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6591e26
minor updates nextflow.config
kdavydzenka Sep 25, 2024
12c2d17
minor updates tumorevo.nf
kdavydzenka Sep 25, 2024
21229e8
updates signature_deconvolution subworkflow config
kdavydzenka Sep 26, 2024
d6b0544
updates signature_deconvolution subworkflow config
kdavydzenka Sep 26, 2024
cb7b274
updates Sigprofiler config
kdavydzenka Sep 29, 2024
9115494
Updated tests for annotate_driver and get_position_rel
RodTol Sep 30, 2024
cac6b5c
added check_max to config and tinc param
Sep 30, 2024
f98f9bb
Merge branch 'dev' of github.com:caravagnalab/tumourevo into dev
Sep 30, 2024
4ebcc48
working publish_dir mode
giorgiagandolfi Sep 30, 2024
4d1e074
mc subclonal deconvolution
giorgiagandolfi Sep 30, 2024
a5c9acc
updating images for subclonal deconvolution
elena-buscaroli Oct 1, 2024
f9c4c71
fixing minor bugs
elena-buscaroli Oct 1, 2024
9fcc5d9
fixing minor bugs
elena-buscaroli Oct 1, 2024
12ab6a3
minor bugs
elena-buscaroli Oct 1, 2024
c870402
bugs fix Sigprofiler
kdavydzenka Oct 2, 2024
547f9f2
bugs fix Sigprofiler
kdavydzenka Oct 2, 2024
541e60a
minor updates Sigprofiler
kdavydzenka Oct 2, 2024
e31c2e0
minor updates Sigprofiler
kdavydzenka Oct 2, 2024
edb82ae
minor updates Sigprofiler
kdavydzenka Oct 2, 2024
d8e15ec
Sigprofiler conf update
kdavydzenka Oct 3, 2024
8ceb4e5
add utils functions Sigprofiler
kdavydzenka Oct 3, 2024
0edac65
minor updates Sigprofiler
kdavydzenka Oct 3, 2024
0b3023b
solve minor bug Sigprofiler
kdavydzenka Oct 3, 2024
a897c9a
solve minor bug Sigprofiler
kdavydzenka Oct 3, 2024
e91fe00
mc in the sigprofiler volume path
elena-buscaroli Oct 3, 2024
3271d83
mc
elena-buscaroli Oct 3, 2024
6149d21
updating docker containers
elena-buscaroli Oct 3, 2024
cf21caf
mc in orfeo config
elena-buscaroli Oct 3, 2024
68fdce0
check if trees is null
elena-buscaroli Oct 3, 2024
fd60b8f
fix bugs in ctree module
elena-buscaroli Oct 4, 2024
036e7e3
Merge branch 'dev' of https://github.com/caravagnalab/tumourevo into dev
elena-buscaroli Oct 4, 2024
4d623d9
fixing minor bug in ctree
elena-buscaroli Oct 4, 2024
5143727
fixing but in annotation_cache_init
elena-buscaroli Oct 4, 2024
fd05749
change ctree folder structure
elena-buscaroli Oct 4, 2024
81fbc91
keep only diploid segments for subcl deconvolution
elena-buscaroli Oct 4, 2024
eb1df81
update ctree to fix special case
elena-buscaroli Oct 4, 2024
4ac0da9
tinc branching
Oct 4, 2024
58e37b2
Merge branch 'dev' of github.com:caravagnalab/tumourevo into dev
Oct 4, 2024
4de37eb
typo in ctree
elena-buscaroli Oct 4, 2024
82384b7
minor tinc
valerianilucrezia Oct 7, 2024
6877acf
minor updates Sigprofiler
kdavydzenka Oct 7, 2024
d4fa1ca
minor updates Sigprofiler
kdavydzenka Oct 7, 2024
7cceddb
minor updates Sigprofiler
kdavydzenka Oct 7, 2024
34845c5
minor updates SparseSig
kdavydzenka Oct 7, 2024
881e4ec
minor updates SparseSig
kdavydzenka Oct 7, 2024
307abc5
minor bugs fix Sigprofiler
kdavydzenka Oct 8, 2024
3440dcd
bugs fix files grouping signature_deconvolution
kdavydzenka Oct 8, 2024
bcf4e1e
minor updates config Sigprofiler
kdavydzenka Oct 8, 2024
0015656
minor updates config SparseSignatures
kdavydzenka Oct 8, 2024
ea8d7d0
minor updates config Signatures
kdavydzenka Oct 8, 2024
9df57fc
working Sigprofiler
