HPC test done. Finalize.

modules/combine_roary_ilp.nf

@@ -23,18 +23,6 @@ process combine_roary_ilp {
     mkdir prokka
     cp *.gff prokka/
 
-    # copy the py script to execute it here with the extended command. 
-    # However this might fail if baseDir can not be reached from the (singularity) container.
-    # If so, download the script from GitHub as a fallback.
-    #if cp "$baseDir/bin/combine_roary_ilp.py" .; then
-    #  echo "Script copied successfully."
-    #else
-    #  echo "Script could not be copied. Download from GitHub."
-    #  git clone https://github.com/hoelzer-lab/ribap.git ribap-tmp
-    #  cp ribap-tmp/bin/combine_roary_ilp.py .
-    #  rm -r ribap-tmp
-    #fi
-
     # setrecursionlimit see: https://github.com/hoelzer-lab/ribap/issues/66
     python -c "import sys;sys.setrecursionlimit(${params.set_recursion_limit});exec(open('combine_roary_ilp.py').read())" ${strain_ids} ${ident}/gene_presence_absence.csv solved/ holy_python_ribap_"${ident}".csv ${ident} > ribap_roary"${ident}"_summary.txt
     """

modules/generate_html.nf

@@ -16,26 +16,6 @@ process generate_html {
 
   script:
     """
-    ## Try to copy the file
-    #if cp "$baseDir/data/web.tar.gz" .; then
-    #  echo "File copied successfully."
-    #else
-    #  # the command might fail when singularity is used, see: https://github.com/hoelzer-lab/ribap/issues/67
-    #  echo "File copy failed. Attempting to download the file..."
-    #  if wget --no-check-certificate https://osf.io/fcyjn/download -O web.tar.gz; then
-    #    echo "File downloaded. Check file size"
-    #    # Check if the downloaded file size is larger than 0 bytes
-    #    if [ -s "web.tar.gz" ]; then
-    #        echo "Downloaded file is valid and larger than 0 bytes."
-    #    else
-    #        echo "Downloaded file is empty or invalid."
-    #        rm web.tar.gz
-    #        git clone https://github.com/hoelzer-lab/ribap.git ribap-tmp
-    #        cp ribap-tmp/data/web.tar.gz .
-    #        rm -r ribap-tmp
-    #    fi
-    #  fi
-    #fi
     tar zxvf web.tar.gz
     
     mkdir tree