Release 0.1.0 (#90)

* Add methylation calls to bedmethyl * Output whatshap stats, and add pipeline presets * Fix mosdepth not running for all samples * Fix methylation sample mix * fix dipcall not working * Add fastq and bam stats * fix dipcall not working * Rework modules and subworkflows to match new-found knowledge about single element channels * Added TRGT for pacbio-data * Fix repeat versions * Fix samtools index publishdirs * Add back --secondary=no to minimap2 align * Fix cramino phased and unphased * Update README.md * Fix dipcall sample name in vcf * Fix trgt container adress * try again to fix trgt container adress * remove TRVZ because it will create too many processes * completely remove TRVZ * update modules conf, missing output files, index bams and fix containers * Fix minimap2 index always using default params * minimap index needs to be built separate for dipcall as well * tweak process requirements * Improve whatshap phasing * Add hiphase * add missing bcftools modules * Add samplesheet, extra_gcvf and extra_snfs validation * update hifiasm * completely remove PED and rely on samplesheet * fix methylation bug * update modkit, removes now unneccesary creation of haplotype bams * Formatting, remove unneccessary inputs * fix leftover flag in pileup * Add skip for phasing and remove more PED references * Simplify sniffles, and put back dipcall par * Update README.md * Add skip for QC * Update hiphase output files * Add hificnv to workflow * nf-download not working.. * add config * Add missing file column to snfs schema * Add hificnv to workflow * nf-download not working.. * add config * Update README.md Remove reference to ped-file * Update README.md * Update align.nf If using BAM-files as input for pbmm2, then don't output those. * Replaces pbmm2 with minimap2, using the nf-core modules * Fix typo * Add missing diff..linting fails because of the container URL, not sure how to fix? * linting working for all but samtools/faidx * Update README.md * Added DeepTrio support (incl. GPU for both DV and DT), trios extractedfrom PED-file * Update README.md * Small clean up. * Add deeptrio, GPU support and fastqc (should get better at keeping features separate) * fix minimap2 singularity version * Added dipcall * Add dipcall as process * Might have messed up git stash * Rewrite fix_trio process in Groovy, add hifiasm-trio and dipcall * Merge updated TEMPLATE * Update modules after TEMPLATE upgrade * More modules fixes to bring it closer to nf-core * Prettier * Replace fix_trio process for deeptrio input * remove nf-core images and add pipeline summary * Update README.md * fix color * Allow to skip either assembly or read_map calling * Update docs * Remove references to non-existing slack * Add tandem-regions and reference back to sniffles + skip snv-calling * reorganise publishdirs * move yak-versions into trio workflow * Fix non-trio hifiasm and add more rememberable skips * Fix dipcall module? * Update genome_assembly.nf * See if this way works * See if this way works-2 * See if this way works-3 * nf-core download would not pull docker image when the container is specified inside single quotes * Update dipcall to use PED-file in non-trio mode * Update base config to better represent needs * Change hifiasm to nf-core module, but make it output lowQ beds as well * add mosdepth * fix dipcall bug * Revert "fix dipcall bug" This reverts commit 36b9768. * Revert "Revert "fix dipcall bug"" - sorry git log This reverts commit 713272e. * Hope to have fixed all dipcall bugs - but need more testing * Change local GLNexus to nf-core module * Make tandem_repeats optional, since it might not be that great? * Update README.md * Add methylation calls to bedmethyl * Output whatshap stats, and add pipeline presets * Fix mosdepth not running for all samples * Fix methylation sample mix * fix dipcall not working * Add fastq and bam stats * fix dipcall not working * Rework modules and subworkflows to match new-found knowledge about single element channels * Added TRGT for pacbio-data * Fix repeat versions * Fix samtools index publishdirs * Add back --secondary=no to minimap2 align * Fix cramino phased and unphased * Fix dipcall sample name in vcf * Update README.md * Fix trgt container adress * try again to fix trgt container adress * remove TRVZ because it will create too many processes * completely remove TRVZ * update modules conf, missing output files, index bams and fix containers * Fix minimap2 index always using default params * minimap index needs to be built separate for dipcall as well * tweak process requirements * Improve whatshap phasing * Add hiphase * add missing bcftools modules * Add samplesheet, extra_gcvf and extra_snfs validation * update hifiasm * completely remove PED and rely on samplesheet * fix methylation bug * update modkit, removes now unneccesary creation of haplotype bams * Formatting, remove unneccessary inputs * fix leftover flag in pileup * Add skip for phasing and remove more PED references * Simplify sniffles, and put back dipcall par * Update README.md * Add skip for QC * Update hiphase output files * Add missing file column to snfs schema * Update README.md Remove reference to ped-file * Annotate variants with one database * Change to list of dbs * Fix anno overwriting input with output * Fix anno