Skip to content
Draft
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
170 commits
Select commit Hold shift + click to select a range
6611217
Add proteoform to pipeline output
JuliaGraf May 26, 2025
3cfc6f0
Update changelog
JuliaGraf May 26, 2025
f1a4385
Lint Changelog
JuliaGraf May 27, 2025
d332972
Merge pull request #376 from JuliaGraf/proteoform
jonasscheid May 27, 2025
18a2222
Template update for nf-core/tools version 3.3.1
nf-core-bot Jun 3, 2025
aae99a1
initial commit
janaHoffmann1 Jun 3, 2025
110bcef
merge template
jonasscheid Jun 4, 2025
9c4bf03
add default snap
jonasscheid Jun 4, 2025
ebfce73
fix ro-crate-metadata
jonasscheid Jun 5, 2025
5dd26cf
fix maintainers
jonasscheid Jun 5, 2025
7b9212c
fix some nf-core linting warnings and bump mqc version
jonasscheid Jun 5, 2025
c2447d4
fix default nf-test
jonasscheid Jun 5, 2025
2ce1816
fix trailing whitespace
jonasscheid Jun 5, 2025
e2702e7
nf-test.yml aktualisieren
jonasscheid Jun 5, 2025
1f041cf
fix pyopenms version parsing, update snapshot
jonasscheid Jun 10, 2025
2d657df
Merge branch 'template-merge-331' of https://github.com/jonasscheid/m…
jonasscheid Jun 10, 2025
6cceff2
Put result file temporarily on ignore list due to float rounding inco…
jonasscheid Jun 12, 2025
b05cd9f
Put result file temporarily on ignore list due to float rounding inco…
jonasscheid Jun 12, 2025
cc7dcdf
add mqc_length_dist file to ignore list
jonasscheid Jun 12, 2025
1f5f47f
update snapshot
jonasscheid Jun 12, 2025
fc16d95
Change lineplots to box plots
JuliaGraf Jun 17, 2025
21873d1
Add peptide intensity box plots
JuliaGraf Jun 17, 2025
abb9ae5
Change to log2
JuliaGraf Jun 17, 2025
c9478b5
Update assets/multiqc_config.yml
jonasscheid Jun 17, 2025
adc185f
Update CHANGELOG.md
jonasscheid Jun 17, 2025
b56ca9f
Merge pull request #382 from JuliaGraf/boxplots
jonasscheid Jun 17, 2025
a47b375
Round all float values to 5 decimals to ensure stable checksums
jonasscheid Jun 17, 2025
19f5607
Merge branch 'dev' into template-merge-331
jonasscheid Jun 18, 2025
61b50f5
Update base.config
jonasscheid Jun 18, 2025
7fd77ef
Update CHANGELOG.md
jonasscheid Jun 18, 2025
0a32468
check result files for same peptide content
jonasscheid Jun 18, 2025
3f8ba1a
Merge pull request #385 from nf-core/fix-config-fullname
jonasscheid Jun 18, 2025
19d6e93
Merge branch 'dev' into template-merge-331
jonasscheid Jun 18, 2025
8278f39
update to epicore version 0.1.5
janaHoffmann1 Jun 18, 2025
dc956e8
change pipeline params
janaHoffmann1 Jun 18, 2025
31d2964
ignore snapping md5sum, check content
jonasscheid Jun 20, 2025
6d6f49a
remove duplicated percolator test. Testing percolator is contained in…
jonasscheid Jun 20, 2025
b81dfc0
Add nftest for ionannotator, increase fdr threshold to perform meanin…
jonasscheid Jun 20, 2025
43484b7
add mokapot nftest
jonasscheid Jun 20, 2025
7d13b19
add speclib nftest
jonasscheid Jun 20, 2025
d4dc8ee
fix mokapot and speclib tests
jonasscheid Jun 20, 2025
e79532c
increase mokapot testfdr to let testruns pass, ignore all mqc/*.txt f…
jonasscheid Jun 20, 2025
b2de994
changelog
jonasscheid Jun 20, 2025
f8cd215
update CHANGELOG
janaHoffmann1 Jun 23, 2025
6cb8756
Make descriptions visible in the report
JuliaGraf Jun 23, 2025
77a99dc
solve merge conflicts
janaHoffmann1 Jun 24, 2025
aa172d6
fix merge of mhcquant
janaHoffmann1 Jun 24, 2025
a8783b4
fix lint and pre-commit error
janaHoffmann1 Jun 24, 2025
0a4cbdb
Merge pull request #379 from jonasscheid/template-merge-331
jonasscheid Jun 25, 2025
90d5f6e
Merge branch 'dev' into epicore
janaHoffmann1 Jun 27, 2025
4e85d7e
Change count to frequency in length distribution, count unique sequen…
JuliaGraf Jun 27, 2025
8f73ef8
Add descriptions for all plots
JuliaGraf Jun 27, 2025
72d4218
move epicore.nf to main/epicore.nf
janaHoffmann1 Jun 27, 2025
d4f3753
add epicore environment.yml
janaHoffmann1 Jun 27, 2025
40c1176
update ro-crate-metadata
janaHoffmann1 Jun 27, 2025
5ae3b3e
rename params to epicore_*, remove all non changing epicore params fr…
janaHoffmann1 Jun 30, 2025
b37ec13
