diff --git a/.editorconfig b/.editorconfig index b78de6e655..b6b3190776 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,7 +8,7 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{md,yml,yaml,html,css,scss,js,cff}] +[*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 # These files are edited and tested upstream in nf-core/modules diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index c4081e839b..6490c68307 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -45,6 +45,6 @@ body: * Nextflow version _(eg. 22.10.1)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ - * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ * Version of nf-core/sarek _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 6f7814ecbf..b3a687b63a 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sare - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md) +- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 269ede0e4c..d731915357 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -15,7 +15,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/awsfulltest_germline.yml b/.github/workflows/awsfulltest_germline.yml index d8bc5860bd..f43848c827 100644 --- a/.github/workflows/awsfulltest_germline.yml +++ b/.github/workflows/awsfulltest_germline.yml @@ -1,4 +1,4 @@ -name: nf-core AWS full size tests somatic +name: nf-core AWS full size tests germline # This workflow is triggered on published releases. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch @@ -8,14 +8,14 @@ on: types: [published] workflow_dispatch: jobs: - run-tower-somatic: + run-tower-germline: name: Run AWS full tests if: github.repository == 'nf-core/sarek' runs-on: ubuntu-latest steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,4 +25,8 @@ jobs: { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test" } - profiles: test_full_somatic,aws_tower + profiles: test_full_germline,aws_tower + - uses: actions/upload-artifact@v3 + with: + name: Tower debug log file + path: tower_action_*.log diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 9a0a932d5f..ebcb22e0d3 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 07fb1c0226..70d2466f02 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,7 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/sarek' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/sarek ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/sarek ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml new file mode 100644 index 0000000000..694e90ecb1 --- /dev/null +++ b/.github/workflows/clean-up.yml @@ -0,0 +1,24 @@ +name: "Close user-tagged issues and PRs" +on: + schedule: + - cron: "0 0 * * 0" # Once a week + +jobs: + clean-up: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v7 + with: + stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." + stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." + close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 858d622efc..888cb4bc35 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.7" + python-version: "3.8" architecture: "x64" - name: Install dependencies diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000000..0c31cdb99f --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,5 @@ +repos: + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v2.7.1" + hooks: + - id: prettier diff --git a/README.md b/README.md index 59b8ee4d53..dd49f72153 100644 --- a/README.md +++ b/README.md @@ -13,9 +13,7 @@ [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/sarek) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23sarek-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/sarek) -[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core) -[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23sarek-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/sarek)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction @@ -47,36 +45,49 @@ By default, the pipeline currently performs the following:

-## Quick Start +## Usage -1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`) +> **Note** +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +> with `-profile test` before running the workflow on actual data. -2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. +First, prepare a samplesheet with your input data that looks as follows: -3. Download the pipeline and test it on a minimal dataset with a single command: +`samplesheet.csv`: - ```bash - nextflow run nf-core/sarek -profile test,YOURPROFILE --outdir - ``` +```csv +patient,sample,lane,fastq_1,fastq_2 +ID1,S1,L002,ID1_S1_L002_R1_001.fastq.gz,ID1_S1_L002_R2_001.fastq.gz +``` - Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. +Each row represents a pair of fastq files (paired end). - > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. - > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. - > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. +Now, you can run the pipeline using: -4. Start running your own analysis! - - ```bash - nextflow run nf-core/sarek --input samplesheet.csv --outdir --genome GATK.GRCh38 -profile - ``` +```bash +nextflow