modules

Nextflow modules used in SAGC Nextflow pipelines.

Coding guidelines

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)