output file * Add VEP annotation * Update README and schema etc. * Add 'hack' to be able to run ONT-files in TRGT * Update README * Update README.md * Update README.md * Split alignment for faster processing * Call variants per regions in bed/fai * Extracting regions from extra gVCFs takes too long * Singularity image does not contain jemalloc * Grab correct one * glnexus will load full files into db even with bed * split DV input in 13 instead of n regions in BED * forgot wf * Clean up, remove PMD/DT as snv-callers, and ONT_R9 as preset * Remove index split alignments & update README * Update README * Update README.md * Update README.md * Add grouptuple size so downstream wf's don't have to wait for all samples to complete * pipeline would freeze depending on number of regions specified * better outputdirs for aligned reads * Update docs with pipeline parameters * Update README * Update README.md * Remove nf-core reference * Split module configs * Fix most process outdirs * minimap2 soft-clips supplementary reads by default * update hificnv config * Add expected CN-files (for XX/XY), MAF-vcf and option to use an exclude regions file. Also update HiFiCNV version to v.0.1.7 * Use BED file for mosdepth * Fix mosdepth running without BED * Update samtools_cat_sort_index.nf Fix args bug * Fix sniffles args bug * Update short_variant_calling.config Merged SNV-vcfs output files were misssing * Fix actually skipping CNV workflow is specifying so * Update qc_aligned_reads.nf Fix mosdepth bed input * Update qc_aligned_reads.nf * Update split_bed_chunks.py Sometimes, the BED-output was with decimals. Difference between system? * Update split_bed_chunks.py * Update split_bed_chunks.py Check that BED-file does not contain any spaces instead. * Update README.md * adding codeowners * Add test profile and data (#33) Add small test profile and data, hg38 asset files and code formatting. * Update pipeline to run with a small test dataset (#35) Reduce memory requirements, allow gzipped reference, single sample run and add BED file in modkit. * Template merge 2.13.1 (#38) Merge template version 2.13.1 * Fix bcftools merge (#43) Fix bcftools merge --------- Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> * Add Revio BAM test data and a multisample-BAM samplesheet (#50) Add BAM test data and a multisample-BAM samplesheet * Add support for uBAM and multisample test (#51) Add ubam support and multisample test * Update usage docs (#53) update usage docs --------- Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> * use biocontainer for glnexus * change to pacbio registry * run pre-commit * Update CHANGELOG * Fixed mosdepth input channel bug when bedfile is not provided * Update module configs (#65) Update config output directories and add minimal documentation * Fix checking whether input files exist (#67) * Add back files exist check, and fromSamplesheet * Add CNV calling workflow to test profile (#68) * Don't skip cnv calling workflow * Updated CHANGELOG.md * Add SNV annotation test data (#76) * Fix path in snp_dbs.csv (#77) * Refactor parameters validation (#69) * Refactor parateters validation --------- Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> * Add SNV annotation to test profile (#75) * fix version reporting (#84) * Run a single phasing software instead of three in parallel (#83) * Remove leftover print (#88) * Release prep v.0.1.0 (#89) * bump versions * clear changelog * Name change: Skierfe -> Nallo (#39) Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> * Change testdata location (#91) * move test data * add dummy samplesheet * Update sniffles module (#92) Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> * update deepvariant module (#93) * Add stubs (#94) * update download pipeline (#95) * Update README.md * Update README.md * Update docs/usage.md * Update docs/usage.md * Update docs/usage.md * Update docs/usage.md * Update docs/usage.md * Delete annotations directory (#97) * Delete assets/test_data directory (#99) * Update download_pipeline.yml (#96) * Update snv_annotation.config (#98) Full size test fails because only `BCFTOOLS_NORM_SINGLESAMPLE` and not `BCFTOOLS_NORM` was actually decomposing variants. * Update conf/modules/structural_variant_calling.config Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> * Apply suggestions from code review and full test issues (#107) * Add review suggestions + full test changes * Update CODEOWNERS (#112) * Update CODEOWNERS Change the code-owners to the GitHub team. This way we can more easily change the team and not having to update the CODEOWNERS * Fixed org * Update whatshap stats version to avoid ZeroDivisionError (#133) * Update whatshap stats version to avoid ZeroDivisionError * Update release date * Update bcftools merge (#134) * Bump date in changelog * Since sex is now numberic, update branching criteria * Was fixed before, but was overwritten --------- Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> Co-authored-by: Ram Nanduri <Ram.Nanduri@skane.se> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Anders Lind <64251477+pbiology@users.noreply.github.com>
genomic-medicine-sweden · May 8, 2024 · eda623d · eda623d
1 parent 1f87ebe
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,22 +2,15 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.

