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[Do not merge!] Pseudo PR for first release #133

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c27dd8b
Adjust output docs to match process/subworkflow name again
tillenglert May 31, 2023
5c59d21
Update chanelog
tillenglert May 31, 2023
87c569c
Rename script from input_to_datamodel module
tillenglert May 31, 2023
ae0b640
[automated] Fix linting with Prettier
nf-core-bot May 31, 2023
aecbe37
Standardise commenting in main workflow
tillenglert May 31, 2023
eb724e1
Apply suggestions from code review
tillenglert Jun 6, 2023
fbf8233
Changed documentation and function name
tillenglert Jun 6, 2023
824a295
rename subworkflow and check samplesheet module
tillenglert Jun 6, 2023
90db8b8
Update Epytope version to 3.3.1
tillenglert May 30, 2023
f7172f0
Reduce peptide length in test_mouse
tillenglert May 30, 2023
6a759dc
Update Changelog
tillenglert May 30, 2023
75abe53
[automated] Fix linting with Prettier
nf-core-bot May 30, 2023
0e519b5
Update conf/test_mouse.config
tillenglert Jun 6, 2023
823a8e9
Shorten documentation in test_mouse
tillenglert Jun 7, 2023
46c6d07
Add statistical test to binding ratio boxplots
skrakau Jun 23, 2023
3f48477
Improve R command line args handling and add param show_pvalue
skrakau Jun 23, 2023
4603399
Update container
skrakau Jun 27, 2023
b4515e0
Merge pull request #75 from tillenglert/Peptide_Length-in-samplesheet…
tillenglert Jun 28, 2023
1258b11
Merge 'dev' into add_tests
skrakau Jun 28, 2023
a1fc576
Change show_pvalue param to hide_pvalue
skrakau Jun 28, 2023
279ca11
Update CHANGELOG
skrakau Jun 28, 2023
408dd7b
Apply suggestions from code review
skrakau Jun 28, 2023
d16d3aa
Fix whitespace
skrakau Jun 28, 2023
0dc3b19
Merge pull request #80 from skrakau/add_tests
skrakau Jun 28, 2023
6c33af9
Include metapep logo in Multiqc
tillenglert Jul 4, 2023
5fbc76c
Adjusted used resource request labels
skrakau Jul 4, 2023
52a434d
patch multiqc
tillenglert Jul 13, 2023
dc4145f
Add Multiqc to output docs again
tillenglert Jul 13, 2023
9d1cdd1
Update Changelog
tillenglert Jul 13, 2023
2bcce52
Add methods and references
tillenglert Jul 13, 2023
b30c217
[automated] Fix linting with Prettier
nf-core-bot Jul 13, 2023
62b7d12
Add epytope to methods and references
tillenglert Jul 13, 2023
1b605b1
Template update nf-core tools 2.9
tillenglert Jul 13, 2023
1d62acf
Add Entrez to description
tillenglert Jul 13, 2023
4c07afd
Update Citations
tillenglert Jul 14, 2023
93c90a3
update changelog
tillenglert Jul 14, 2023
df629b1
[automated] Fix linting with Prettier
nf-core-bot Jul 14, 2023
78851e6
Include the citations.md file in the methods description
tillenglert Jul 14, 2023
8913959
Merge pull request #87 from tillenglert/Template_update_2.9
tillenglert Jul 19, 2023
60e894e
Merge branch 'dev' into multiqc
tillenglert Jul 19, 2023
c8e3cf4
Merge branch 'dev' into Citations
tillenglert Jul 19, 2023
75f14b3
generalise citations style
tillenglert Jul 19, 2023
e7810b8
Merge pull request #88 from tillenglert/Citations
tillenglert Jul 24, 2023
e38e7b8
Merge branch 'dev' into multiqc
tillenglert Jul 24, 2023
654ef58
