reduce script to just the smallest possible i-o

main.nf

@@ -32,94 +32,96 @@ process copy_files_from_bucket_to_demultiplexing {
     path("project_apscale/*")
 
   script: """
-
-  # Create the apscale-Project
-  # apscale --create_project project
   mkdir -p project_apscale/2_demultiplexing/data/
-  # Copy data from bucket to demultiplexing
-  find ${filepath}/* -regex ".*\\\\.fastq\\\\.gz" -exec cp {} project_apscale/2_demultiplexing/data/ \\;
-  find ${filepath}/* -regex ".*\\\\.fastq" -exec cp {} project_apscale/2_demultiplexing/data/ \\;
-
-  # Getting a prepared Settings-file and prepare it for exchanging the placeholders
-  cp -f ../../../settings_with_placeholders.xlsx .
-  DIR=unzipped_settings
-  mkdir \$DIR
-  unzip -d \$DIR settings_with_placeholders.xlsx
-
-
-
-  # Exchanging the placeholders with the given values
-  # Because booleans are strings in xlsx and strings are saved as ids in tables refering to the sharedStrings.xml
-  # False == 8, True == 15
-
-  sed -i "s/placeholder_maxdiffpct/$params.pe_merging_maxdiffpct/g" \$DIR/xl/worksheets/sheet2.xml
-  sed -i "s/placeholder_maxdiffs/$params.pe_merging_maxdiffs/g" \$DIR/xl/worksheets/sheet2.xml
-  sed -i "s/placeholder_minovlen/$params.pe_merging_minovlen/g" \$DIR/xl/worksheets/sheet2.xml
-
-
-  if [ "$params.primer_trimming_anchoring" = "true" ]
-  then
-    sed -i "s/placeholder_anchoring/15/g" \$DIR/xl/worksheets/sheet3.xml
-  else
-    sed -i "s/placeholder_anchoring/8/g" \$DIR/xl/worksheets/sheet3.xml
-  fi
-
-
-  sed -i "s/placeholder_max_ee/$params.quality_filtering_max_ee/g" \$DIR/xl/worksheets/sheet4.xml
-  sed -i "s/placeholder_min_length/$params.quality_filtering_min_length/g" \$DIR/xl/worksheets/sheet4.xml
-  sed -i "s/placeholder_max_length/$params.quality_filtering_max_length/g" \$DIR/xl/worksheets/sheet4.xml
-
-
-  sed -i "s/placeholder_min_size_to_pool/$params.dereplication_pooling_size_of_pool/g" \$DIR/xl/worksheets/sheet5.xml
-
-
-  sed -i "s/placeholder_pct_id/$params.otu_clustering_pct_id/g" \$DIR/xl/worksheets/sheet6.xml
-
-  if [ "$params.otu_clustering_to_excel" = "true" ]
-  then
-    sed -i "s/placeholder_otu_clusterung_to_excel/15/g" \$DIR/xl/worksheets/sheet6.xml
-  else
-    sed -i "s/placeholder_otu_clusterung_to_excel/8/g" \$DIR/xl/worksheets/sheet6.xml
-  fi
-
-
-  sed -i "s/placeholder_alpha/$params.denoising_alpha/g" \$DIR/xl/worksheets/sheet7.xml
-  sed -i "s/placeholder_minsize/$params.denoising_minsize/g" \$DIR/xl/worksheets/sheet7.xml
-
-  if [ "$params.denoising_to_excel" = "true" ]
-  then
-    sed -i "s/placeholder_denoising_to_excel/15/g" \$DIR/xl/worksheets/sheet7.xml
-  else
-    sed -i "s/placeholder_denoising_to_excel/8/g" \$DIR/xl/worksheets/sheet7.xml
-  fi
-
-
-  sed -i "s/placeholder_minimum_similarity/$params.lulu_filtering_minimum_similarity/g" \$DIR/xl/worksheets/sheet8.xml
-  sed -i "s/placeholder_minimum_relative_cooccurence/$params.lulu_filtering_minimum_relative_cooccurence/g" \$DIR/xl/worksheets/sheet8.xml
-  sed -i "s/placeholder_minimum_ratio/$params.lulu_filtering_minimum_ratio/g" \$DIR/xl/worksheets/sheet8.xml
-
-  if [ "$params.lulu_filtering_to_excel" = "true" ]
-  then
-    sed -i "s/placeholder_lulu_to_excel/15/g" \$DIR/xl/worksheets/sheet8.xml
-  else
-    sed -i "s/placeholder_lulu_to_excel/8/g" \$DIR/xl/worksheets/sheet8.xml
-  fi
-
-
-  sed -i "s/placeholder_p5_primer/$params.primer_trimming_p5_primer/g" \$DIR/xl/sharedStrings.xml
-  sed -i "s/placeholder_p7_primer/$params.primer_trimming_p7_primer/g" \$DIR/xl/sharedStrings.xml
-
-
-
-  #Zipping the settings-sheets back into a one Settings-File and replacing the one in the project
-  cd \$DIR
-  zip -r ../Settings.xlsx *
-  cd ..
-  cp -f Settings.xlsx project_apscale/Settings.xlsx
-
-
-  # Run the actual apscale-Project
-  # apscale --run_apscale "project_apscale"