run nf-core/sarek \ + -profile \ + --input samplesheet.csv \ + --outdir +``` See [usage docs](https://nf-co.re/sarek/usage) for all of the available options when running the pipeline. ## Documentation -The nf-core/sarek pipeline comes with documentation about the pipeline [usage](https://nf-co.re/sarek/usage), [parameters](https://nf-co.re/sarek/parameters) and [output](https://nf-co.re/sarek/output). +> **Warning:** +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those +> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). + +For more details, please refer to the [usage documentation](https://nf-co.re/sarek/usage) and the [parameter documentation](https://nf-co.re/sarek/parameters). + +## Pipeline output + +To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/sarek/results) tab on the nf-core website pipeline page. +For more details about the output files and reports, please refer to the +[output documentation](https://nf-co.re/sarek/output). ## Credits diff --git a/conf/base.config b/conf/base.config index bee4acce1a..1945ad9aa9 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,7 +15,7 @@ process { shell = ['/bin/bash', '-euo', 'pipefail'] // memory errors which should be retried. otherwise error out - errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' diff --git a/conf/igenomes.config b/conf/igenomes.config index 4e8cad67ef..9e5916ff32 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -103,6 +103,11 @@ params { vep_species = 'homo_sapiens' vep_version = '108.2' } + 'CHM13' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" + bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" + } 'GRCm38' { bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" chr_dir = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes" diff --git a/conf/test/test_full.config b/conf/test/test_full.config index fe9a414d03..af1a46dbe5 100644 --- a/conf/test/test_full.config +++ b/conf/test/test_full.config @@ -10,6 +10,8 @@ ---------------------------------------------------------------------------------------- */ +cleanup = true + params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index 3e2d2beaf3..19499dcc5d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -30,6 +30,29 @@ work # Directory containing the nextflow working files # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` +If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. + +Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. + +> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> The above pipeline run specified with a params file in yaml format: + +```bash +nextflow run nf-core/sarek -profile docker -params-file params.yaml +``` + +with `params.yaml` containing: + +```yaml +input: './samplesheet.csv' +outdir: './results/' +genome: 'GRCh37' +input: 'data' +<...> +``` + +You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). + ## Input: Sample sheet configurations You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use the parameter `--input` to specify its location. It has to be a comma-separated file with at least 3 columns, and a header row as shown in the examples below. @@ -299,6 +322,10 @@ Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 3.1 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. +To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. + +> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. + # Core Nextflow arguments > **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). @@ -308,7 +335,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. > We highly recommend the use of `Docker` or `Singularity` containers for full pipeline reproducibility, however when this is not possible, `Conda` is also supported. @@ -333,8 +360,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `apptainer` + - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `conda` - - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. ## `-resume` @@ -370,105 +399,19 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: +To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. -```bash -[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) -Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' - -Caused by: - Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) - -Command executed: - STAR \ - --genomeDir star \ - --readFilesIn WT_REP1_trimmed.fq.gz \ - --runThreadN 2 \ - --outFileNamePrefix WT_REP1. \ - - -Command exit status: - 137 - -Command output: - (empty) - -Command error: - .