Merge pull request #84 from tillenglert/multiqc
tillenglert Jul 25, 2023
6993717
Bugfix peptide Lengths and include log instead of tsv
tillenglert Aug 1, 2023
4c05d74
python black
tillenglert Aug 1, 2023
a610d08
update Changelog
tillenglert Aug 1, 2023
aba423c
software_versions for plot_entity_binding_ratios
tillenglert Aug 1, 2023
6e5d95b
Remove headers, unnecessary imports and commented code
tillenglert Aug 1, 2023
a3663d2
update changelog
tillenglert Aug 1, 2023
5630b21
Merge pull request #86 from skrakau/adjust_resources
skrakau Aug 1, 2023
33eb79d
Merge pull request #90 from tillenglert/script_headers
tillenglert Aug 2, 2023
ec2ee2b
Merge branch 'dev' into bugfix/peptide_lengths
tillenglert Aug 2, 2023
3ee1efa
Review comment
tillenglert Aug 2, 2023
fc14e3f
Merge pull request #89 from tillenglert/bugfix/peptide_lengths
tillenglert Aug 2, 2023
ba29802
Add new parameter to
tillenglert Aug 2, 2023
0740fe1
Include new parameter in process_input
tillenglert Aug 2, 2023
87633e5
Additional checks in epytope_predict to circumvent errors
tillenglert Aug 2, 2023
8efd391
python black
tillenglert Aug 2, 2023
1f902d6
Update Changelog
tillenglert Aug 2, 2023
3f4ba65
Add check for peptide length parameter and replace exit with error
tillenglert Aug 2, 2023
cba996e
Add comment on check
tillenglert Aug 2, 2023
81bfb31
update changelog
tillenglert Aug 2, 2023
488ce19
Add test to allow all peptide lengths for mouse test
tillenglert Aug 2, 2023
e02e13a
Change larger mosue test including also taxa to reduce the number of …
tillenglert Aug 2, 2023
3ae3c66
Add test taxa only
tillenglert Aug 3, 2023
a88ebc0
add test bins only
tillenglert Aug 3, 2023
432c4d3
Add tests to gh ci
tillenglert Aug 3, 2023
c6ba6ed
Add correct name and remove ncbi from test all peptide lengths
tillenglert Aug 3, 2023
e859215
Add test taxa to tests run with gh secrets
tillenglert Aug 3, 2023
119a158
Add comment to add ncbi mail and pw
tillenglert Aug 3, 2023
e1c5c07
remove todos in test profile
tillenglert Aug 3, 2023
39fa300
Add tests for mhcflurry and mhcnuggets
tillenglert Aug 3, 2023
5d65ada
Adjust line in usage.md for test not needing any configuration additi…
tillenglert Aug 3, 2023
b277395
Use mhc2 alleles test for mhcnuggets class 2
tillenglert Aug 3, 2023
7e65b30
[automated] Fix linting with Prettier
nf-core-bot Aug 4, 2023
9c9cd5f
update changelog
tillenglert Aug 4, 2023
69a6953
Update workflow overview figures
tillenglert Aug 11, 2023
fa15159
Add white background to overview figure
tillenglert Aug 11, 2023
17da32b
Update changelog
tillenglert Aug 11, 2023
4e49f61
change parameter name
tillenglert Sep 8, 2023
0a4d1b3
Update nextflow_schema.json
tillenglert Sep 8, 2023
210b4fe
Apply suggestions from code review
tillenglert Sep 8, 2023
2968449
Update parameter allow_inconsistent_pep_lengths
tillenglert Sep 8, 2023
713ace9
Merge pull request #91 from tillenglert/feature/allow_allpep_lengths
tillenglert Sep 11, 2023
3f69f4b
Merge pull request #92 from tillenglert/bugfix/peptide_length_check
tillenglert Sep 11, 2023
93a9cff
Update Overview Figure
tillenglert Sep 11, 2023
20435fd
Merge branch 'dev' into overview_figure_update
tillenglert Sep 11, 2023