remove else block of --epicore, update channel parsing
janaHoffmann1 Jul 1, 2025
140b54b
Control how outliers are displayed in box plots
JuliaGraf Jul 3, 2025
fa7575a
Update CHANGELOG.md
JuliaGraf Jul 3, 2025
258ea8c
Coarsen binning for TICs and move general stats to the top
JuliaGraf Jul 7, 2025
b8351e1
Update CHANGELOG.md
JuliaGraf Jul 7, 2025
e19f45e
Merge pull request #388 from JuliaGraf/fix_binning
jonasscheid Jul 7, 2025
326adbe
Template update for nf-core/tools version 3.3.2
nf-core-bot Jul 8, 2025
0d88fe9
Initial commit
JuliaGraf Jul 14, 2025
e52263f
Enable patient-specific fasta
JuliaGraf Jul 14, 2025
a611fa4
Fix bug
JuliaGraf Jul 14, 2025
0686df4
Move definition of fasta channel to else clause
JuliaGraf Jul 14, 2025
6949096
Remove test data
JuliaGraf Jul 14, 2025
595ec0e
Update modules.config
jonasscheid Jul 15, 2025
4488bbc
Merge pull request #392 from nf-core/fix-global-idfilter-config
jonasscheid Jul 15, 2025
112d9ee
Remove ext field from the meta-map after branching
JuliaGraf Jul 15, 2025
836e9fe
Add additional file extensions for fastas
JuliaGraf Jul 15, 2025
faa7d6a
Add warning if both --fasta and samplesheet fastas are provided
JuliaGraf Jul 15, 2025
698deb8
Fix typo
JuliaGraf Jul 15, 2025
1532c72
Update CHANGELOG.md
JuliaGraf Jul 15, 2025
5335657
Update usage.md
JuliaGraf Jul 15, 2025
75aaab3
Merge the two if-else clauses
JuliaGraf Jul 15, 2025
5b0b6ca
Remove --fasta parameter from test config
JuliaGraf Jul 15, 2025
5113177
Fix linting
JuliaGraf Jul 15, 2025
4a83eee
Only create decoy database once per sample+condition
JuliaGraf Jul 16, 2025
be4787e
Fix bug
JuliaGraf Jul 16, 2025
423f490
merge tempalte
jonasscheid Jul 22, 2025
5d56ef5
fix linting
jonasscheid Jul 22, 2025
9281066
update snapshots
jonasscheid Jul 22, 2025
667657b
Merge pull request #393 from jonasscheid/template-merge-332
jonasscheid Jul 23, 2025
29f09d9
add groupKey to sample-specific fasta track
jonasscheid Jul 23, 2025
95acf63
Merge pull request #391 from JuliaGraf/fasta
jonasscheid Jul 23, 2025
1ca6d32
update output columns in output.md, add description to html plots, ch…
janaHoffmann1 Jul 31, 2025
5f51794
update to epicore v0.1.6
janaHoffmann1 Jul 31, 2025
f393274
Merge branch 'dev' into epicore
jonasscheid Jul 31, 2025
da7e3a4
add epicore test
janaHoffmann1 Jul 31, 2025
bca54b6
add epicore snapshot file
janaHoffmann1 Aug 1, 2025
32dab70
fix lint errors
janaHoffmann1 Aug 1, 2025
67d0350
update epicore test
janaHoffmann1 Aug 1, 2025
6b83105
Update modules/local/epicore/environment.yml
janaHoffmann1 Aug 1, 2025
7a55d79
Update docs/output.md
janaHoffmann1 Aug 1, 2025
33a92ed
Update docs/output.md
janaHoffmann1 Aug 1, 2025
034777e
Update docs/output.md
janaHoffmann1 Aug 1, 2025
182e5fb
Update docs/output.md
janaHoffmann1 Aug 1, 2025
7f24f6a
Update docs/output.md
janaHoffmann1 Aug 1, 2025
7359cb6
fix epicore version output
janaHoffmann1 Aug 4, 2025
10d6ec2
update version in epicore test, add epicore to full test
janaHoffmann1 Aug 4, 2025
35f4bb3
fix whitespaces
janaHoffmann1 Aug 4, 2025
26638e7
Merge pull request #386 from janaHoffmann1/epicore
janaHoffmann1 Aug 4, 2025
de921b1
Merge branch 'dev' into boxplots
JuliaGraf Aug 4, 2025
1079fc6
Merge pull request #387 from JuliaGraf/boxplots
jonasscheid Aug 4, 2025
5098b24
Write out FDR-filtered global FDR peptide list, instead of 100% FDR list
jonasscheid Aug 5, 2025
8a31c55
Save global fdr filtered speclib in global_fdr output folder
jonasscheid Aug 5, 2025
819a777
Fix correct channel emit
jonasscheid Aug 5, 2025
a459cd7
Update MS2rescore container (new DeepLC version)
steffenlem Aug 13, 2025
870b636
update snapshots
jonasscheid Sep 11, 2025
160c0c3
update CHANGELOG
jonasscheid Sep 11, 2025
17bdb2e
Merge pull request #394 from nf-core/jonasscheid-patch-global-fdr
jonasscheid Sep 11, 2025
e3d0319
Update easypqp container version to 0.1.53
jonasscheid Sep 11, 2025
99525be
Update easypqp version to 0.1.53
jonasscheid Sep 11, 2025
83f2a3a
Update easypqp version to 0.1.53
jonasscheid Sep 11, 2025
9847879