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. -Work dir: - /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb +### Custom Containers -Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -``` - -#### For beginners - -A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. -Therefore you can go to the [parameter documentation of sarek](https://nf-co.re/sarek/3.1.1/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. -In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. -If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below. +In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. -#### Advanced option on process level +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. -To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). -We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`. -If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). -The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. -The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. -Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. -The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. - -```nextflow -process { - withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' { - memory = 100.GB - } -} -``` +### Custom Tool Arguments -> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. -> -> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. +A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -### Updating containers (advanced users) - -The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. - -1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19) -2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) -3. Create the custom config accordingly: - - - For Docker: - - ```nextflow - process { - withName: PANGOLIN { - container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` - - - For Singularity: - - ```nextflow - process { - withName: PANGOLIN { - container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` - - - For Conda: - - ```nextflow - process { - withName: PANGOLIN { - conda = 'bioconda::pangolin=3.0.5' - } - } - ``` - -> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. ## nf-core/configs @@ -498,7 +441,7 @@ nextflow run nf-core/sarek -r 3.0.1 -profile test, Expected run output: -``` +```bash [42/360944] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX (genome.fasta) [100%] 1 of 1 ✔ [- ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX - [- ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE - @@ -624,28 +567,28 @@ From 'Reference files' https://github.com/VanLoo-lab/ascat: 1. Fetch the GC content correction and replication timing (RT) correction files from the [Dropbox links provided by the ASCAT developers](https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS) and intersect the SNP coordinates with the exome target coordinates. If the target file has 'chr' prefixes, make a copy with these removed first. Extract the GC and RT information for only the on target SNPs and zip the results. -``` +```bash sed -e 's/chr//' targets_with_chr.bed > targets.bed for t in GC RT do unzip ${t}_G1000_hg38.zip - cut -f 1-3 ${t}_G1000_hg38.txt > ascat_${t}_snps_hg38.txt - tail -n +2 ascat_${t}_snps_hg38.txt | awk '{ print $2 "\t" $3-1 "\t" $3 "\t" $1 }' > ascat_${t}_snps_hg38.bed - bedtools intersect -a ascat_${t}_snps_hg38.bed -b targets.bed | awk '{ print $1 "_" $3 }' > ascat_${t}_snps_on_target_hg38.txt + cut -f 1-3 ${t}_G1000_hg38.txt > ascat_${t}_snps_hg38.txt + tail -n +2 ascat_${t}_snps_hg38.txt | awk '{ print $2 "\t" $3-1 "\t" $3 "\t" $1 }' > ascat_${t}_snps_hg38.bed + bedtools intersect -a ascat_${t}_snps_hg38.bed -b targets.bed | awk '{ print $1 "_" $3 }' > ascat_${t}_snps_on_target_hg38.txt - head -n 1 ${t}_G1000_hg38.txt > ${t}_G1000_on_target_hg38.txt - grep -f ascat_${t}_snps_on_target_hg38.txt ${t}_G1000_hg38.txt >> ${t}_G1000_on_target_hg38.txt - zip ${t}_G1000_on_target_hg38.zip ${t}_G1000_on_target_hg38.txt + head -n 1 ${t}_G1000_hg38.txt > ${t}_G1000_on_target_hg38.txt + grep -f ascat_${t}_snps_on_target_hg38.txt ${t}_G1000_hg38.txt >> ${t}_G1000_on_target_hg38.txt + zip ${t}_G1000_on_target_hg38.zip ${t}_G1000_on_target_hg38.txt - rm ${t}_G1000_hg38.zip + rm ${t}_G1000_hg38.zip done ``` 2. Download the Battenberg 1000G loci and alleles files. The steps below follow downloading from the [Battenberg repository at the Oxford University Research Archive](https://ora.ox.ac.uk/objects/uuid:08e24957-7e76-438a-bd38-66c48008cf52). The files are also available via Dropbox links from the same page as the GC and RT correction files above. -``` +```bash wget https://ora.ox.ac.uk/objects/uuid:08e24957-7e76-438a-bd38-66c48008cf52/files/rt435gd52w mv rt345gd52w battenberg.zip jar xf battenberg.zip @@ -660,7 +603,7 @@ mv *loci* battenberg_loci_on_target_hg38/ 3. Copy the `targets_with_chr.bed` and `GC_G1000_on_target_hg38.txt` files into the newly created `battenberg_loci_on_target_hg38` folder before running the next set of steps. ASCAT generates a list of GC correction loci with sufficient coverage in a sample, then intersects that with the list of all loci with tumour logR values in that sample. If the intersection is <10% the size of the latter, it will fail with an error. Because the Battenberg loci/allele sets are very dense, subsetting to on-target regions is still too many loci. This script ensures that all SNPs with GC correction information are included in the loci list, plus a random sample of another 30% of all on target loci. You may need to vary this proportion depending on your set of targets. A good rule of thumb is that the size of your GC correction loci list should be about 15% the size of your total loci list. This allows for a margin of error. -``` +```bash cd battenberg_loci_on_target_hg38/ rm *chrstring* rm 1kg.phase3.v5a_GRCh38nounref_loci_chr23.txt @@ -680,7 +623,7 @@ zip battenberg_loci_on_target_hg38.zip battenberg_loci_on_target_hg38_chr*.txt 4. Extract the alleles for the same set of SNPs. Uses a short R script defined below. -``` +```bash cd ../battenberg_alleles_on_target_hg38/ rm 1kg.phase3.v5a_GRCh38nounref_allele_index_chr23.txt for i in {1..22} X @@ -693,7 +636,7 @@ zip battenberg_alleles_on_target_hg38.zip battenberg_alleles_on_target_hg38_chr* Rscript `intersect_ascat_alleles.R` -``` +```bash #!