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Release 2.5.0 #284

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merged 147 commits into from
Oct 10, 2023
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6151b2c
Template update for nf-core/tools version 2.8
nf-core-bot Apr 28, 2023
e7695cb
Resolve conflicts
jonasscheid May 15, 2023
e586c40
resolve more conflicts
jonasscheid May 15, 2023
d7a1ccb
fix linting
jonasscheid May 15, 2023
9c1244f
Merge pull request #264 from nf-core/nf-core-template-merge-2.8
jonasscheid May 15, 2023
c78ad22
update openms version, rename parser
jonasscheid May 19, 2023
e558b0e
add skip_quantification to small test datase
jonasscheid May 26, 2023
4889f37
adjust changelog
jonasscheid May 26, 2023
60fc60a
Merge pull request #266 from jonasscheid/dev
jonasscheid May 28, 2023
60b5456
Add bruker converter tdf2mzml
jonasscheid May 30, 2023
aa687e2
fix linting
jonasscheid May 30, 2023
5bc762c
Merge pull request #267 from jonasscheid/dev
jonasscheid May 31, 2023
69d5875
fix rawfileparser output bug
jonasscheid Jun 2, 2023
58847d2
Merge pull request #268 from jonasscheid/dev
jonasscheid Jun 5, 2023
97dd090
Added DeepLC script
Jun 20, 2023
ea476f4
Call deeplc after comet
Jun 20, 2023
b3e1d96
Changed input variable of DeepLC
Jun 20, 2023
55a0f06
Added shebang to deeplc script
Jun 20, 2023
0598e6b
Adjusted paramter names for deeplc script
Jun 20, 2023
d69ff73
Fixed parameter name in deeplc script
Jun 20, 2023
8e6ae4b
Fix input/output parameter names
Jun 20, 2023
1bbecd9
Added default error calculation
Jun 21, 2023
f3fcdf7
Added deeplc features to percolator
Jun 21, 2023
c03395c
Fixed deeplc output
Jun 21, 2023
32df09f
Updated schema with DeepLC parameters
Jun 22, 2023
296f96e
Updated changelog
Jun 22, 2023
0a242fe
Linting
Jun 22, 2023
ad407a5
Fixed linting changes
Jun 22, 2023
a1b0105
Added newline at EOF
Jun 22, 2023
a7998db
Fixed mail template
Jun 22, 2023
5537a84
Python black
Jun 22, 2023
42ce78b
Renamed channel comet out
Jun 22, 2023
16e8cd8
Fixed input channel for comet
Jun 22, 2023
89d3796
Added handling of non canonical amino acids for DeepLC module
Jun 22, 2023
572ab70
Added support for noncanonical peptides
Jun 23, 2023
289e487
Merge pull request #269 from steffenlem/deeplc
jonasscheid Jun 23, 2023
6ce2d4f
Added MS2pip
Jun 23, 2023
47eb403
lint
Jun 23, 2023
e643d0f
Ran Prettier
Jun 24, 2023
dbcfea5
Merge pull request #270 from steffenlem/ms2pip
jonasscheid Jun 24, 2023
4fde366
Add filefilter to clean mzml before search
jonasscheid Jun 27, 2023
34b989a
add changes to changelog
jonasscheid Jun 27, 2023
185a63b
update version
jonasscheid Jun 27, 2023
236ffa6
Merge pull request #271 from jonasscheid/filefilter
steffenlem Jun 27, 2023
375b192
Added case insensitive check for file extension
Jun 29, 2023
69d3f7b
Added option for default comet parameters file
Jun 29, 2023
4dafa29
Update changelog
Jun 29, 2023
0401fb4
Merge pull request #272 from steffenlem/dev
steffenlem Jun 29, 2023
6879ff0
Optimize resource allocations
jonasscheid Jun 29, 2023
ec7e9b3
add changelog
jonasscheid Jun 29, 2023
df64ea5
typo
jonasscheid Jun 29, 2023
49e8c37
Merge branch 'dev' into dev
jonasscheid Jun 29, 2023
42d61d1
Merge pull request #273 from jonasscheid/dev
steffenlem Jun 29, 2023
42927e0
Template update for nf-core/tools version 2.9
nf-core-bot Jun 30, 2023
8f3e242
Fixed extra flag for ms2pip
Jul 11, 2023
801355f
debug template update
Jul 12, 2023
14b71c2
add loading modules.conf again
Jul 19, 2023
c7bc5bd
changelog
jonasscheid Jul 19, 2023
e147260
fix nextflow version for fulltest
jonasscheid Jul 19, 2023
15f94ef
fix gh ci for fulltest
jonasscheid Jul 19, 2023
621fdeb
add novel params to fulltest
jonasscheid Jul 19, 2023
b1a7fb4
fix old conda implementation in modules
jonasscheid Jul 19, 2023
7b88d9c
adjust authors
jonasscheid Jul 19, 2023
706538d
remove fastqc from citations
jonasscheid Jul 19, 2023
9ac8f45
prettier
jonasscheid Jul 19, 2023
516f054
adjust license
jonasscheid Jul 19, 2023
795ec22
Update nextflow.config
jonasscheid Jul 20, 2023
5ac3e94
Merge pull request #274 from nf-core/nf-core-template-merge-2.9
jonasscheid Jul 20, 2023
7a0ec5b
Merge remote-tracking branch 'upstream/dev' into dev
Jul 27, 2023
047c8d8
Fixed parameter calling in psmfeatureextractor
steffenlem Aug 18, 2023
013dc25
Merge pull request #275 from steffenlem/dev
jonasscheid Aug 18, 2023
a58c7ed
refactor naming
jonasscheid Aug 18, 2023
da5ab1f
more naming changes
jonasscheid Aug 18, 2023
5f13484
more namings
jonasscheid Aug 18, 2023
5784677
Restructure quant part 1
jonasscheid Aug 18, 2023
71cf0f9
Add post-alignment merger for featurefinder
jonasscheid Aug 18, 2023
1956dcf
ensure percolator tdc
jonasscheid Aug 28, 2023
b79c8a7
Merge branch 'dev' of https://github.com/jonasscheid/mhcquant into dev
jonasscheid Aug 28, 2023
bc326d4
Merge pull request #279 from jonasscheid/dev
jonasscheid Aug 30, 2023
ce8b6b7
