Update readme/template

README.md

@@ -27,6 +27,7 @@ See `utils/template.nf` for a process template which uses the following guidelin
 - Use the original tool version numbering
 - Use CamelCase for tool, command and process names
 - Use lowercase with words separated by underscores for params, inputs, outputs and scripts.
+- Use 4 spaces per indentation level.
 - All input and output identifiers should reflect their conceptual identity. Use informative names like unaligned_sequences, reference_genome, phylogeny, or aligned_sequences instead of foo_input, foo_file, result, input, output, and so forth.
 - Define two labels for each process, containing toolname, version and command separated by an underscore.
     - BWA_0.7.17
@@ -42,16 +43,16 @@ See `utils/template.nf` for a process template which uses the following guidelin
 - Use separate process input channels as much as possible. Use tuples for linked inputs only. 
     ```
     input:
-          tuple sample_id, rg_id, bam, bai
-          path genome_fasta
+          val(analysis_id)
+          tuple(sample_id, path(bam), path(bai))
     ```
 - Define named process output channels. This ensures that outputs can be referenced in external scope by their respective names. Indicate whether an output channel is optional. 
     ```
     output:
-          path "my_file.txt", emit: my_file
-          path "my_optional_file.txt",  optional: my_optional_file, emit: my_optional_file
-          ......
+          path("my_file.txt", emit: my_file)
+          path("my_optional_file.txt",  optional: my_optional_file, emit: my_optional_file)
     ```
+- Use `params` for resource files, for example `genome.fasta`, `database.vcf`.
 
 ## GUIX
 1. Creating squashfs immage

Utils/template.nf

@@ -6,15 +6,15 @@ process Command {
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
+        val(analysis_id)
         tuple(sample_id, path(input_file))
 
     output:
         tuple(sample_id, path(output_file), emit: output_file)
-        path("*.{tsv,txt}", emit: my_output)
+        path("log.txt", emit: log)
 
-
     script:
         """
-        tool command ${params.optional}
+        tool command ${params.optional} ${analysis_id} ${params.resource_file} ${input_file} 
         """
 }