/usr/bin/env Rscript args = commandArgs(trailingOnly=TRUE) @@ -709,14 +652,13 @@ write.table(out, args[3], col.names=T, row.names=F, quote=F, sep="\t") 5. Move or copy all of the zip files you've created to a suitable location. Specify these in your parameters, e.g. -``` +```json { - "ascat_alleles": "/path/to/battenberg_alleles_on_target_hg38.zip", - "ascat_loci": "/path/to/battenberg_loci_on_target_hg38.zip", - "ascat_loci_gc": "/path/to/GC_G1000_on_target_hg38.zip", - "ascat_loci_rt": "/path/to/RT_G1000_on_target_hg38.zip" + "ascat_alleles": "/path/to/battenberg_alleles_on_target_hg38.zip", + "ascat_loci": "/path/to/battenberg_loci_on_target_hg38.zip", + "ascat_loci_gc": "/path/to/GC_G1000_on_target_hg38.zip", + "ascat_loci_rt": "/path/to/RT_G1000_on_target_hg38.zip" } - ``` ## What are the bwa/bwa-mem2 parameters? diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 4d29681431..9b34804d6d 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -84,6 +84,7 @@ class NfcoreSchema { 'stub-run', 'test', 'w', + 'with-apptainer', 'with-charliecloud', 'with-conda', 'with-dag', diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 255cbcdf57..c3c286c6e0 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the main.nf workflow in the nf-core/sarek pipeline // +import nextflow.Nextflow + class WorkflowMain { // @@ -21,8 +23,8 @@ class WorkflowMain { // // Generate help string // - public static String help(workflow, params, log) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.tsv --genome GRCh38 -profile docker" + public static String help(workflow, params) { + def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh38 -profile docker" def help_string = '' help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) help_string += NfcoreSchema.paramsHelp(workflow, params, command) @@ -34,7 +36,7 @@ class WorkflowMain { // // Generate parameter summary log string // - public static String paramsSummaryLog(workflow, params, log) { + public static String paramsSummaryLog(workflow, params) { def summary_log = '' summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) @@ -49,7 +51,7 @@ class WorkflowMain { public static void initialise(workflow, params, log) { // Print help to screen if required if (params.help) { - log.info help(workflow, params, log) + log.info help(workflow, params) System.exit(0) } @@ -61,7 +63,7 @@ class WorkflowMain { } // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params, log) + log.info paramsSummaryLog(workflow, params) // Validate workflow parameters via the JSON schema if (params.validate_params) { diff --git a/lib/WorkflowSarek.groovy b/lib/WorkflowSarek.groovy index 2251f6f748..2dc499dbf9 100755 --- a/lib/WorkflowSarek.groovy +++ b/lib/WorkflowSarek.groovy @@ -13,9 +13,8 @@ class WorkflowSarek { public static void initialise(params, log) { genomeExistsError(params, log) - - if (!params.fasta) { - Nextflow.error("Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.") + if (!params.fasta && params.step == 'annotate') { + Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." } } @@ -61,7 +60,9 @@ class WorkflowSarek { def description_html = engine.createTemplate(methods_text).make(meta) return description_html - }// + } + + // // Exit pipeline if incorrect --genome key provided // private static void genomeExistsError(params, log) { diff --git a/modules.json b/modules.json index 2c5a5a0f5c..bec75f9710 100644 --- a/modules.json +++ b/modules.json @@ -57,7 +57,7 @@ }, "cat/fastq": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "38b16706fa3a9d4ee2bf46fa5805e7397e275cdd", "installed_by": ["modules"] }, "cnvkit/antitarget": { @@ -102,12 +102,12 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "7101db4432d3268b7fcb5b8f75fa0a022dc5561b", + "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", "installed_by": ["modules"] }, "deepvariant": { "branch": "master", - "git_sha": "58b5e78506e66f7ecd610fa825890ed9fb98b793", + "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", "installed_by": ["modules"] }, "dragmap/align": { @@ -129,7 +129,7 @@ "ensemblvep/vep": { "branch": "master", "git_sha": "ac924c4ba0be25f79248b51be0c9fbfa404b6030", - "installed_by": ["modules", "vcf_annotate_ensemblvep"] + "installed_by": ["vcf_annotate_ensemblvep", "modules"] }, "fastp": { "branch": "master", @@ -168,7 +168,7 @@ }, "gatk4/applybqsrspark": { "branch": "master", - "git_sha": "643756685546fa61f5c8fba439af746c090b9180", + "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", "installed_by": ["modules"] }, "gatk4/applyvqsr": { @@ -183,7 +183,7 @@ }, "gatk4/baserecalibratorspark": { "branch": "master", - "git_sha": "643756685546fa61f5c8fba439af746c090b9180", + "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", "installed_by": ["modules"] }, "gatk4/calculatecontamination": { @@ -193,7 +193,7 @@ }, "gatk4/cnnscorevariants": { "branch": "master", - "git_sha": "643756685546fa61f5c8fba439af746c090b9180", + "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { @@ -263,7 +263,7 @@ }, "gatk4/markduplicatesspark": { "branch": "master", - "git_sha": "700486852c27d8d44bd750799c69f208bb624fed", + "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", "installed_by": ["modules"] }, "gatk4/mergemutectstats": { @@ -318,7 +318,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba", + "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", "installed_by": ["modules"] }, "samblaster": { @@ -378,7 +378,7 @@ }, "snpeff/snpeff": { "branch": "master", - "git_sha": "75027bf77472b1f4fd2cdd7e46f83119dfb0f2c6", + "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71", "installed_by": ["modules", "vcf_annotate_snpeff"] }, "strelka/germline": { @@ -404,7 +404,7 @@ "tabix/tabix": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules", "vcf_annotate_ensemblvep"] + "installed_by": ["vcf_annotate_ensemblvep", "modules"] }, "tiddit/sv": { "branch": "master", @@ -413,7 +413,7 @@ }, "untar": { "branch": "master", - "git_sha": "cc1f997fab6d8fde5dc0e6e2a310814df5b53ce7", + "git_sha": "38b16706fa3a9d4ee2bf46fa5805e7397e275cdd", "installed_by": ["modules"] }, "unzip": { @@ -432,7 +432,7 @@ "nf-core": { "vcf_annotate_ensemblvep": { "branch": "master", - "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653", + "git_sha": "ca2bf9212707e83717934ec6c5d4cab42b39ca69", "installed_by": ["subworkflows"] }, "vcf_annotate_snpeff": { diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 8a0b5600c2..c5359bf93f 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -5,7 +5,7 @@ process CAT_FASTQ { conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'docker.io/library/ubuntu:20.04' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index c836598e49..8a39e309fb 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -1,6 +1,7 @@ name: cat_fastq description: Concatenates fastq files keywords: + - cat - fastq - concatenate tools: @@ -16,7 +17,7 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: - type: list + type: file description: | List of input FastQ files to be concatenated. output: diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 60b546a012..c32657de7a 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,7 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom + - dump - version tools: - custom: diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py old mode 100644 new mode 100755 diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf index 434fcc0e4b..afc5e444b3 100644 --- a/modules/nf-core/deepvariant/main.nf +++ b/modules/nf-core/deepvariant/main.nf @@ -2,7 +2,7 @@ process DEEPVARIANT { tag "$meta.id" label 'process_medium' - container "google/deepvariant:1.4.0" + container "docker.io/google/deepvariant:1.4.0" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml index 63868b2597..97f068ec1f 100644 --- a/modules/nf-core/deepvariant/meta.yml +++ b/modules/nf-core/deepvariant/meta.yml @@ -3,6 +3,7 @@ description: DeepVariant is an analysis pipeline that uses a deep neural network keywords: - variant calling - machine learning + - neural network tools: - deepvariant: description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data diff --git a/modules/nf-core/gatk4/applybqsrspark/main.nf b/modules/nf-core/gatk4/applybqsrspark/main.nf index 208c6b5b02..e920a2554d 100644 --- a/modules/nf-core/gatk4/applybqsrspark/main.nf +++ b/modules/nf-core/gatk4/applybqsrspark/main.nf @@ -3,7 +3,7 @@ process GATK4_APPLYBQSR_SPARK { label 'process_low' conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" - container 'broadinstitute/gatk:4.4.0.0' + container 'docker.io/broadinstitute/gatk:4.4.0.0' input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applybqsrspark/meta.yml b/modules/nf-core/gatk4/applybqsrspark/meta.yml index bc6a8ebfd8..9acdecc5af 100644 --- a/modules/nf-core/gatk4/applybqsrspark/meta.yml +++ b/modules/nf-core/gatk4/applybqsrspark/meta.yml @@ -3,6 +3,7 @@ description: Apply base quality score recalibration (BQSR) to a bam file keywords: - bqsr - bam + - gatk tools: - gatk4: description: | diff --git a/modules/nf-core/gatk4/baserecalibratorspark/main.nf b/modules/nf-core/gatk4/baserecalibratorspark/main.nf index 8578585657..8857dbc382 100644 --- a/modules/nf-core/gatk4/baserecalibratorspark/main.nf +++ b/modules/nf-core/gatk4/baserecalibratorspark/main.nf @@ -3,7 +3,7 @@ process GATK4_BASERECALIBRATOR_SPARK { label 'process_low' conda "bioconda::gatk4=4.4.0.0 conda-forge::openjdk=8.0.312" - container 'broadinstitute/gatk:4.4.0.0' + container 