millironx/nf-core_modules
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drpatelh 2020-10-15 11:02:04 +01:00
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README.md
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@ -80,7 +80,7 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
nextflow.enable.dsl = 2
include { FASTQC } from './modules/nf-core/software/fastqc/main'
include { FASTQC } from './modules/nf-core/software/fastqc/main' addParams( options: [:] )
```
5. We have plans to add other utility commands to help developers install and maintain modules downloaded from this repository so watch this space!
@ -170,7 +170,7 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
- A module file SHOULD only define input and output files as command-line parameters to be executed within the process.
- All other parameters MUST be provided as a string i.e. `options.args` where `options` is a Groovy Map that MUST be provided in the `input` section of the process.
- All other parameters MUST be provided as a string i.e. `options.args` where `options` is a Groovy Map that MUST be provided via the Nextflow `addParams` option when including the module via `include` in the parent workflow.
- If the tool supports multi-threading then you MUST provide the appropriate parameter using the Nextflow `task` variable e.g. `--threads $task.cpus`.
@ -207,7 +207,7 @@ The [Nextflow `publishDir`](https://www.nextflow.io/docs/latest/process.html#pub
```nextflow
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
```
The `saveFiles` function can be found in the [`functions.nf`](software/fastqc/functions.nf) file of utility functions that will be copied into all module directories. It uses the various publishing `options` specified as input to the module to construct and append the relevant output path to `params.outdir`.