992820b
Merge branch 'dev' into CI_tests
tillenglert Sep 11, 2023
8ab5217
Apply suggestions from code review
tillenglert Sep 11, 2023
1dfc608
Update conf/test_mhcnuggets_2.config
tillenglert Sep 12, 2023
2d34c3e
Add/change tests according to suggestions
tillenglert Sep 12, 2023
2d115ad
Update Overview figure according to suggestions
tillenglert Sep 12, 2023
b9d4fd5
Split out downstream visualisations chunk size parameter
tillenglert Sep 12, 2023
69e7106
Reduce chunk size by scaling in merge predictions buffer
tillenglert Sep 12, 2023
5c3cdda
Use parameter to reduce files ending up in merge predictions buffer
tillenglert Sep 12, 2023
05d95e3
typo in parameter
tillenglert Sep 12, 2023
dbc777a
Update Overview figure
tillenglert Sep 13, 2023
abbbfa2
Merge pull request #94 from tillenglert/overview_figure_update
tillenglert Sep 13, 2023
d657603
Use 4kk as chunk size -> number of jobs reduced to 160
tillenglert Sep 13, 2023
7579adb
Fix typo in peptide lengths
tillenglert Sep 13, 2023
dced421
Update CHANGELOG
tillenglert Sep 13, 2023
8160cfb
create versioning directory in test-datasets
tillenglert Sep 14, 2023
1fc49b3
Merge branch 'dev' into CI_tests
tillenglert Sep 14, 2023
151d7e4
[automated] Fix linting with Prettier
nf-core-bot Sep 14, 2023
5021b67
Add label long to epitope prediction as for MHCflurry the processes r…
tillenglert Sep 18, 2023
4873e95
Optional merge buffer
tillenglert Sep 18, 2023
b5edc16
Update Changelog
tillenglert Sep 18, 2023
eb225ce
reduce number of characters for output in prediction
tillenglert Sep 19, 2023
4b12f2b
Update nf schema
tillenglert Sep 19, 2023
8cf98c3
Merge pull request #95 from tillenglert/bugfix/peptide_lengths
tillenglert Sep 19, 2023
4b9bc5c
Merge branch 'dev' into feature/Chunk_size_rework
tillenglert Sep 19, 2023
d93322e
more verbose multimap and branch
tillenglert Sep 26, 2023
15ec56f
Change to samplesheet instead of input
tillenglert Sep 26, 2023
4d7bd0c
rename samplesheet for mouse assembly only
tillenglert Sep 26, 2023
fe1e70a
Update CHANGELOG.md
tillenglert Sep 26, 2023
6b61415
Merge pull request #96 from tillenglert/feature/Chunk_size_rework
tillenglert Sep 27, 2023
c51f7ad
Merge branch 'dev' into CI_tests
tillenglert Oct 2, 2023
2e8e11b
Merge pull request #93 from tillenglert/CI_tests
tillenglert Oct 16, 2023
f794e93
Merge branch 'dev' into nf-core-template-merge-2.10
tillenglert Oct 16, 2023
1c478e0
Forgot to add test_all to nextflow.config
tillenglert Oct 16, 2023
defbdba
Update Changelog
tillenglert Oct 16, 2023
07b5974
Remove test_bins and test_tiny
tillenglert Oct 16, 2023
8bea247
Merge pull request #98 from tillenglert/bugfix/CI_test_all
tillenglert Oct 17, 2023
2a50309
Merge branch 'dev' into nf-core-template-merge-2.10
tillenglert Oct 17, 2023
5f72aae
reset multiqc config
tillenglert Oct 17, 2023
f2d4247
fix linting
tillenglert Oct 17, 2023
2601169
Merge pull request #97 from nf-core/nf-core-template-merge-2.10
tillenglert Nov 10, 2023
eb93b26
Merge remote-tracking branch 'upstream/nf-core-template-merge-2.13' i…
tillenglert Feb 27, 2024
cc489dd
Readd schema_input.json -> needs to be adjusted to our needs