adjust such that quant_fdr can be used
jonasscheid Sep 4, 2023
cb0dca8
restructure quant such that map alignment comes after percolator
jonasscheid Sep 17, 2023
a9cfc37
Update to openms 3.0.0
jonasscheid Sep 18, 2023
4021716
replace dev container with mulled container on quay
jonasscheid Sep 18, 2023
c26ddf4
Depricate old rt prediction
jonasscheid Sep 18, 2023
9488a4b
depricate openms rt prediction
jonasscheid Sep 18, 2023
d43c040
depricate openms rt prediction
jonasscheid Sep 18, 2023
b0ff42b
remove fastq image in docs
jonasscheid Sep 18, 2023
791258d
adjust ffid settings
jonasscheid Sep 19, 2023
ab0e4fd
Update publishing files
jonasscheid Sep 20, 2023
8e5ae21
Add scoreswitcher for quant and optional filefilter
jonasscheid Sep 20, 2023
35c1919
cosmetics
jonasscheid Sep 20, 2023
2967a5b
Adjust publihsed files
jonasscheid Sep 20, 2023
8c9c92d
filefilter optional in schema
jonasscheid Sep 20, 2023
c3e01cb
updated docs
jonasscheid Sep 20, 2023
c600bf4
bump version
jonasscheid Sep 20, 2023
386788b
bump openms conda version
jonasscheid Sep 20, 2023
c0d83a6
linting
jonasscheid Sep 20, 2023
46835a9
merge dev into feature branch, fix conflict
jonasscheid Sep 20, 2023
4ceb045
update changelog
jonasscheid Sep 20, 2023
e48f525
remove fastqc
jonasscheid Sep 20, 2023
0b43c85
fix typo
jonasscheid Sep 20, 2023
2e81e78
update citations
jonasscheid Sep 20, 2023
565d0fd
fix lint
jonasscheid Sep 20, 2023
61b58e8
fix typo
jonasscheid Sep 20, 2023
72ca114
fix citation
jonasscheid Sep 20, 2023
3eecfbf
fix wrong channel elements in ionannotator and cleanup
jonasscheid Sep 21, 2023
7bcd973
fix ionannotator input for mzml files
jonasscheid Sep 21, 2023
195694d
Template update for nf-core/tools version 2.10
nf-core-bot Sep 25, 2023
5940636
harmonize exporter modules between id and quant
jonasscheid Sep 27, 2023
12b2e1a
add requested comment
jonasscheid Sep 27, 2023
fad924e
cosmetics
jonasscheid Sep 27, 2023
bf62f77
adjust filenaming in maptransformer
jonasscheid Sep 27, 2023
75d9eed
Refactor grouping
jonasscheid Sep 28, 2023
d2ce44e
Encapsulate quant in subworkflow
jonasscheid Sep 28, 2023
83d6063
Add test profi
jonasscheid Sep 28, 2023
d55446a
prettier
jonasscheid Sep 28, 2023
370e957
adjust ci
jonasscheid Sep 28, 2023
24d7597
add test profiles to nextflow.config
jonasscheid Sep 28, 2023
33425a8
styling
jonasscheid Sep 28, 2023
1c5bf30
add ionannotator test
jonasscheid Sep 28, 2023
04bc8f3
merge template updaet
jonasscheid Oct 2, 2023
4137f91
addd subwayplot
jonasscheid Oct 2, 2023
fa5ec53
update changelog
jonasscheid Oct 2, 2023
f30e857
fix nfcore linting
jonasscheid Oct 2, 2023
91dff6b
set white background of subway plot
jonasscheid Oct 2, 2023
ad742b9
limit mem for ci
jonasscheid Oct 2, 2023
6baac65
limit cpus for ci
jonasscheid Oct 2, 2023
dd66c39
spectrum batch size limit on ci tests to prevent crashing workflows
jonasscheid Oct 3, 2023
d59e1f4
Update pyopenms to latest version in ionannotator
jonasscheid Oct 3, 2023
07b9713
increase speed of ci test
jonasscheid Oct 3, 2023
86c740c
typo
jonasscheid Oct 3, 2023
3b0d487
remove unused dependency
jonasscheid Oct 3, 2023
758e8f2
speed up ci quant and fulltest
jonasscheid Oct 3, 2023
cff9bc9
Add comments to subworkflows
jonasscheid Oct 3, 2023
d59d2e5
update changelog
jonasscheid Oct 3, 2023
87141eb
Merge pull request #280 from jonasscheid/rearrange_quant
jonasscheid Oct 3, 2023
f76dd19
incorporate feedback
jonasscheid Oct 7, 2023
6877012
Movve quant test to test full bc of github limitations
jonasscheid Oct 8, 2023
f76fb7f
move quant test solely to test_full
jonasscheid Oct 8, 2023
2bf573d
update warning for refine fdr
jonasscheid Oct 8, 2023
090aaa3
prettier
jonasscheid Oct 8, 2023
0d0f46b
remove deeplc and ms2pip from test_full since test stops bc of runtime
jonasscheid Oct 8, 2023
6d11bcc
reduce test_full bc no more storage of device (github)
jonasscheid Oct 8, 2023
db8ad1d
remove class1 and class2 from test_full
jonasscheid Oct 8, 2023
9f10857
only use quant in test_full due to space issue on gh
jonasscheid Oct 8, 2023
eb6d692
feedback
jonasscheid Oct 9, 2023
1990be7
Merge pull request #285 from jonasscheid/rearrange_quant
jonasscheid Oct 9, 2023
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1 change: 1 addition & 0 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
Expand Down
2 changes: 1 addition & 1 deletion .editorconfig
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
5 changes: 3 additions & 2 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
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/mhcquant then the best place to ask is on the nf-core Slack [#mhcquant](https://nfcore.slack.com/channels/mhcquant) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::info
If you need help using or modifying nf-core/mhcquant then the best place to ask is on the nf-core Slack [#mhcquant](https://nfcore.slack.com/channels/mhcquant) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::