kdavydzenka Oct 9, 2024
e6da7b6
working SparseSignatures
kdavydzenka Oct 9, 2024
0e51010
working SparseSignatures
kdavydzenka Oct 9, 2024
ab17640
working signature_deconvolution
kdavydzenka Oct 9, 2024
10b5fcf
modify NV in join_pos
valerianilucrezia Oct 9, 2024
d673643
Merge branch 'dev' of https://github.com/caravagnalab/tumourevo into dev
valerianilucrezia Oct 9, 2024
23f8183
working ctree and singularity config
elena-buscaroli Oct 9, 2024
bcea464
Merge branch 'dev' of https://github.com/caravagnalab/tumourevo into dev
elena-buscaroli Oct 9, 2024
1cf47a9
annotate_driver test
Sep 20, 2024
7fe6416
formatter test
Sep 20, 2024
899317b
subclonal_deconvolution test
Sep 20, 2024
934a0d9
QC test
Sep 20, 2024
75d1ab5
lifter test wip
Sep 20, 2024
4d6a971
fix data paths
Sep 23, 2024
0d29a01
signature deconvolution worflow test
Oct 11, 2024
febff3f
fix divergent branches
Oct 11, 2024
5112b1a
new qc workflow
valerianilucrezia Oct 14, 2024
c0a60fb
update main
valerianilucrezia Oct 14, 2024
209d906
minor updates Signatures config
kdavydzenka Oct 16, 2024
b57eb3f
Merge pull request #17 from caravagnalab/subworkflow_tests-bth
brandon-hastings Oct 17, 2024
f975110
genome handling update
kdavydzenka Oct 17, 2024
e10e5b2
minor update
kdavydzenka Oct 17, 2024
be33f02
minor update signatures
kdavydzenka Oct 22, 2024
afd1ac2
minor update signatures
kdavydzenka Oct 22, 2024
9d31736
add SPN01 samplesheet
valerianilucrezia Oct 24, 2024
03914eb
minor update BSgenome hg38 function call
kdavydzenka Oct 24, 2024
fbd962a
solving bug BSgenome hg38 SparseSignatures
kdavydzenka Oct 25, 2024
c54ef41
solving bug BSgenome hg38
kdavydzenka Oct 25, 2024
eb3ca26
mc
kdavydzenka Oct 25, 2024
615cb7b
branching tinc
Oct 30, 2024
cd5c3c3
Merge branch 'dev' of github.com:caravagnalab/tumourevo into dev
Oct 30, 2024
ecaf1cf
working tinc branching
Oct 30, 2024
714bdd1
new QC and driver workflows
valerianilucrezia Nov 3, 2024
c196e9a
removing "remove_tail" parameter
elena-buscaroli Nov 5, 2024
60cf7e5
solve annotate driver
valerianilucrezia Nov 5, 2024
472050a
add
valerianilucrezia Nov 5, 2024
e763581
new qc logic
valerianilucrezia Nov 5, 2024
bcb9560
Fix ctree-pyclonevi
giorgiagandolfi Nov 8, 2024
f1f258c
add filter flag + minor CNAqc & driver_annot
valerianilucrezia Nov 15, 2024
d11c8c0
Merge branch 'dev' of https://github.com/caravagnalab/tumourevo into dev
valerianilucrezia Nov 15, 2024
7c74b2a
Fix minor issue CNAqc,sigprofiler config
giorgiagandolfi Nov 18, 2024
b94ce4b
minor vcf
valerianilucrezia Nov 19, 2024
8573055
minor pileup
valerianilucrezia Nov 19, 2024
b3cae36
first documentation update
Nov 20, 2024
1b23f5f
Merge branch 'dev' of github.com:caravagnalab/tumourevo into dev
Nov 20, 2024
a07ab7b
minor formatter
valerianilucrezia Nov 20, 2024
8f7198d
sigprofiler
Nov 20, 2024
0ede756
Update output.md
giorgiagandolfi Nov 20, 2024
500050c
sigprofiler changes
Nov 20, 2024
078e1e9
Merge branch 'dev' of github.com:caravagnalab/tumourevo into dev
Nov 20, 2024
b7be366
SigProfiler config updates
kdavydzenka Nov 21, 2024
f6ea3cc
update
kdavydzenka Nov 21, 2024
36e1eb6
minor updates
kdavydzenka Nov 21, 2024
8abe3e7
minor updates
kdavydzenka Nov 22, 2024
98a1eda
minor updates
kdavydzenka Nov 22, 2024
3bb15a8
minor updates
kdavydzenka Nov 22, 2024
