Updated sftp_user.json and some templates

CHANGELOG.md

@@ -8,8 +8,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ### Credits
 
+Code contributions to the new version:
+
+- [Victor Lopez](https://github.com/victor5lm)
+
 ### Template fixes and updates
 
+- Updated sftp_user.json, added the locus-tag option for the PROKKA process in the bacass config file and changed new_service.py so that integrity is checked only for the samples of interest [#363](https://github.com/BU-ISCIII/buisciii-tools/pull/363).
+
 ### Modules
 
 #### Added enhancements

bu_isciii/new_service.py

@@ -103,12 +103,19 @@ def check_md5(self):
         md5_dir = os.path.dirname(md5_file_path)
         os.chdir(md5_dir)
 
+        # Regex pattern to match sample names in .fastq.gz files
+        sample_names_pattern = "|".join(
+            [
+                f"{sample['sample_name']}.*\\.fastq\\.gz"
+                for sample in self.service_samples
+            ]
+        )
+
         # md5sum command
         stderr.print(f"[blue]Checking MD5 integrity for {md5_file_path}")
         try:
-            subprocess.run(
-                ["md5sum", "-c", os.path.basename(md5_file_path)], check=True
-            )
+            cmd = f"grep -E '{sample_names_pattern}' {md5_file_path} | md5sum -c"
+            subprocess.run(cmd, shell=True, check=True, executable="/bin/bash")
             stderr.print("[green]MD5 check passed!")
         except subprocess.CalledProcessError as e:
             stderr.print(f"[red]ERROR: MD5 check failed: {e.stderr}")

bu_isciii/templates/assembly/DOC/hpc_slurm_assembly.config

@@ -195,7 +195,8 @@ process {
         ext.args = {
             [
                 '--force',
-                params.prokka_args ? "${params.prokka_args}" : ''
+                params.prokka_args ? "${params.prokka_args}" : '',
+                "--locustag ${meta.id}"
             ].join(' ').trim()
         }
         publishDir = [

bu_isciii/templates/sftp_user.json

@@ -55,5 +55,6 @@
     "bioinfoadm": ["test"],
     "s.varona": ["misc"],
     "nlabiod": ["Labarbovirus"],
-    "jmgonzalez": ["Lablegionella"]
+    "jmgonzalez": ["Lablegionella"],
+    "alberto.campoy": ["Labvirusres"]
 }