Extract reads for viral taxids

.github/CODEOWNERS

@@ -0,0 +1,8 @@
+##############################################################
+#
+# List of approvers/reviewers for meta-val
+#
+##############################################################
+
+# These owners will be the default owners for everything in the repo.
+* @genomic-medicine-sweden/taxprofiler-devs

.github/CONTRIBUTING.md

@@ -1,23 +1,23 @@
-# nf-core/metaval: Contributing Guidelines
+# genomic-medicine-sweden/meta-val: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-core/metaval.
+Many thanks for taking an interest in improving genomic-medicine-sweden/meta-val.
 
-We try to manage the required tasks for nf-core/metaval using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for genomic-medicine-sweden/meta-val 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 ;)
 
 > [!NOTE]
-> If you need help using or modifying nf-core/metaval then the best place to ask is on the nf-core Slack [#metaval](https://nfcore.slack.com/channels/metaval) channel ([join our Slack here](https://nf-co.re/join/slack)).
+> If you need help using or modifying genomic-medicine-sweden/meta-val then the best place to ask is by creating an [issue](https://github.com/genomic-medicine-sweden/meta-val/issues).
 
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/metaval, the standard workflow is as follows:
+If you'd like to write some code for genomic-medicine-sweden/meta-val, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/metaval issues](https://github.com/nf-core/metaval/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 [nf-core/metaval repository](https://github.com/nf-core/metaval) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [genomic-medicine-sweden/meta-val issues](https://github.com/genomic-medicine-sweden/meta-val/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/meta-val repository](https://github.com/genomic-medicine-sweden/meta-val) 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
@@ -61,11 +61,11 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/metaval documentation](https://nf-co.re/metaval/usage) and don't hesitate to get in touch on the nf-core Slack [#metaval](https://nfcore.slack.com/channels/metaval) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [metaval documentation](https://github.com/genomic-medicine-sweden/meta-val) and don't hesitate to get in touch on by creating an [issue](https://github.com/genomic-medicine-sweden/meta-val/issues).
 
 ## Pipeline contribution conventions
 
-To make the nf-core/metaval 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/meta-val 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
 
@@ -115,7 +115,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/nf-core/metaval/codespaces)
+- Open the repo in [Codespaces](https://github.com/genomic-medicine-sweden/meta-val/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -8,7 +8,7 @@ body:
         Before you post this issue, please check the documentation:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/metaval pipeline documentation](https://nf-co.re/metaval/usage)
+        - [genomic-medicine-sweden/meta-val pipeline documentation](https://nf-co.re/metaval/usage)
 
   - type: textarea
     id: description
@@ -47,4 +47,4 @@ body:
         * 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 nf-core/metaval _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of genomic-medicine-sweden/meta-val _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -4,4 +4,4 @@ contact_links:
     about: Please join the nf-core community here
   - name: "Slack #metaval channel"
     url: https://nfcore.slack.com/channels/metaval
-    about: Discussion about the nf-core/metaval pipeline
+    about: Discussion about the genomic-medicine-sweden/meta-val pipeline

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/metaval pipeline
+description: Suggest an idea for the genomic-medicine-sweden/meta-val pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,22 +1,22 @@
 <!--
-# nf-core/metaval pull request
+# genomic-medicine-sweden/meta-val pull request
 
-Many thanks for contributing to nf-core/metaval!
+Many thanks for contributing to genomic-medicine-sweden/meta-val!
 
 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/nf-core/metaval/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/genomic-medicine-sweden/meta-val/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/nf-core/metaval/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/metaval _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/genomic-medicine-sweden/meta-val/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the genomic-medicine-sweden/meta-val _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 <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.github/workflows/awsfulltest.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/metaval'
+    if: github.repository == 'genomic-medicine-sweden/meta-val'
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via Seqera Platform

.github/workflows/awstest.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   run-platform:
     name: Run AWS tests
-    if: github.repository == 'nf-core/metaval'
+    if: github.repository == 'genomic-medicine-sweden/meta-val'
     runs-on: ubuntu-latest
     steps:
       # Launch workflow using Seqera Platform CLI tool action

.github/workflows/branch.yml

@@ -11,9 +11,9 @@ 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 == 'nf-core/metaval'
+        if: github.repository == 'genomic-medicine-sweden/meta-val'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/metaval ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == genomic-medicine-sweden/meta-val ]] && [[ $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

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/metaval') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/meta-val') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

.github/workflows/fix-linting.yml

@@ -9,7 +9,7 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'nf-core/metaval'
+      github.repository == 'genomic-medicine-sweden/meta-val'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
@@ -86,4 +86,4 @@ jobs:
           issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/nf-core/metaval/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/genomic-medicine-sweden/meta-val/actions/runs/${{ github.run_id }}) for more details.

.nf-core.yml

@@ -1,8 +1,8 @@
 lint:
   files_exist: false
-    - assets/nf-core-metaval_logo_light.png
-    - docs/images/nf-core-metaval_logo_light.png
-    - docs/images/nf-core-metaval_logo_dark.png
+    - assets/nf-core-meta-val_logo_light.png
+    - docs/images/nf-core-meta-val_logo_light.png
+    - docs/images/nf-core-meta-val_logo_dark.png
     - assets/samplesheet.csv
   files_unchanged: false
     - assets/sendmail_template.txt
@@ -15,6 +15,18 @@ lint:
     - assets/email_template.html
     - assets/email_template.txt
     - docs/README.md
-    - pyproject.toml
+
+  multiqc_config:
+    - report_comment
+
+  nextflow_config:
+    - manifest.name
+    - manifest.homePage
+
 repository_type: pipeline
+template:
+  author: LilyAnderssonLee
+  description: nf-core/taxprofiler post processing
+  name: metaval
+  prefix: genomic-medicine-sweden
 nf_core_version: "2.14.1"

CHANGELOG.md

@@ -1,14 +1,17 @@
-# nf-core/metaval: Changelog
+# genomic-medicine-sweden/meta-val: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## v1.0dev - [date]
 
-Initial release of nf-core/metaval, created with the [nf-core](https://nf-co.re/) template.
-
 ### `Added`
 
+Extract taxIDs of viruses
+Extract Kraken2 reads with KrakenTools
+Extract Centrifuge reads
+Extract DIAMOND reads
+
 ### `Fixed`
 
 ### `Dependencies`

CITATIONS.md

@@ -1,4 +1,4 @@
-# nf-core/metaval: Citations
+# genomic-medicine-sweden/meta-val: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 
@@ -18,6 +18,9 @@
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [KrakenTools](https://www.nature.com/articles/s41596-022-00738-y)
+  > Lu J, Rincon N, Wood DE, et al. Metagenome analysis using the Kraken software suite. Nat Protoc. 2022;17(12). doi:10.1038/s41596-022-00738-y
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)