ed7bfa2
minor updates
kdavydzenka Nov 22, 2024
0e50cfe
minor updates
kdavydzenka Nov 22, 2024
0a452e9
minor updates
kdavydzenka Nov 22, 2024
5f7cea2
mc in documentation for local website
elena-buscaroli Nov 22, 2024
0c6458a
yml for website
elena-buscaroli Nov 22, 2024
b18096b
adding last version piepline schema
elena-buscaroli Nov 22, 2024
ee3112b
updating workflow
elena-buscaroli Nov 22, 2024
4ce82f2
adding --wrirable-tmpfs for proper Sigprofiler functioning
kdavydzenka Nov 25, 2024
4f97324
Fix typo in config file
giorgiagandolfi Nov 26, 2024
253fe76
add some links
nicola-calonaci Nov 26, 2024
4bd25f5
documnation typo
nicola-calonaci Nov 26, 2024
57431cf
documnation typo 2
nicola-calonaci Nov 26, 2024
acb8126
Update credits
nicola-calonaci Dec 3, 2024
1d58ade
remove files in home directory
nicola-calonaci Dec 5, 2024
cb9e22d
remove unutilised modules
nicola-calonaci Dec 5, 2024
f313bb4
remove unutilised bin files
nicola-calonaci Dec 5, 2024
45e84a1
config files updated
nicola-calonaci Dec 5, 2024
4163754
removed markdown documentation website
nicola-calonaci Dec 5, 2024
afacb0c
update usage documentation
nicola-calonaci Dec 5, 2024
9768ff3
update config files
nicola-calonaci Dec 5, 2024
3b8e880
update viber error strategy
nicola-calonaci Dec 5, 2024
fdb83f7
fixe old name evoverse to tumourevo
nicola-calonaci Dec 5, 2024
8673d43
add complete test + some minor
valerianilucrezia Dec 6, 2024
f30b5fb
Merge pull request #18 from caravagnalab/dev
nicola-calonaci Dec 6, 2024
37d1238
minor
valerianilucrezia Dec 9, 2024
a8206d5
Merge pull request #19 from caravagnalab/dev
nicola-calonaci Dec 9, 2024
fdddb61
Template update for nf-core/tools version 3.1.0
nf-core-bot Dec 12, 2024
f5e9335
add modules.json
valerianilucrezia Dec 12, 2024
ebd690c
grouping of params in schema
valerianilucrezia Dec 16, 2024
e103577
Template update for nf-core/tools version 3.1.1
nf-core-bot Dec 20, 2024
1b1dd25
Merge branch 'dev' into nf-core-template-merge-3.1.0
nicola-calonaci Dec 20, 2024
7e61aa5
Merge pull request #20 from nf-core/nf-core-template-merge-3.1.0
nicola-calonaci Dec 20, 2024
5602757
Merge branch 'nf-core:dev' into dev
valerianilucrezia Dec 20, 2024
e6f80d8
modules json update
valerianilucrezia Dec 20, 2024
e37f0d4
fix some tests
valerianilucrezia Dec 20, 2024
6dfdbaa
solved all pipeline test, missing only module test
valerianilucrezia Dec 20, 2024
dd97255
resolve test of module with nf-core modules patch
valerianilucrezia Dec 20, 2024
732caf6
Revert "resolve test of module with nf-core modules patch"
valerianilucrezia Dec 20, 2024
d526c37
add .diff files
valerianilucrezia Dec 20, 2024
5894fe3
add modules.json
valerianilucrezia Dec 20, 2024
60237f6
fix last 2 test
valerianilucrezia Dec 30, 2024
77ee2d6
fix pre-commit
valerianilucrezia Dec 30, 2024
037e056
change usage
valerianilucrezia Dec 30, 2024
131b602
minor
valerianilucrezia Dec 30, 2024
1e11d1f
adjust pre-commit p1
valerianilucrezia Dec 30, 2024
b145c97
fix pre-commit final
valerianilucrezia Dec 30, 2024
cc787a9
minor in docs
valerianilucrezia Jan 7, 2025
15ca6fc
minor schema
valerianilucrezia Jan 7, 2025
5f102db
minor in test config
valerianilucrezia Jan 7, 2025
5844459
remove check_max, + minors
valerianilucrezia Jan 9, 2025
737bebf
