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Add link to functions file

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drpatelh 2020-08-06 16:26:57 +01:00
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commit c98b32dfa8
2 changed files with 6 additions and 4 deletions
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8
README.md
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@ -126,8 +126,6 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
- `*.fastq.gz` and NOT `*.fastq` - `*.fastq.gz` and NOT `*.fastq`
- `*.bam` and NOT `*.sam` - `*.bam` and NOT `*.sam`
- The process definition MUST NOT contain a `when` statement.
- Where applicable, each module command MUST emit a file `<SOFTWARE>.version.txt` containing a single line with the software's version in the format `<VERSION_NUMBER>` or `0.7.17` e.g. - Where applicable, each module command MUST emit a file `<SOFTWARE>.version.txt` containing a single line with the software's version in the format `<VERSION_NUMBER>` or `0.7.17` e.g.
```bash ```bash
@ -136,6 +134,8 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
If the software is unable to output a version number on the command-line then a variable called `VERSION` can be manually specified to create this file e.g. [homer/annotatepeaks module](https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf). If the software is unable to output a version number on the command-line then a variable called `VERSION` can be manually specified to create this file e.g. [homer/annotatepeaks module](https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf).
- The process definition MUST NOT contain a `when` statement.
#### Naming conventions #### Naming conventions
- The directory structure for the module name must be all lowercase e.g. [`software/bwa/mem/`](software/bwa/mem/). The name of the software (i.e. `bwa`) and tool (i.e. `mem`) MUST be all one word. - The directory structure for the module name must be all lowercase e.g. [`software/bwa/mem/`](software/bwa/mem/). The name of the software (i.e. `bwa`) and tool (i.e. `mem`) MUST be all one word.
@ -174,7 +174,7 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
- Software requirements SHOULD be declared within the module file using the Nextflow `container` directive e.g. go to the [BWA BioContainers webpage](https://biocontainers.pro/#/tools/bwa), click on the `Pacakages and Containers` tab, sort by `Version` and get the portion of the link after the `docker pull` command where `Type` is Docker. You may need to double-check that you are using the latest version of the software because you may find that containers for older versions have been rebuilt more recently. - Software requirements SHOULD be declared within the module file using the Nextflow `container` directive e.g. go to the [BWA BioContainers webpage](https://biocontainers.pro/#/tools/bwa), click on the `Pacakages and Containers` tab, sort by `Version` and get the portion of the link after the `docker pull` command where `Type` is Docker. You may need to double-check that you are using the latest version of the software because you may find that containers for older versions have been rebuilt more recently.
- If the software is available on Conda the software should also be defined using the Nextflow `conda` directive. Software MUST be pinned to the channel (i.e. `bioconda`) and version (i.e. `0.7.17`) e.g. `bioconda::bwa=0.7.17`. Pinning the build too e.g. `bioconda::bwa=0.7.17=h9402c20_2` is not currently a requirement. - If the software is available on Conda it MUST also be defined using the Nextflow `conda` directive. Software MUST be pinned to the channel (i.e. `bioconda`) and version (i.e. `0.7.17`) e.g. `bioconda::bwa=0.7.17`. Pinning the build too is not currently a requirement e.g. `bioconda::bwa=0.7.17=h9402c20_2`.
- If required, multi-tool containers may also be available on BioContainers e.g. [`bwa` and `samtools`](https://biocontainers.pro/#/tools/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40). It is also possible for a multi-tool container to be built and added to BioContainers by submitting a pull request on their [`multi-package-containers`](https://github.com/BioContainers/multi-package-containers) repository. - If required, multi-tool containers may also be available on BioContainers e.g. [`bwa` and `samtools`](https://biocontainers.pro/#/tools/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40). It is also possible for a multi-tool container to be built and added to BioContainers by submitting a pull request on their [`multi-package-containers`](https://github.com/BioContainers/multi-package-containers) repository.
@ -190,7 +190,7 @@ The [Nextflow `publishDir`](https://www.nextflow.io/docs/latest/process.html#pub
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
``` ```
The `saveFiles` function can be found in the `functions.nf` file of utility functions that will be copied into all modules directories. It uses the various publishing `options` specified as input to the module to construct and append the relevant output path to `params.outdir`. The `saveFiles` function can be found in the [`functions.nf`](software/fastqc/functions.nf) file of utility functions that will be copied into all modules directories. It uses the various publishing `options` specified as input to the module to construct and append the relevant output path to `params.outdir`.
We also use a standardised parameter called `params.publish_dir_mode` that can be used to alter the file publishing method (default: `copy`). We also use a standardised parameter called `params.publish_dir_mode` that can be used to alter the file publishing method (default: `copy`).

2
software/SOFTWARE/TOOL/main.nf
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@ -34,6 +34,8 @@ process SOFTWARE_TOOL {
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
// TODO nf-core: Fetch "docker pull" address for latest BioContainer image of software: e.g. https://biocontainers.pro/#/tools/samtools // TODO nf-core: Fetch "docker pull" address for latest BioContainer image of software: e.g. https://biocontainers.pro/#/tools/samtools
// Click on the Pacakages and Containers tab, sort by Version and get the portion of the link after the docker pull command where Type is Docker.
// You may need to double-check that you are using the latest version of the software because you may find that containers for older versions have been rebuilt more recently.
// If required, multi-tool containers may also be available and are usually named to start with "mulled". // If required, multi-tool containers may also be available and are usually named to start with "mulled".
container "quay.io/biocontainers/samtools:1.10--h9402c20_2" container "quay.io/biocontainers/samtools:1.10--h9402c20_2"