tillenglert Feb 27, 2024
ff65c32
Implement metapep input to input_schema.json
tillenglert Mar 3, 2024
7979436
fix merge errors and implement template further
tillenglert Mar 3, 2024
3350cca
Update Multiqc
tillenglert Mar 3, 2024
b307183
fix unifying models and reimplement
tillenglert Mar 3, 2024
69e02e4
fix model information subbranch
tillenglert Mar 3, 2024
81b245a
Merge remote-tracking branch 'upstream/nf-core-template-merge-2.13.1'…
tillenglert Mar 4, 2024
dbb2bed
fix mhcflury permission error -> docker issue
tillenglert Mar 4, 2024
29180b3
python ruff formatting
tillenglert Mar 4, 2024
1c8c6b7
fix and deprecate docker.userEmulation
tillenglert Mar 8, 2024
9c9c9ad
Add allele regex to schema_input.json
tillenglert Mar 8, 2024
eb12e89
Remove TODO from metapep.nf
tillenglert Mar 8, 2024
166b154
Add citations text and bibliography to utils
tillenglert Mar 8, 2024
10cbd27
Merge pull request #106 from tillenglert/template_update_2.13
tillenglert Mar 11, 2024
a9ee974
Copy CHangelog to clean branch
tillenglert Mar 11, 2024
c079cf9
[automated] Fix code linting
nf-core-bot Mar 11, 2024
a81e448
Merge pull request #110 from tillenglert/changelog_cleanup
tillenglert Mar 18, 2024
cd80158
Add strain level check
tillenglert Mar 18, 2024
c7a331b
Add the option for assembly id within the input tsv for taxids
tillenglert Mar 18, 2024
4dad83e
Add the format of the input taxa tsv to the input documentation
tillenglert Mar 18, 2024
ab26aeb
make the tsv format readable
tillenglert Mar 18, 2024
c14056b
Add CI test for specific assembly taxa input
tillenglert Mar 18, 2024
cea89e3
[automated] Fix code linting
nf-core-bot Mar 18, 2024
f7235c8
Refactor input tsv check
tillenglert Mar 19, 2024
13a6637
Add warning of mixed specific assemblyID and taxID and output log of …
tillenglert Mar 19, 2024
363ff60
Append the documentation by a section about the input type taxa and s…
tillenglert Mar 19, 2024
61647d1
[automated] Fix code linting
nf-core-bot Mar 19, 2024
6641b10
Add log of Entrez download to output.md
tillenglert Mar 19, 2024
529a553
[automated] Fix code linting
nf-core-bot Mar 19, 2024
2b1f02b
Remove dead code of bare proteins input path
tillenglert Mar 19, 2024
7af27d7
Readability
tillenglert Mar 20, 2024
6791c90
Chunked efetch and esummary for more than 9999 protein ids (maximum o…
tillenglert Mar 20, 2024
909cc17
Comments and casting assembly length to int
tillenglert Mar 20, 2024
1431ed0
Add maximum number of chunks parameter
tillenglert Mar 26, 2024
5329034
Add information on how to use the assembly_ids for reproducibility
tillenglert Mar 26, 2024
3edf5e4
Add the usage of taxa_assemblies.tsv
tillenglert Mar 26, 2024
60d3d98
readd deleted sentence
tillenglert Mar 26, 2024
abbd7ce
remove whitespaces in download_proteins.nf
tillenglert Mar 26, 2024
a00fec5
Append some words on how to use the pipeline in a second run in regar…
tillenglert Mar 26, 2024
acedaa6
Update docs/usage.md
tillenglert Mar 26, 2024
b0a8c71
Merge pull request #111 from tillenglert/dl_proteins_input
tillenglert Mar 26, 2024
ea5c060
Add maximum chunk number in prediciton chunk generation
tillenglert Mar 27, 2024
37afb83