add params description of mobster/viber/pyclone + modify test
valerianilucrezia Jan 10, 2025
82c8f3b
add test_full
valerianilucrezia Jan 10, 2025
75edf2a
updating docker image and adding version.yml
elena-buscaroli Jan 13, 2025
ce58a4a
add ctree, TINC, joinCNAqc
valerianilucrezia Jan 14, 2025
06d77a6
adding version.yml to pyclone-vi
elena-buscaroli Jan 14, 2025
9235e0a
add yml and modify config
valerianilucrezia Jan 15, 2025
9ff326e
solve out problem
valerianilucrezia Jan 15, 2025
7d34604
update docker tag version + adding version.yml
kdavydzenka Jan 15, 2025
207dbb9
adding SparseSig, Sigprofiler params
kdavydzenka Jan 16, 2025
01a59f8
adding SparseSig, Sigprofiler params
kdavydzenka Jan 16, 2025
0b85989
uniform dir + minor updates
kdavydzenka Jan 16, 2025
a95d8cb
fix versions.yml in subclonal deconvolution
elena-buscaroli Jan 17, 2025
4a18f9a
fix versions yml
kdavydzenka Jan 19, 2025
ab58b77
Template update for nf-core/tools version 3.1.2
nf-core-bot Jan 20, 2025
071a3f2
fix yml version
kdavydzenka Jan 21, 2025
327e5a6
fix typo in annotate_driver
giorgiagandolfi Jan 21, 2025
46ca31a
adding version yml
kdavydzenka Jan 21, 2025
011dec5
adding version yml
kdavydzenka Jan 21, 2025
55ede79
fix trailing whitespace SigProfiler
kdavydzenka Jan 21, 2025
3e5ca68
adding version.yml to tinc
giorgiagandolfi Jan 22, 2025
6307915
fix sigprofiler module + mc subworkflow
giorgiagandolfi Jan 22, 2025
35e03a8
update ensemblvep.config
valerianilucrezia Jan 22, 2025
8c96e7e
fix sigprofiler output dir + versions.yml
giorgiagandolfi Jan 23, 2025
50eb4c9
finalize output.md
giorgiagandolfi Jan 23, 2025
08c3df0
Add resources selectors
elena-buscaroli Jan 23, 2025
f2ff14b
fixing trailing whitespaces
elena-buscaroli Jan 23, 2025
9129bea
nf-core modules patch
elena-buscaroli Jan 23, 2025
c7d9e34
Template update for nf-core/tools version 3.2.0
nf-core-bot Jan 27, 2025
98f8875
updating resources labels
elena-buscaroli Jan 27, 2025
1ac0b56
Merge pull request #24 from caravagnalab/dev
nicola-calonaci Jan 27, 2025
3311711
Merge branch 'dev' into nf-core-template-merge-3.2.0
nicola-calonaci Jan 27, 2025
3d51362
Merge pull request #23 from nf-core/nf-core-template-merge-3.2.0
nicola-calonaci Jan 27, 2025
b74cc13
Fixed plugin typo
nicola-calonaci Jan 27, 2025
a02c350
removing obsolete modules.config
elena-buscaroli Jan 29, 2025
c76acb9
updating test.config params
elena-buscaroli Jan 29, 2025
0a42b17
update modules.json removing old nf-core modules
elena-buscaroli Jan 29, 2025
eb273f6
adding templates
elena-buscaroli Jan 29, 2025
c222384
deleting auxiliary scripts included in templates
elena-buscaroli Jan 29, 2025
dd8583c
deleting auxiliary scripts included in templates
elena-buscaroli Jan 29, 2025
7a1f850
updating docker containers and setting templates
elena-buscaroli Jan 29, 2025
21c6732
update nextflow.config
elena-buscaroli Jan 29, 2025
7a5b5df
Merge pull request #25 from caravagnalab/dev
nicola-calonaci Jan 30, 2025
bfff6c9
first release checks
elena-buscaroli Jan 30, 2025
9cbb632
fix pre-commit
valerianilucrezia Jan 30, 2025
b81f17f
Merge pull request #26 from caravagnalab/dev
nicola-calonaci Jan 30, 2025
4f76f56
documentation typos and input csv fixed
vvvirgy Feb 21, 2025
67a7d4d
fixing documentation
vvvirgy Feb 25, 2025
7d05550