+  echo Hello World > project_apscale/2_demultiplexing/data/out.txt
+
+#  # Create the apscale-Project
+#  # apscale --create_project project
+#  mkdir -p project_apscale/2_demultiplexing/data/
+#  # Copy data from bucket to demultiplexing
+#  find ${filepath}/* -regex ".*\\\\.fastq\\\\.gz" -exec cp {} project_apscale/2_demultiplexing/data/ \\;
+#  find ${filepath}/* -regex ".*\\\\.fastq" -exec cp {} project_apscale/2_demultiplexing/data/ \\;
+#
+#  # Getting a prepared Settings-file and prepare it for exchanging the placeholders
+#  cp -f ../../../settings_with_placeholders.xlsx .
+#  DIR=unzipped_settings
+#  mkdir \$DIR
+#  unzip -d \$DIR settings_with_placeholders.xlsx
+#
+#
+#
+#  # Exchanging the placeholders with the given values
+#  # Because booleans are strings in xlsx and strings are saved as ids in tables refering to the sharedStrings.xml
+#  # False == 8, True == 15
+#
+#  sed -i "s/placeholder_maxdiffpct/$params.pe_merging_maxdiffpct/g" \$DIR/xl/worksheets/sheet2.xml
+#  sed -i "s/placeholder_maxdiffs/$params.pe_merging_maxdiffs/g" \$DIR/xl/worksheets/sheet2.xml
+#  sed -i "s/placeholder_minovlen/$params.pe_merging_minovlen/g" \$DIR/xl/worksheets/sheet2.xml
+#
+#
+#  if [ "$params.primer_trimming_anchoring" = "True" ]
+#  then
+#    sed -i "s/placeholder_anchoring/15/g" \$DIR/xl/worksheets/sheet3.xml
+#  else
+#    sed -i "s/placeholder_anchoring/8/g" \$DIR/xl/worksheets/sheet3.xml
+#  fi
+#
+#
+#  sed -i "s/placeholder_max_ee/$params.quality_filtering_max_ee/g" \$DIR/xl/worksheets/sheet4.xml
+#  sed -i "s/placeholder_min_length/$params.quality_filtering_min_length/g" \$DIR/xl/worksheets/sheet4.xml
+#  sed -i "s/placeholder_max_length/$params.quality_filtering_max_length/g" \$DIR/xl/worksheets/sheet4.xml
+#
+#
+#  sed -i "s/placeholder_min_size_to_pool/$params.dereplication_pooling_size_of_pool/g" \$DIR/xl/worksheets/sheet5.xml
+#
+#
+#  sed -i "s/placeholder_pct_id/$params.otu_clustering_pct_id/g" \$DIR/xl/worksheets/sheet6.xml
+#
+#  if [ "$params.otu_clustering_to_excel" = "True" ]
+#  then
+#    sed -i "s/placeholder_otu_clusterung_to_excel/15/g" \$DIR/xl/worksheets/sheet6.xml
+#  else
+#    sed -i "s/placeholder_otu_clusterung_to_excel/8/g" \$DIR/xl/worksheets/sheet6.xml
+#  fi
+#
+#
+#  sed -i "s/placeholder_alpha/$params.denoising_alpha/g" \$DIR/xl/worksheets/sheet7.xml
+#  sed -i "s/placeholder_minsize/$params.denoising_minsize/g" \$DIR/xl/worksheets/sheet7.xml
+#
+#  if [ "$params.denoising_to_excel" = "True" ]
+#  then
+#    sed -i "s/placeholder_denoising_to_excel/15/g" \$DIR/xl/worksheets/sheet7.xml
+#  else
+#    sed -i "s/placeholder_denoising_to_excel/8/g" \$DIR/xl/worksheets/sheet7.xml
+#  fi
+#
+#
+#  sed -i "s/placeholder_minimum_similarity/$params.lulu_filtering_minimum_similarity/g" \$DIR/xl/worksheets/sheet8.xml
+#  sed -i "s/placeholder_minimum_relative_cooccurence/$params.lulu_filtering_minimum_relative_cooccurence/g" \$DIR/xl/worksheets/sheet8.xml
+#  sed -i "s/placeholder_minimum_ratio/$params.lulu_filtering_minimum_ratio/g" \$DIR/xl/worksheets/sheet8.xml
+#
+#  if [ "$params.lulu_filtering_to_excel" = "True" ]
+#  then
+#    sed -i "s/placeholder_lulu_to_excel/15/g" \$DIR/xl/worksheets/sheet8.xml
+#  else
+#    sed -i "s/placeholder_lulu_to_excel/8/g" \$DIR/xl/worksheets/sheet8.xml
+#  fi
+#
+#
+#  sed -i "s/placeholder_p5_primer/$params.primer_trimming_p5_primer/g" \$DIR/xl/sharedStrings.xml
+#  sed -i "s/placeholder_p7_primer/$params.primer_trimming_p7_primer/g" \$DIR/xl/sharedStrings.xml
+#
+#
+#
+#  #Zipping the settings-sheets back into a one Settings-File and replacing the one in the project
+#  cd \$DIR
+#  zip -r ../Settings.xlsx *
+#  cd ..
+#  cp -f Settings.xlsx project_apscale/Settings.xlsx
+#
+#
+#  # Run the actual apscale-Project
+#  # apscale --run_apscale "project_apscale"
   """
 }