Fixed Typos

Author: olabiyi

Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina/workflow_code/post_processing.config

@@ -3,18 +3,18 @@ params {
 
     publishDir_mode    = "link" // "copy", "link", "symlink"
     //-------- Parameters used to generate README.txt  ------------------//
-    name               = "Olabiyi A. Obayomi"  // name of analyst
-    email              = "olabiyi.a.obayomi@nasa.gov" // email of analyst
+    name               = "FirstName M. LastName"  // name of analyst
+    email              = "name@nasa.gov" // email of analyst
     // Genelab pipeline document protocol id used to process the data
     protocol_id        = "GL-DPPD-7104-B"  
-    GLDS_accession     =  "GLDS-487"
-    OSD_accession      =  "OSD-487"
+    GLDS_accession     =  "" // e.g "GLDS-487"
+    OSD_accession      =  "" // e.g "OSD-487"
     assay_suffix       =  "_GLAmpSeq"
     readme             = "README${params.assay_suffix}.txt"
     processing_zip_file = "processing_info${params.assay_suffix}.zip"
     /* extra parameters and arguments to GL-gen-processed-amplicon-data-readme command
     run `GL-gen-processed-amplicon-readme --help` for extra parameters that can be set
-     "--raw-reads-dir  '../Raw_Sequence_Data/' "  for Metagenomics
+     "--raw-reads-dir  '../Raw_Sequence_Data/' "
      "--primers-already-trimmed" for Amplicon: if primers were trimmed prior to analysis
      */ 
     readme_extra  =  "" 
@@ -53,9 +53,9 @@ params {
         main              = "./main.nf"
         config            = "./nextflow.config" 
         samples           = "./unique-sample-IDs.txt"
-        assay_table       = "" //"../Genelab/a_GLDS-487_amplicon-sequencing_16s_illumina-1.txt"
-        isa_zip           = "../Genelab/OSD-487_metadata_GLDS-487-ISA.zip"
-        runsheet          = "../Genelab/GLfile.csv"
+        assay_table       = "" // e.g. "../Genelab/a_GLDS-487_amplicon-sequencing_16s_illumina-1.txt"
+        isa_zip           = "" // e.g.  "../Genelab/OSD-487_metadata_GLDS-487-ISA.zip"
+        runsheet          = "" // e.g "../Genelab/GLfile.csv"
         software_versions = "../Metadata/software_versions.txt"
     }
 

Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina/workflow_code/post_processing.nf

@@ -34,7 +34,7 @@ if(params.help){
   println("  --email [STRING] The analyst's email address. E.g. 'mail@nasa.gov'.  Default: mail@nasa.gov")
   println("  --assay_suffix [STRING]  Genelab's assay suffix. Default: _GLAmpSeq.")
   println("  --output_prefix [STRING] Unique name to tag onto output files. Default: empty string.")
-  println("  --V_V_guidelines_link [URL] Genelab metagenomics data validation and verification guidelines link. Default: https://genelab-tools.arc.nasa.gov/confluence/pages/viewpage.action?pageId=8225175.")
+  println("  --V_V_guidelines_link [URL] Genelab metagenomics data validation and verification guidelines link. Default: https://genelab-tools.arc.nasa.gov/confluence/pages/viewpage.action?pageId=2428598.")
   println("  --target_files [STRING] A comma separated list of target files and/or directories to find in processing_info.zip. Default: main.nf,nextflow.config,unique-sample-IDs.txt,envs/,bin/,config/,modules/.")
   println()
   println("File Suffixes:")
@@ -50,8 +50,8 @@ if(params.help){
   println()
   println("Extra parameters to scripts:")
   println("      --readme_extra [STRING] Extra parameters and arguments to GL-gen-processed-amplicon-data-readme command. Run 'GL-gen-processed-amplicon-readme --help' for extra parameters that can be set. Example '--raw-reads-dir  ../Raw_Sequence_Data/'. Default: empty string")
-  println("      --validation_extra [STRING] Extra parameters and arguments to GL-validate-processed-amplicon-data command. Run 'GL-validate-processed-amplicon-data --help' for extra parameters that can be set. Example '--single-ended --R1-used-as-single-ended-data --skip_raw_multiqc'. Default: '--skip_raw_multiqc' ")
-  println("      --file_association_extra [STRING] Extra parameters and arguments to GL-gen-amplicon-file-associations-table command. Run 'GL-gen-amplicon-file-associations-table --help' for extra parameters that can be set. Example '--single-ended --R1-used-as-single-ended-data'. Default: '--use-sample-names-from-assay-table' ")
+  println("      --validation_extra [STRING] Extra parameters and arguments to GL-validate-processed-amplicon-data command. Run 'GL-validate-processed-amplicon-data --help' for extra parameters that can be set. Example '--single-ended --R1-used-as-single-ended-data --skip_raw_multiqc'. Default: empty string ")
+  println("      --file_association_extra [STRING] Extra parameters and arguments to GL-gen-amplicon-file-associations-table command. Run 'GL-gen-amplicon-file-associations-table --help' for extra parameters that can be set. Example '--single-ended --R1-used-as-single-ended-data'. Default: empty string ")
   println()
   println("Files:")
   println("    --files.main  [PATH] The main workflow script used for processing. Default: ./main.nf")