minor vcf_parser vep field
valerianilucrezia Mar 21, 2025
e637392
minor changes vcf2CNAqc
giorgiagandolfi Mar 24, 2025
c660c1a
mc mobster template script
giorgiagandolfi Apr 14, 2025
30d6368
mc viber template script
giorgiagandolfi Apr 14, 2025
6fcf262
minor config
valerianilucrezia May 4, 2025
b1aed61
minor to VIBER - solve opt error
valerianilucrezia May 22, 2025
e1fb504
minor updates sparsesignatures save mutCounts data
kdavydzenka May 26, 2025
02b5191
add bcftools filtering + change parser
valerianilucrezia Jun 9, 2025
a414bc9
minor
valerianilucrezia Jun 10, 2025
0cf0bbd
minor updates signature
kdavydzenka Jun 10, 2025
317d95b
minor updates signature
kdavydzenka Jun 10, 2025
bf32aba
minor updates signature
kdavydzenka Jun 10, 2025
4d38d6e
minor updates signature
kdavydzenka Jun 10, 2025
b968508
minor updates signature
kdavydzenka Jun 10, 2025
caff4a9
minor updates signature
kdavydzenka Jun 10, 2025
54617f8
minor updates Sigprofiler: DBS and ID fit
kdavydzenka Jun 13, 2025
e7d9c55
minor updates Sigprofiler: DBS and ID fit
kdavydzenka Jun 13, 2025
6066232
minor fix sigprofiler
kdavydzenka Jun 13, 2025
b6c529b
minor sigprofiler
valerianilucrezia Jun 15, 2025
f4e2fd6
modify driver filter
valerianilucrezia Jun 16, 2025
09cd468
minor sparcsesignature main_script.R
valerianilucrezia Jun 16, 2025
e23779b
minor driver
valerianilucrezia Jun 17, 2025
b3bac4e
minor update Sigprofiler
kdavydzenka Aug 1, 2025
3c3b2e9
add support to Battenberg calls
valerianilucrezia Aug 20, 2025
ea6dd15
add nf-core modules
valerianilucrezia Sep 17, 2025
83e6339
correct lint
valerianilucrezia Sep 17, 2025
265e4d5
minor
valerianilucrezia Sep 18, 2025
15dce65
new nf module
valerianilucrezia Sep 20, 2025
571e5ac
remove unused params
valerianilucrezia Sep 20, 2025
81585f6
solve lint
valerianilucrezia Sep 20, 2025
97fb97e
minor to docs
valerianilucrezia Sep 22, 2025
9c88736
minor nextflow.config
valerianilucrezia Sep 22, 2025
d22c07a
solve lint
valerianilucrezia Sep 22, 2025
83b4ef8
solve issue with nextflow.config
valerianilucrezia Sep 22, 2025
7def2b2
Merge pull request #35 from caravagnalab/dev
valerianilucrezia Sep 22, 2025
9aa2ad2
add new container and yml
valerianilucrezia Sep 22, 2025
81ac6a5
minor lint
valerianilucrezia Sep 22, 2025
c49bef6
prettier check
valerianilucrezia Sep 22, 2025
d2a6497
add conda support
valerianilucrezia Sep 22, 2025
ba7c7f6
solve test_full and change label
valerianilucrezia Sep 24, 2025
24dd7af
Merge pull request #36 from caravagnalab/dev
valerianilucrezia Sep 24, 2025
a981bb5
add last nf-core modules
valerianilucrezia Oct 27, 2025
9fadf37
update pipeline schema
valerianilucrezia Oct 27, 2025
5081ec9
vep patch
valerianilucrezia Oct 27, 2025
13b3c86
Merge pull request #38 from caravagnalab/dev
valerianilucrezia Oct 27, 2025
efee22e
solve vep error
valerianilucrezia Oct 30, 2025
3ac619e
Merge pull request #39 from caravagnalab/dev
valerianilucrezia Oct 30, 2025
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20 changes: 20 additions & 0 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
// Configure properties specific to VS Code.
"vscode": {
// Set *default* container specific settings.json values on container create.
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python"
},