## Contribution workflow

Expand Down Expand Up @@ -116,4 +118,3 @@ To get started:
Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
- [Dockerfile](.devcontainer/Dockerfile)
4 changes: 2 additions & 2 deletions .github/ISSUE_TEMPLATE/bug_report.yml
Original file line number Diff line number Diff line change
Expand Up @@ -42,9 +42,9 @@ body:
attributes:
label: System information
description: |
* Nextflow version _(eg. 22.10.1)_
* 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 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/mhcquant _(eg. 1.1, 1.5, 1.8.2)_
3 changes: 2 additions & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mhcq

- [ ] 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/mhcquant/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/mhcquant _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/mhcquant/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/mhcquant _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>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
Expand Down
14 changes: 11 additions & 3 deletions .github/workflows/awsfulltest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,18 +14,26 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: nf-core/tower-action@v3
uses: seqeralabs/action-tower-launch@v2
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mhcquant/work-${{ github.sha }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-${{ github.sha }}"
}
profiles: test_full,aws_tower
profiles: test_full

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json
10 changes: 7 additions & 3 deletions .github/workflows/awstest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -12,18 +12,22 @@ 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@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mhcquant/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-test-${{ github.sha }}"
}
profiles: test,aws_tower
profiles: test

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json
2 changes: 1 addition & 1 deletion .github/workflows/branch.yml
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ jobs:
- name: Check PRs
if: github.repository == 'nf-core/mhcquant'
run: |
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mhcquant ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mhcquant ]] && [[ $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
Expand Down
24 changes: 12 additions & 12 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ jobs:
strategy:
matrix:
NXF_VER:
- "22.10.1"
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
Expand All @@ -37,27 +37,28 @@ jobs:

- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --spectrum_batch_size 5000 --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

test_additional_params:
name: Run pipeline with additional params
# 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/mhcquant') }}"
profile:
name: Run profile tests
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
strategy:
matrix:
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- NXF_VER: "22.10.1"
- NXF_VER: "23.04.0"
NXF_EDGE: ""
# Test latest edge release of Nextflow
- NXF_VER: ""
NXF_EDGE: "1"
tests: ["test_deeplc", "test_ms2pip", "test_ionannotator", "test_quant", "test_full"]
steps:
- name: Check out pipeline code
uses: actions/checkout@v2

- name: Install Nextflow
env:
NXF_VER: ${{ matrix.NXF_VER }}
Expand All @@ -67,7 +68,6 @@ jobs:
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Run pipeline with additional params
- name: Run pipeline with profile ${{ matrix.tests }}
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT --spectrum_batch_size 2000 --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --max_memory '6.GB' --max_cpus 2 --spectrum_batch_size 5000 --outdir ./results
24 changes: 24 additions & 0 deletions .github/workflows/clean-up.yml
Original file line number Diff line number Diff line change
@@ -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 }}"
2 changes: 1 addition & 1 deletion .github/workflows/linting.yml
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ jobs:

- uses: actions/setup-python@v4
with:
python-version: "3.7"
python-version: "3.11"
architecture: "x64"

- name: Install dependencies
Expand Down
68 changes: 68 additions & 0 deletions .github/workflows/release-announcments.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,68 @@
name: release-announcements
# Automatic release toot and tweet anouncements
on:
release:
types: [published]
workflow_dispatch:

jobs:
toot:
runs-on: ubuntu-latest
steps:
- uses: rzr/fediverse-action@master
with:
access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
host: "mstdn.science" # custom host if not "mastodon.social" (default)
# GitHub event payload
# https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
message: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

Please see the changelog: ${{ github.event.release.html_url }}

send-tweet:
runs-on: ubuntu-latest

steps:
- uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install dependencies
run: pip install tweepy==4.14.0
- name: Send tweet
shell: python
run: |
import os
import tweepy

client = tweepy.Client(
access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
)
tweet = os.getenv("TWEET")
client.create_tweet(text=tweet)
env:
TWEET: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

Please see the changelog: ${{ github.event.release.html_url }}
TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}

bsky-post:
runs-on: ubuntu-latest
steps:
- uses: zentered/[email protected]
with:
post: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

Please see the changelog: ${{ github.event.release.html_url }}
env:
BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
#
5 changes: 5 additions & 0 deletions .gitpod.yml
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image: nfcore/gitpod:latest
tasks:
- name: Update Nextflow and setup pre-commit
command: |
pre-commit install --install-hooks
nextflow self-update

vscode:
extensions: # based on nf-core.nf-core-extensionpack
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5 changes: 5 additions & 0 deletions .pre-commit-config.yaml
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repos:
- repo: https://github.com/pre-commit/mirrors-prettier
rev: "v2.7.1"
hooks:
- id: prettier
30 changes: 29 additions & 1 deletion CHANGELOG.md
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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).

## v2.4.1 nfcore/mhcquant "Maroon Gold Boxer" (patch) - 2023/04/04
## v2.5.0 - nfcore/mhcquant "Angry Bird" - 2023/10/04

### `Added`

- Support for brukers tdf format by adding tdf2mzml converter [#263](https://github.com/nf-core/mhcquant/issues/263)
- DeepLC retention time prediction
- MS2PIP peak intensity prediction
- Added OpenMS FileFilter to clean mzml after parsing to remove artifacts like empty spectra or precursors with charge 0 (optional)
- Made file extension check case insensitive
- Added option to provide a default comet parameters file
- Optimize resource allocations
- Template update 2.9 [#274](https://github.com/nf-core/mhcquant/pull/274)
- Improved quantification such that merged FDR-filtered runs can be quantified properly
- Template update 2.10 [#282](https://github.com/nf-core/mhcquant/pull/282)

### `Fixed`

- [#266](https://github.com/nf-core/mhcquant/pull/266) New OpenMS version 3.0.0 fixes duplicated ID bug [#250](https://github.com/nf-core/mhcquant/issues/250)

### `Dependencies`

- [#266](https://github.com/nf-core/mhcquant/pull/266) Switched from OpenMS version 2.8.0 to newest version 3.0.0 [#265](https://github.com/nf-core/mhcquant/issues/265)
- [#266](https://github.com/nf-core/mhcquant/pull/266) Bumped ThermoRawFileParser version from 1.4.0 to 1.4.2

### `Deprecated`

- OpenMS RT prediction

## v2.4.1 nfcore/mhcquant "Young Shark" (patch) - 2023/04/04

### `Added`

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6 changes: 4 additions & 2 deletions CITATIONS.md
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> Röst H, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walze M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13 741–748 (2016). doi: 10.1038/nmeth.3959. PubMed PMID: 27575624

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> 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.

## Software packaging/containerisation tools
Expand All @@ -47,5 +46,8 @@

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

> Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
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