Add hidden and missed files

.github/CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# genomic-medicine-sweden/skierfe: Contributing Guidelines
+# genomic-medicine-sweden/nallo: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving genomic-medicine-sweden/skierfe.
+Many thanks for taking an interest in improving genomic-medicine-sweden/nallo.
 
-We try to manage the required tasks for genomic-medicine-sweden/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 genomic-medicine-sweden/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 [genomic-medicine-sweden/skierfe issues](https://github.com/genomic-medicine-sweden/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 [genomic-medicine-sweden/skierfe repository](https://github.com/genomic-medicine-sweden/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
@@ -58,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the genomic-medicine-sweden/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
 
@@ -108,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/genomic-medicine-sweden/skierfe/codespaces)
+- Open the repo in [Codespaces](https://github.com/genomic-medicine-sweden/nallo/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -49,6 +49,6 @@ body:
 
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
 
-        * Version of genomic-medicine-sweden/skierfe _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of genomic-medicine-sweden/nallo _(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: ""
     url: https://google.com
-    about: Discussion about the nf-core/skierfe pipeline
+    about: Discussion about the nf-core/nallo pipeline

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the genomic-medicine-sweden/skierfe pipeline
+description: Suggest an idea for the genomic-medicine-sweden/nallo pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,21 @@
 <!--
-# genomic-medicine-sweden/skierfe pull request
+# genomic-medicine-sweden/nallo pull request
 
-Many thanks for contributing to genomic-medicine-sweden/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/genomic-medicine-sweden/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/genomic-medicine-sweden/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 (`nf-test test main.nf.test -profile test,docker`).
 - [ ] 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-tower:
     name: Run AWS full tests
-    if: github.repository == 'fellen31/skierfe'
+    if: github.repository == 'fellen31/nallo'
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
@@ -22,10 +22,10 @@ jobs:
           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/skierfe/work-${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nallo/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/skierfe/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nallo/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
       - uses: actions/upload-artifact@v3

.github/workflows/awstest.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   run-tower:
     name: Run AWS tests
-    if: github.repository == 'fellen31/skierfe'
+    if: github.repository == 'fellen31/nallo'
     runs-on: ubuntu-latest
     steps:
       # Launch workflow using Tower CLI tool action
@@ -17,10 +17,10 @@ jobs:
           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/skierfe/work-${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nallo/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/skierfe/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nallo/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
       - uses: actions/upload-artifact@v3

.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 == 'genomic-medicine-sweden/skierfe'
+        if: github.repository == 'genomic-medicine-sweden/nallo'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == genomic-medicine-sweden/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

.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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/skierfe') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/nallo') }}"
     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 == 'genomic-medicine-sweden/skierfe'
+      github.repository == 'genomic-medicine-sweden/nallo'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
@@ -85,4 +85,4 @@ 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/genomic-medicine-sweden/skierfe/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/genomic-medicine-sweden/nallo/actions/runs/${{ github.run_id }}) for more details.

.nf-core.yml

@@ -1,18 +1,18 @@
 lint:
   files_exist:
     - CODE_OF_CONDUCT.md
-    - assets/nf-core-skierfe_logo_light.png
-    - docs/images/nf-core-skierfe_logo_light.png
-    - docs/images/nf-core-skierfe_logo_dark.png
+    - assets/nf-core-nallo_logo_light.png
+    - docs/images/nf-core-nallo_logo_light.png
+    - docs/images/nf-core-nallo_logo_dark.png
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
     - conf/modules.config
   files_unchanged:
     - CODE_OF_CONDUCT.md
-    - assets/nf-core-skierfe_logo_light.png
-    - docs/images/nf-core-skierfe_logo_light.png
-    - docs/images/nf-core-skierfe_logo_dark.png
+    - assets/nf-core-nallo_logo_light.png
+    - docs/images/nf-core-nallo_logo_light.png
+    - docs/images/nf-core-nallo_logo_dark.png
     - .github/ISSUE_TEMPLATE/bug_report.yml
     - .github/CONTRIBUTING.md
   multiqc_config:

subworkflows/local/utils_nfcore_nallo_pipeline/main.nf

@@ -1,5 +1,5 @@
 //
-// Subworkflow with functionality specific to the genomic-medicine-sweden/skierfe pipeline
+// Subworkflow with functionality specific to the genomic-medicine-sweden/nallo pipeline
 //
 
 /*