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Add link to functions file
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2 changed files with 6 additions and 4 deletions
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@ -126,8 +126,6 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
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- `*.fastq.gz` and NOT `*.fastq`
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- `*.bam` and NOT `*.sam`
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- The process definition MUST NOT contain a `when` statement.
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- 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.
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```bash
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@ -136,6 +134,8 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
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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).
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- The process definition MUST NOT contain a `when` statement.
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#### Naming conventions
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- 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.
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@ -174,7 +174,7 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
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- 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.
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- 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.
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- 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`.
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- 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.
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@ -190,7 +190,7 @@ The [Nextflow `publishDir`](https://www.nextflow.io/docs/latest/process.html#pub
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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```
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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`.
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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`.
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We also use a standardised parameter called `params.publish_dir_mode` that can be used to alter the file publishing method (default: `copy`).
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@ -34,6 +34,8 @@ process SOFTWARE_TOOL {
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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// TODO nf-core: Fetch "docker pull" address for latest BioContainer image of software: e.g. https://biocontainers.pro/#/tools/samtools
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// 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.
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// 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.
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// If required, multi-tool containers may also be available and are usually named to start with "mulled".
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container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
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