// Add the IDs of extensions you want installed when the container is created.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
}
37 changes: 37 additions & 0 deletions .editorconfig
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
root = true

[*]
charset = utf-8
end_of_line = lf
insert_final_newline = true
trim_trailing_whitespace = true
indent_size = 4
indent_style = space

[*.{md,yml,yaml,html,css,scss,js}]
indent_size = 2

# These files are edited and tested upstream in nf-core/modules
[/modules/nf-core/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
[/subworkflows/nf-core/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset

[/assets/email*]
indent_size = unset

# ignore python and markdown
[*.{py,md}]
indent_style = unset

# ignore ro-crate metadata files
[**/ro-crate-metadata.json]
insert_final_newline = unset
3 changes: 3 additions & 0 deletions .gitattributes
Original file line number Diff line number Diff line change
@@ -1 +1,4 @@
*.config linguist-language=nextflow
*.nf.test linguist-language=nextflow
modules/nf-core/** linguist-generated
subworkflows/nf-core/** linguist-generated
6 changes: 6 additions & 0 deletions .github/.dockstore.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
# Dockstore config version, not pipeline version
version: 1.2
workflows:
- subclass: nfl
primaryDescriptorPath: /nextflow.config
publish: True
104 changes: 86 additions & 18 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -1,43 +1,50 @@
# nf-core/evoverse: Contributing Guidelines
# `nf-core/tumourevo`: Contributing Guidelines

Hi there!
Many thanks for taking an interest in improving nf-core/evoverse.
Many thanks for taking an interest in improving nf-core/tumourevo.

We try to manage the required tasks for nf-core/evoverse using GitHub issues, you probably came to this page when creating one.
We try to manage the required tasks for nf-core/tumourevo using GitHub issues, you probably came to this page when creating one.
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/evoverse then the best place to ask is on the nf-core Slack [#evoverse](https://nfcore.slack.com/channels/evoverse) channel ([join our Slack here](https://nf-co.re/join/slack)).
> [!NOTE]
> If you need help using or modifying nf-core/tumourevo then the best place to ask is on the nf-core Slack [#tumourevo](https://nfcore.slack.com/channels/tumourevo) channel ([join our Slack here](https://nf-co.re/join/slack)).

## Contribution workflow

If you'd like to write some code for nf-core/evoverse, the standard workflow is as follows:
If you'd like to write some code for nf-core/tumourevo, the standard workflow is as follows:

1. Check that there isn't already an issue about your idea in the [nf-core/evoverse issues](https://github.com/nf-core/evoverse/issues) to avoid duplicating work
* If there isn't one already, please create one so that others know you're working on this
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/evoverse repository](https://github.com/nf-core/evoverse) to your GitHub account
3. Make the necessary changes / additions within your forked repository
4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
1. Check that there isn't already an issue about your idea in the [nf-core/tumourevo issues](https://github.com/nf-core/tumourevo/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/tumourevo repository](https://github.com/nf-core/tumourevo) to your GitHub account
3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged

If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).

## Tests

You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:

```bash
nf-test test --profile debug,test,docker --verbose
```

When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

There are typically two types of tests that run:

### Lint Tests
### Lint tests

`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.

If any failures or warnings are encountered, please follow the listed URL for more documentation.