Update easypqp container version to 0.1.53
jonasscheid Sep 11, 2025
3644224
Add '--diannpqp' argument to module configurations
jonasscheid Sep 11, 2025
c36f52b
Update easypqp version to 0.1.53 in tests
jonasscheid Sep 11, 2025
7977a34
Merge branch 'nf-core:dev' into dev
steffenlem Sep 11, 2025
d2b018e
Update EasyPQP version in CHANGELOG
jonasscheid Sep 11, 2025
ac3e51f
Merge pull request #395 from steffenlem/dev
jonasscheid Sep 11, 2025
2e4e215
Merge pull request #396 from nf-core/bump-easypqp
jonasscheid Sep 11, 2025
0796acf
Update labels for global configurations
jonasscheid Sep 15, 2025
8206507
Add high memory and CPU processing configuration
jonasscheid Sep 15, 2025
57b9436
Fix changelog entry for FDR-filtered peptide list
jonasscheid Sep 15, 2025
deda148
Merge pull request #397 from nf-core/fix-globalfdr-ressource_allocation
jonasscheid Sep 15, 2025
20e4ba8
Initial plan
Copilot Sep 15, 2025
552ee83
Update README with new subworkflows and global FDR documentation
Copilot Sep 15, 2025
7a9b2d5
Update usage documentation with new subworkflows and features
Copilot Sep 15, 2025
a547bd0
Address reviewer feedback: restructure documentation and consolidate …
Copilot Sep 15, 2025
42cf58e
Remove mokapot from complete workflow example
Copilot Sep 15, 2025
c8bc8ab
Merge pull request #399 from nf-core/copilot/fix-72f40d13-378b-4ce8-b…
jonasscheid Sep 15, 2025
ed63780
lint
jonasscheid Sep 15, 2025
5205b44
sync ro crate
jonasscheid Sep 15, 2025
0aed628
Update README.md
jonasscheid Sep 16, 2025
fbc0e1d
Update docs/usage.md
jonasscheid Sep 16, 2025
1cdd1f5
Update docs/usage.md
jonasscheid Sep 16, 2025
da6155a
fix linting
jonasscheid Sep 17, 2025
9f7c2a5
update snapshots with release version
jonasscheid Sep 18, 2025
2d30adf
Merge pull request #400 from nf-core/update-docs
jonasscheid Sep 18, 2025
9368daa
Add a column for unique accessions
JuliaGraf Sep 23, 2025
80c5a3a
Remove special character from column name to resolve bug
JuliaGraf Sep 23, 2025
527305b
Update changelog
JuliaGraf Sep 24, 2025
08479da
Merge pull request #403 from JuliaGraf/unique_accessions
JuliaGraf Sep 24, 2025
3337406
Initial plan
Copilot Sep 24, 2025
44d2cca
Add default values to nextflow_schema.json from nextflow.config params
Copilot Sep 24, 2025
803b559
Update nextflow_schema.json
jonasscheid Sep 24, 2025
5f5a327
Update nextflow_schema.json
jonasscheid Sep 24, 2025
6f9fed2
fix nf-core lint
jonasscheid Sep 24, 2025
5ccdaef
fix trailing whitespace
jonasscheid Oct 2, 2025
772dea5
add nf-core bot automations
jonasscheid Oct 2, 2025
d38ea69
specify mhcquant as target repo
jonasscheid Oct 2, 2025
1d9eabe
Update DOI to MHCquant2 publication
jonasscheid Oct 2, 2025
46f7af4
add .vscode/settings.json to nf-core.yml to run nf-core pipelines lin…
jonasscheid Oct 2, 2025
b334333
update ro-create
jonasscheid Oct 2, 2025
9cbef27
Merge pull request #404 from nf-core/copilot/fix-20167b1f-b3d6-4467-b…
jonasscheid Oct 6, 2025
c27bbb1
Initial plan
Copilot Oct 7, 2025
27e3b78
Change "false" to false in assets/multiqc_config.yml
Copilot Oct 7, 2025
44dfa86
Add changelog update script for CI integration
jonasscheid Oct 7, 2025
f3b745d
Merge pull request #407 from nf-core/copilot/fix-boolean-value-in-config
jonasscheid Oct 7, 2025
659eb7c
Implementation attempt to update-snapshots using nf-core bot
jonasscheid Oct 7, 2025
813545e
Delete .github/workflows/update-textual-snapshots.yml
jonasscheid Oct 8, 2025
906babc
Delete .github/workflows/changelog.yml
jonasscheid Oct 8, 2025
f553b79
Merge pull request #406 from nf-core/update-doi
jonasscheid Oct 8, 2025
22c6306
Update .github/workflows/update-snapshots.yml
jonasscheid Oct 13, 2025
9e1e619
Merge pull request #405 from nf-core/add-nfcore-bot
jonasscheid Oct 13, 2025
3c1e3ec
don't rely on deeplc rt, take comet rt
jonasscheid Oct 17, 2025
ff13347
update changelog
jonasscheid Oct 17, 2025
6142b97
Merge pull request #411 from jonasscheid/fix-409
jonasscheid Oct 17, 2025
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
43 changes: 0 additions & 43 deletions .editorconfig