Merge branch 'dev' into Download_Proteins_todos
tillenglert Mar 27, 2024
b39ab38
Merge branch 'dev' into cleanup_proteins_type_input
tillenglert Mar 27, 2024
fe66069
Merge pull request #112 from tillenglert/cleanup_proteins_type_input
tillenglert Mar 27, 2024
797dcb7
Update bin/download_proteins_entrez.py
tillenglert Mar 27, 2024
81f19da
fix chunking end of chunk
tillenglert Mar 27, 2024
679143c
Merge pull request #115 from tillenglert/Download_Proteins_todos
tillenglert Apr 12, 2024
b5fd2e5
Add warning that maximum chunk number is reduced
tillenglert Apr 19, 2024
617e7b4
Change description of parameter a bit
tillenglert Apr 19, 2024
db30e03
Move chunk size increase to top of the code to circumvent an error fo…
tillenglert Apr 19, 2024
2058f83
Merge branch 'dev' into maximum_chunk_number
tillenglert Apr 19, 2024
835a2eb
Remove TODOs and add contributors
tillenglert Apr 19, 2024
797223f
[automated] Fix code linting
nf-core-bot Apr 19, 2024
8e97db1
init nf test and add initial test for pipeline
tillenglert Apr 19, 2024
7745229
Change CI to include nf-test (no ncbi credentials)
tillenglert Apr 19, 2024
7cdbefd
fix ci paths to samplesheets
tillenglert Apr 19, 2024
83e85e5
remove nf-test nextflow.config for now
tillenglert Apr 19, 2024
5190cdb
Create placeholder tests for all test profiles (still no ncbi login)
tillenglert Apr 19, 2024
56ba42f
fix coassembly placeholder
tillenglert Apr 19, 2024
11d5b6e
add linting exceptions
tillenglert Apr 19, 2024
2e7a802
Adjust contributors
skrakau Apr 19, 2024
0d30528
Add additional test profiles
tillenglert Apr 22, 2024
4799088
Merge pull request #117 from tillenglert/README_Todos
tillenglert Apr 22, 2024
34aa983
Merge remote-tracking branch 'upstream/dev' into dev
tillenglert Apr 22, 2024
218e00f
Merge branch 'dev' into maximum_chunk_number
tillenglert Apr 22, 2024
643061a
Add additional test profiles, needing the github secrets
tillenglert Apr 26, 2024
7ccb3dd
Code Review
tillenglert Apr 26, 2024
8453941
enable conda
tillenglert May 3, 2024
03da0ce
update subworkflow utils
tillenglert May 3, 2024
f5cecb9
Catch divide by zero error in process_input subworkflow
tillenglert May 8, 2024
d6abf00
update nf-test to latest version
tillenglert May 8, 2024
5300d5a
code review
tillenglert May 8, 2024
f711619
Update .github/workflows/ci.yml
tillenglert May 8, 2024
34759b4
forgot to change tag to profile
tillenglert May 8, 2024
7045007
Remove the checking out of test data
tillenglert May 8, 2024
44e2b07
remove "raw"/"endraw"
tillenglert May 8, 2024
5d05bfa
Merge pull request #121 from tillenglert/update-utils-subworkflow
tillenglert May 8, 2024
a5a9ec8
Merge branch 'dev' into nf-test_implementation
tillenglert May 8, 2024
1e19b9a
Merge branch 'dev' into maximum_chunk_number
tillenglert May 8, 2024
046772d
Merge branch 'dev' into enable-conda
tillenglert May 8, 2024
936ebbc
Merge pull request #120 from tillenglert/enable-conda
tillenglert May 8, 2024
a91dfe7
Merge branch 'dev' into nf-test_implementation
tillenglert May 8, 2024
b2947e8
Merge branch 'dev' into maximum_chunk_number
tillenglert May 8, 2024
ec9292e
Merge pull request #116 from tillenglert/maximum_chunk_number
