_stats.csv
 ln -s ../../ANALYSIS/*/01-PikaVirus-results/all_samples_virus_table_filtered.csv ./pikavirus_table.csv
 
 #conda activate viralrecon_report
-echo "python ./excel_generator.py -r ./references.tmp" > _01_generate_excel_files.sh
+echo "python ./excel_generator.py -r ./references.tmp --merge_lineage_files" > _01_generate_excel_files.sh
 #Cleaning temp files and broken symbolic links
 echo "find . -xtype l -delete" > _02_clean_folders.sh
 echo 'for dir in */; do find ${dir} -xtype l -delete; done' >> _02_clean_folders.sh
@@ -46,3 +46,9 @@ cd variants_annot; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; do a
 cd assembly_spades; rsync -rlv ../../../ANALYSIS/*/*/assembly/spades/rnaviral/*.scaffolds.fa.gz .; gunzip *.scaffolds.fa.gz; cd -
 cd abacas_assembly; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; do arr=($in); ln -s ../../../ANALYSIS/*/*${arr[1]}*/assembly/spades/rnaviral/abacas/${arr[0]}.abacas.fasta ./${arr[0]}_${arr[1]}.abacas.fasta; done; cd -
 ln -s ../../ANALYSIS/*/all_samples_filtered_BLAST_results.xlsx .
+
+#Auxiliar script useful for multiple hosts if samples have pattern to distinguish: e.g. HOSTPATTERN1 = 'MONKEY'
+
+#cat ../viralrecon_results | sed 's@../../@../../../@g' | sed 's/entrega01/HOSTPATTERN1_results/g' > results_wgs
+#sed -i 's@ANALYSIS/\*/@ANALYSIS/*HOSTPATTERN1*/@g' results_wgs.sh
+#sed 's/HOSTPATTERN1/HOSTPATTERN2/g' results_wgs > results_gf.sh
diff --git a/setup.py b/setup.py
old mode 100644
new mode 100755
index ba13fa2f..dcda6436
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import setup, find_packages
 
-version = "2.0.0"
+version = "2.1.0"
 
 with open("README.md") as f:
     readme = f.read()