This file was deleted.

2 changes: 1 addition & 1 deletion .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ If you wish to contribute a new step, please use the following coding standards:
5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
6. Add sanity checks and validation for all relevant parameters.
7. Perform local tests to validate that the new code works as expected.
8. If applicable, add a new test command in `.github/workflow/ci.yml`.
8. If applicable, add a new test in the `tests` directory.
9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.

Expand Down
69 changes: 69 additions & 0 deletions .github/actions/get-shards/action.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
name: "Get number of shards"
description: "Get the number of nf-test shards for the current CI job"
inputs:
max_shards:
description: "Maximum number of shards allowed"
required: true
paths:
description: "Component paths to test"
required: false
tags:
description: "Tags to pass as argument for nf-test --tag parameter"
required: false
outputs:
shard:
description: "Array of shard numbers"
value: ${{ steps.shards.outputs.shard }}
total_shards:
description: "Total number of shards"
value: ${{ steps.shards.outputs.total_shards }}
runs:
using: "composite"
steps:
- name: Install nf-test
uses: nf-core/setup-nf-test@v1
with:
version: ${{ env.NFT_VER }}
- name: Get number of shards
id: shards
shell: bash
run: |
# Run nf-test with dynamic parameter
nftest_output=$(nf-test test \
--profile +docker \
$(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
--dry-run \
--ci \
--changed-since HEAD^) || {
echo "nf-test command failed with exit code $?"
echo "Full output: $nftest_output"
exit 1
}
echo "nf-test dry-run output: $nftest_output"
# Default values for shard and total_shards
shard="[]"
total_shards=0
# Check if there are related tests
if echo "$nftest_output" | grep -q 'No tests to execute'; then
echo "No related tests found."
else
# Extract the number of related tests
number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
total_shards="$shards_to_run"
else
echo "Unexpected output format. Falling back to default values."
fi
fi
# Write to GitHub Actions outputs
echo "shard=$shard" >> $GITHUB_OUTPUT
echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
# Debugging output
echo "Final shard array: $shard"
echo "Total number of shards: $total_shards"
109 changes: 109 additions & 0 deletions .github/actions/nf-test/action.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,109 @@
name: "nf-test Action"
description: "Runs nf-test with common setup steps"
inputs:
profile:
description: "Profile to use"
required: true
shard:
description: "Shard number for this CI job"
required: true
total_shards:
description: "Total number of test shards(NOT the total number of matrix jobs)"
required: true
paths:
description: "Test paths"
required: true
tags:
description: "Tags to pass as argument for nf-test --tag parameter"
required: false
runs:
using: "composite"
steps:
- name: Setup Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ env.NXF_VERSION }}"

