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Merge pull request #447 from nf-core/dev
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Release 3.0.0
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@rannick
rannick authored Nov 27, 2023
2 parents c3b0f9f + 4ae96ff commit f5ecf8d
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Showing 177 changed files with 5,018 additions and 2,742 deletions.
1 change: 1 addition & 0 deletions .devcontainer/devcontainer.json
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Expand Up @@ -2,6 +2,7 @@
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
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4 changes: 3 additions & 1 deletion .github/CONTRIBUTING.md
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Expand Up @@ -9,7 +9,9 @@ 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 ;)

> If you need help using or modifying nf-core/rnafusion then the best place to ask is on the nf-core Slack [#rnafusion](https://nfcore.slack.com/channels/rnafusion) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::info
If you need help using or modifying nf-core/rnafusion then the best place to ask is on the nf-core Slack [#rnafusion](https://nfcore.slack.com/channels/rnafusion) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::

## Contribution workflow

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225 changes: 4 additions & 221 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
if: github.repository == 'nf-core/rnafusion'
runs-on: ubuntu-latest
steps:
- name: Launch build arriba workflow via tower
- name: Launch build references workflow via tower
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
Expand All @@ -28,7 +28,7 @@ jobs:
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"arriba": true,
"all": true,
"build_references": true
}
profiles: test_full,aws_tower
Expand All @@ -39,7 +39,7 @@ jobs:
tower_action_*.log
tower_action_*.json
- name: Launch arriba workflow via tower
- name: Launch run workflow via tower
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
Expand All @@ -52,223 +52,6 @@ jobs:
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"arriba": true,
"all": true,
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
- name: Launch build squid workflow via tower
uses: seqeralabs/action-tower-launch@v2
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/rnafusion/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"squid": true,
"build_references": true
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
- name: Launch squid workflow via tower
uses: seqeralabs/action-tower-launch@v2
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/rnafusion/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"squid": true,
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
- name: Launch build starfusion workflow via tower
uses: seqeralabs/action-tower-launch@v2
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/rnafusion/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"starfusion": true,
"build_references": true
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
- name: Launch starfusion workflow via tower
uses: seqeralabs/action-tower-launch@v2
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/rnafusion/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"starfusion": true,
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
- name: Launch build fusioncatcher workflow via tower
uses: seqeralabs/action-tower-launch@v2
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/rnafusion/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"fusioncatcher": true,
"build_references": true
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
- name: Launch fusioncatcher workflow via tower
uses: seqeralabs/action-tower-launch@v2
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/rnafusion/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"fusioncatcher": true,
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
- name: Launch build pizzly workflow via tower
uses: seqeralabs/action-tower-launch@v2
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/rnafusion/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"pizzly": true,
"build_references": true
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
- name: Launch pizzly workflow via tower
uses: seqeralabs/action-tower-launch@v2
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/rnafusion/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"pizzly": true,
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
- name: Launch stringtie workflow via tower
uses: seqeralabs/action-tower-launch@v2
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/rnafusion/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}",
"genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references",
"cosmic_username": "${{ secrets.cosmic_username }}",
"cosmic_passwd": "${{ secrets.cosmic_passwd }}",
"stringtie": true,
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
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