tillenglert May 8, 2024
7001a17
Merge branch 'dev' into nf-test_implementation
tillenglert May 8, 2024
879ee06
ignore actions_ci linting
tillenglert May 8, 2024
ccf2e5b
Prepare merge and solve merge conflicts
tillenglert May 10, 2024
2102af6
add pipeline testdata base path (forgot in one test)
tillenglert May 10, 2024
048c2cc
Also add myself to authors in pipeline manifest (oversight before)
tillenglert May 10, 2024
ccb10aa
update License according to manifest
tillenglert May 10, 2024
d6c467c
remove cache lenient label
tillenglert Jun 7, 2024
e26ff5b
Merge pull request #123 from nf-core/nf-core-template-merge-2.14.1
tillenglert Jun 10, 2024
ce01b45
Merge branch 'dev' into nf-test_implementation
tillenglert Jun 10, 2024
6db5834
Merge pull request #118 from tillenglert/nf-test_implementation
tillenglert Jun 10, 2024
f89574b
Apply stash to new branch:
tillenglert Jun 25, 2024
637bedb
[automated] Fix code linting
nf-core-bot Jun 25, 2024
006d8b8
Add secrets to CI tests
tillenglert Jun 25, 2024
dd327c1
remove nf-test config environment and set in ci
tillenglert Jun 25, 2024
fb3c4c2
Update docs/usage.md
tillenglert Jul 1, 2024
9c5acc0
Merge pull request #124 from tillenglert/ncbi_params2secret
tillenglert Jul 1, 2024
7c899e6
remove testdata
tillenglert Jul 12, 2024
c126e27
Merge pull request #126 from tillenglert/remove_testfiles
tillenglert Jul 17, 2024
57fd30a
nf-test assertions
tillenglert Jul 18, 2024
5ffeb38
Add nf-test snapshots
tillenglert Jul 18, 2024
76ce8da
updated snaps to new sorting strategy
tillenglert Aug 5, 2024
90118eb
Refactoring and Sorting for deterministic table generation
tillenglert Aug 6, 2024
5c9bb1b
Merge pull request #127 from tillenglert/refactor_reproducibility
tillenglert Aug 6, 2024
e431d5b
Merge branch 'dev' into nf-test_assertions_new
tillenglert Aug 6, 2024
707375c
remove bank lines from *.nf.test
tillenglert Aug 6, 2024
3b46b3c
Merge pull request #128 from tillenglert/nf-test_assertions_new
tillenglert Aug 6, 2024
d0711e6
fix plot generation
tillenglert Aug 6, 2024
890b4a1
add figures to tests
tillenglert Aug 6, 2024
8923d02
Merge pull request #129 from tillenglert/bugfix/figure_creation
tillenglert Aug 7, 2024
1f45f7b
prepare release 1.0.0
tillenglert Aug 7, 2024
14a0066
remove "dev" from links to nf-core website and github repository
tillenglert Aug 8, 2024
a09de95
Merge pull request #131 from tillenglert/prepare_release_1.0.0
tillenglert Aug 8, 2024
2a7f521
fix bug in `generate_protein_and_entity_ids.py`
tillenglert Sep 13, 2024
dde3c9b
update test snapshots
tillenglert Sep 13, 2024
825420d
Merge pull request #135 from tillenglert/bugfix/duplicated_rows_prote…
tillenglert Sep 16, 2024
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change module name in modules.config
  • Loading branch information
tillenglert authored and skrakau committed Jun 27, 2023
commit 4df778b2a8ea2fb06899d2dd24f5eec9245a68f5
2 changes: 1 addition & 1 deletion conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ process {
]
}

withName: SAMPLESHEET_CHECK {
withName: INPUT_TO_DATAMODEL {
publishDir = [
path: { "${params.outdir}" },
mode: params.publish_dir_mode,
Expand Down