'docker.io/broadinstitute/gatk:4.4.0.0' input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/baserecalibratorspark/meta.yml b/modules/nf-core/gatk4/baserecalibratorspark/meta.yml index d12f8ec267..a4a73ade51 100644 --- a/modules/nf-core/gatk4/baserecalibratorspark/meta.yml +++ b/modules/nf-core/gatk4/baserecalibratorspark/meta.yml @@ -2,6 +2,8 @@ name: gatk4_baserecalibrator_spark description: Generate recalibration table for Base Quality Score Recalibration (BQSR) keywords: - sort + - bqsr + - gatk tools: - gatk4: description: | diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf index 38dad6cb44..730544f61e 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -3,7 +3,7 @@ process GATK4_CNNSCOREVARIANTS { label 'process_low' //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package + container "docker.io/broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/nf-core/gatk4/markduplicatesspark/main.nf b/modules/nf-core/gatk4/markduplicatesspark/main.nf index b1716584d5..d1388298c1 100644 --- a/modules/nf-core/gatk4/markduplicatesspark/main.nf +++ b/modules/nf-core/gatk4/markduplicatesspark/main.nf @@ -3,7 +3,7 @@ process GATK4_MARKDUPLICATES_SPARK { label 'process_high' conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312" - container 'broadinstitute/gatk:4.4.0.0' + container 'docker.io/broadinstitute/gatk:4.4.0.0' input: tuple val(meta), path(bam) diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ebc29b279d..f93b5ee519 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: MultiQC description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: @@ -37,7 +38,7 @@ output: description: MultiQC report file pattern: "multiqc_report.html" - data: - type: dir + type: directory description: MultiQC data dir pattern: "multiqc_data" - plots: diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index 28973c78b3..cf00c819ac 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -2,6 +2,8 @@ name: SNPEFF_SNPEFF description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation + - variant + - effect prediction tools: - snpeff: description: | @@ -21,7 +23,7 @@ input: description: | vcf to annotate - db: - type: value + type: string description: | which db to annotate with - cache: diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 3384847aa5..a4488c3595 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -5,7 +5,7 @@ process UNTAR { conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'docker.io/library/ubuntu:20.04' }" input: tuple val(meta), path(archive) diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index ea7a3f382a..db241a6e5e 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -3,6 +3,7 @@ description: Extract files. keywords: - untar - uncompress + - extract tools: - untar: description: | diff --git a/nextflow.config b/nextflow.config index 91551d3a1c..68177f1600 100644 --- a/nextflow.config +++ b/nextflow.config @@ -145,8 +145,13 @@ try { } profiles { - debug { process.beforeScript = 'echo $HOSTNAME' } + debug { + cleanup = false + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + } conda { + apptainer.enabled = false charliecloud.enabled = false conda.enabled = true docker.enabled = false @@ -155,6 +160,8 @@ profiles { singularity.enabled = false } mamba { + apptainer.enabled = false + charliecloud.enabled = false conda.enabled = true conda.useMamba = true charliecloud.enabled = false @@ -164,9 +171,12 @@ profiles { singularity.enabled = false } docker { + apptainer.enabled = false + charliecloud.enabled = false + conda.enabled = false docker.enabled = true + docker.registry = 'quay.io' docker.userEmulation = { params.use_gatk_spark ? false : true }.call() - charliecloud.enabled = false podman.enabled = false shifter.enabled = false singularity.enabled = false @@ -175,29 +185,47 @@ profiles { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { - singularity.autoMounts = true - singularity.enabled = true + apptainer.enabled = false charliecloud.enabled = false + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false + singularity.autoMounts = true + singularity.enabled = true } podman { - podman.enabled = true + apptainer.enabled = false charliecloud.enabled = false + conda.enabled = false docker.enabled = false + podman.enabled = true + podman.registry = 'quay.io' shifter.enabled = false singularity.enabled = false } shifter { - shifter.enabled = true + apptainer.enabled = false charliecloud.enabled = false + conda.enabled = false docker.enabled = false podman.enabled = false + shifter.enabled = true singularity.enabled = false } charliecloud { + apptainer.enabled = false charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + singularity.enabled = false + } + apptainer { + apptainer.enabled = true + charliecloud.enabled = false + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false diff --git a/tower.yml b/tower.yml new file mode 100644 index 0000000000..787aedfe92 --- /dev/null +++ b/tower.yml @@ -0,0 +1,5 @@ +reports: + multiqc_report.html: + display: "MultiQC HTML report" + samplesheet.csv: + display: "Auto-created samplesheet with collated metadata and FASTQ paths"