diff --git 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
@@ -18,7 +18,18 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-indent_size = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py,md}]
+indent_style = unset
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -0,0 +1,5 @@
+# These owners will be the default owners for everything in
+# the repo. Unless a later match takes precedence,
+# @global-owner1 and @global-owner2 will be requested for
+# review when someone opens a pull request.
+* @genomic-medicine-sweden/nallo-devs
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,20 +1,20 @@
-# fellen31/skierfe: Contributing Guidelines
+# genomic-medicine-sweden/nallo: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving fellen31/skierfe.
+Many thanks for taking an interest in improving genomic-medicine-sweden/nallo.
 
-We try to manage the required tasks for fellen31/skierfe using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for genomic-medicine-sweden/nallo using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for fellen31/skierfe, the standard workflow is as follows:
+If you'd like to write some code for genomic-medicine-sweden/nallo, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [fellen31/skierfe issues](https://github.com/fellen31/skierfe/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [fellen31/skierfe repository](https://github.com/fellen31/skierfe) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [genomic-medicine-sweden/nallo issues](https://github.com/genomic-medicine-sweden/nallo/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [genomic-medicine-sweden/nallo repository](https://github.com/genomic-medicine-sweden/nallo) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -23,21 +23,27 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
+
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
 There are typically two types of tests that run:
 
 ### Lint tests
 
-`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+Altough this is not a `nf-core` pipeline, `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all their pipelines must adhere to.
+To enforce these and ensure that all pipelines stay in sync, they have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
 ### Pipeline tests
 
-Each `nf-core` pipeline should be set up with a minimal set of test-data.
+This pipeline should be set up with a minimal set of test-data.
 `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
 If there are any failures then the automated tests fail.
 These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
@@ -52,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the fellen31/skierfe code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the genomic-medicine-sweden/nallo code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
@@ -79,7 +85,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 
@@ -102,12 +108,11 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/fellen31/skierfe/codespaces)
+- Open the repo in [Codespaces](https://github.com/genomic-medicine-sweden/nallo/codespaces)
 - Tools installed
   - nf-core
   - Nextflow
 
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,52 +2,53 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-- type: textarea
-  id: description
-  attributes:
-    label: Description of the bug
-    description: A clear and concise description of what the bug is.
-  validations:
-    required: true
-- type: textarea
-  id: command_used
-  attributes:
-    label: Command used and terminal output
-    description: Steps to reproduce the behaviour. Please paste the command you used
-      to launch the pipeline and the output from your terminal.
-    render: console
-    placeholder: '$ nextflow run ...
-
-
-      Some output where something broke
-
-      '
-- type: textarea
-  id: files
-  attributes:
-    label: Relevant files
-    description: 'Please drag and drop the relevant files here. Create a `.zip` archive
-      if the extension is not allowed.
-
-      Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
-      in the directory where you launched the pipeline)_ as well as custom Nextflow
-      configuration files.
-
-      '
-- type: textarea
-  id: system
-  attributes:
-    label: System information
-    description: '* 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)_
-
-      * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
-      * Version of fellen31/skierfe _(eg. 1.1, 1.5, 1.8.2)_
-
-      '
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used
+        to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: "$ nextflow run ...
+
+
+        Some output where something broke
+
+        "
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
+
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
+
+        "
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: "* Nextflow version _(eg. 23.04.0)_
+
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+
+        * Executor _(eg. slurm, local, awsbatch)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
+
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+
+        * Version of genomic-medicine-sweden/nallo _(eg. 1.1, 1.5, 1.8.2)_
+
+        "
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,7 @@
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: ""
+    url: https://google.com
+    about: Discussion about the nf-core/nallo pipeline
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the fellen31/skierfe pipeline
+description: Suggest an idea for the genomic-medicine-sweden/nallo pipeline
 labels: enhancement
 body:
   - type: textarea

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,23 +1,24 @@
 <!--
-# fellen31/skierfe pull request
+# genomic-medicine-sweden/nallo pull request
 
-Many thanks for contributing to fellen31/skierfe!
+Many thanks for contributing to genomic-medicine-sweden/nallo!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/fellen31/skierfe/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/genomic-medicine-sweden/nallo/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] 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/fellen31/skierfe/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/genomic-medicine-sweden/nallo/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -0,0 +1,29 @@
+name: nf-core AWS test
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
+
+on:
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run AWS tests
+    if: github.repository == 'fellen31/nallo'
+    runs-on: ubuntu-latest
+    steps:
+      # Launch workflow using Tower CLI tool action
+      - name: Launch workflow via tower
+        uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nallo/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nallo/results-test-${{ github.sha }}"
+            }
+          profiles: test,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -11,15 +11,15 @@ jobs:
     steps:
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'fellen31/skierfe'
+        if: github.repository == 'genomic-medicine-sweden/nallo'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == fellen31/skierfe ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == genomic-medicine-sweden/nallo ]] && [[ $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
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v1
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -19,25 +19,31 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'fellen31/skierfe') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/nallo') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
+        parameters:
+          - ""
+          - "--input https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/testdata/samplesheet_multisample_bam.csv --split_fastq 250 --parallel_snv 1 --phaser hiphase_sv"
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Run pipeline with test data
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}