- name: Set up Python
uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
with:
python-version: "3.13"

- name: Install nf-test
uses: nf-core/setup-nf-test@v1
with:
version: "${{ env.NFT_VER }}"
install-pdiff: true

- name: Setup apptainer
if: contains(inputs.profile, 'singularity')
uses: eWaterCycle/setup-apptainer@main

- name: Set up Singularity
if: contains(inputs.profile, 'singularity')
shell: bash
run: |
mkdir -p $NXF_SINGULARITY_CACHEDIR
mkdir -p $NXF_SINGULARITY_LIBRARYDIR

- name: Conda setup
if: contains(inputs.profile, 'conda')
uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
with:
auto-update-conda: true
conda-solver: libmamba
conda-remove-defaults: true

- name: Run nf-test
shell: bash
env:
NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
run: |
nf-test test \
--profile=+${{ inputs.profile }} \
$(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
--ci \
--changed-since HEAD^ \
--verbose \
--tap=test.tap \
--shard ${{ inputs.shard }}/${{ inputs.total_shards }}

# Save the absolute path of the test.tap file to the output
echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT

- name: Generate test summary
if: always()
shell: bash
run: |
# Add header if it doesn't exist (using a token file to track this)
if [ ! -f ".summary_header" ]; then
echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
echo "" >> $GITHUB_STEP_SUMMARY
echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
touch .summary_header
fi

if [ -f test.tap ]; then
while IFS= read -r line; do
if [[ $line =~ ^ok ]]; then
test_name="${line#ok }"
# Remove the test number from the beginning
test_name="${test_name#* }"
echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
elif [[ $line =~ ^not\ ok ]]; then
test_name="${line#not ok }"
# Remove the test number from the beginning
test_name="${test_name#* }"
echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
fi
done < test.tap
else
echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
fi

- name: Clean up
if: always()
shell: bash
run: |
sudo rm -rf /home/ubuntu/tests/
4 changes: 2 additions & 2 deletions .github/workflows/awsfulltest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ jobs:
run-platform:
name: Run AWS full tests
# run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
if: github.repository == 'nf-core/mhcquant' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
if: github.repository == 'nf-core/mhcquant' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
runs-on: ubuntu-latest
steps:
- name: Set revision variable
Expand All @@ -37,7 +37,7 @@ jobs:
}
profiles: test_full

- uses: actions/upload-artifact@v4
- uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
with:
name: Seqera Platform debug log file
path: |
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/awstest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ jobs:
}
profiles: test

- uses: actions/upload-artifact@v4
- uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
with:
name: Seqera Platform debug log file
path: |
Expand Down
Loading
Loading