### Pipeline Tests
### Pipeline tests

Each `nf-core` pipeline should be set up with a minimal set of test-data.
`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
Expand All @@ -46,12 +53,73 @@ These tests are run both with the latest available version of `Nextflow` and als

## Patch

: warning: Only in the unlikely and regretful event of a release happening with a bug.
:warning: Only in the unlikely and regretful event of a release happening with a bug.

* On your own fork, make a new branch `patch` based on `upstream/master`.
* Fix the bug, and bump version (X.Y.Z+1).
* A PR should be made on `master` from patch to directly this particular bug.
- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
- Fix the bug, and bump version (X.Y.Z+1).
- Open a pull-request from `patch` to `main`/`master` with the changes.

## Getting help

For further information/help, please consult the [nf-core/evoverse documentation](https://nf-co.re/nf-core/evoverse/docs) and don't hesitate to get in touch on the nf-core Slack [#evoverse](https://nfcore.slack.com/channels/evoverse) channel ([join our Slack here](https://nf-co.re/join/slack)).
For further information/help, please consult the [nf-core/tumourevo documentation](https://nf-co.re/tumourevo/usage) and don't hesitate to get in touch on the nf-core Slack [#tumourevo](https://nfcore.slack.com/channels/tumourevo) channel ([join our Slack here](https://nf-co.re/join/slack)).

## Pipeline contribution conventions

To make the `nf-core/tumourevo` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.

### Adding a new step

If you wish to contribute a new step, please use the following coding standards:

1. Define the corresponding input channel into your new process from the expected previous process channel.
2. Write the process block (see below).
3. Define the output channel if needed (see below).
4. Add any new parameters to `nextflow.config` with a default (see below).
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`.
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`.

### Default values

Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.

Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.

### Default processes resource requirements

Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.

The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.

### Naming schemes

Please use the following naming schemes, to make it easy to understand what is going where.

- initial process channel: `ch_output_from_<process>`
- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`

### Nextflow version bumping

If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`

### Images and figures

For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

## GitHub Codespaces

This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.

To get started:

- Open the repo in [Codespaces](https://github.com/nf-core/tumourevo/codespaces)
- Tools installed
- nf-core
- Nextflow

Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
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name: Bug report
description: Report something that is broken or incorrect
labels: bug
body:
- type: markdown
attributes:
value: |
Before you post this issue, please check the documentation:

- [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [nf-core/tumourevo pipeline documentation](https://nf-co.re/tumourevo/usage)
- type: textarea
id: description
attributes:
label: Description of the bug
description: A clear and concise description of what the bug is.
validations:
required: true

- type: textarea
id: command_used
attributes:
label: Command used and terminal output
description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
render: console
placeholder: |
$ nextflow run ...

Some output where something broke

- type: textarea
id: files
attributes:
label: Relevant files
description: |
Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.

- type: textarea
id: system
attributes:
label: System information
description: |
* 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, Charliecloud, or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of nf-core/tumourevo _(eg. 1.1, 1.5, 1.8.2)_
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contact_links:
- name: Join nf-core
url: https://nf-co.re/join
about: Please join the nf-core community here
- name: "Slack #tumourevo channel"
url: https://nfcore.slack.com/channels/tumourevo
about: Discussion about the nf-core/tumourevo pipeline
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name: Feature request
description: Suggest an idea for the nf-core/tumourevo pipeline
labels: enhancement
body:
- type: textarea
id: description
attributes:
label: Description of feature
description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
validations:
required: true
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# nf-core/evoverse pull request
<!--
# nf-core/tumourevo pull request

Many thanks for contributing to nf-core/evoverse!
Many thanks for contributing to nf-core/tumourevo!

Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).

Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.

Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/tumourevo/tree/master/.github/CONTRIBUTING.md)
-->

## PR checklist

- [ ] This comment contains a description of changes (with reason)
- [ ] 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 necessary, also make a PR on the [nf-core/evoverse branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/evoverse)
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
- [ ] Make sure your code lints (`nf-core lint .`).
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated

**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/evoverse/tree/master/.github/CONTRIBUTING.md)
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/tumourevo/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/tumourevo _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core pipelines lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
- [ ] `README.md` is updated (including new tool citations and authors/contributors).
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