Nextflow modules used in SAGC Nextflow pipelines.

These guidelines were adapted from UMCUGenetics.

See utils/template.nf for a process template which uses the following guidelines.

• Use the Tool/version/Command.nf folder structure of this repository.
• 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
  • BWA_0.7.17_MEM
• Define a tag to each process, containing toolname, command, sample_id and/or rg_id.
  • {"BWA MEM ${sample_id} - ${rg_id}"}
• Add 'set -euo pipefail' to each process.
  • shell = ['/bin/bash', '-euo', 'pipefail']
• Do not define any runtime settings like cpus, memory and time.
• Set process parameters on include:
  • include process from 'path/to/process.nf' params(optional: '')
• Use separate process input channels as much as possible. Use tuples for linked inputs only.

input:
    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)

• Use params for resource files, for example genome.fasta, database.vcf.