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