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[pull] dev from nf-core:dev #8

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298028e
refact: move subworkflow to its own directory
atrigila Nov 27, 2024
1aca475
Merge pull request #541 from atrigila/remove_local_rrnatranscripts
atrigila Nov 28, 2024
914aea0
Merge branch 'dev' into stringtie_workflow_test
atrigila Nov 28, 2024
320b4ca
add no_cosmic option/update fusionreport
rannick Nov 28, 2024
23b9d3e
update changelog
rannick Nov 28, 2024
6514cbb
add option to usage documentation
rannick Nov 28, 2024
cb6671b
prettier
rannick Nov 28, 2024
288c707
remove check for . in .fastq.gz fileformat
rannick Nov 28, 2024
c739e6c
update changelog
rannick Nov 28, 2024
eece50d
Updated tests and fusion containers and conda versions, general confi…
nschcolnicov Nov 28, 2024
8a87c11
test: update nf-core picard/collectrnaseqmetrics to include tests
atrigila Nov 28, 2024
74195e7
docs: update changelog
atrigila Nov 28, 2024
3029fdf
Merge pull request #551 from atrigila/picard
atrigila Nov 28, 2024
3058f0c
Merge branch 'dev' of https://github.com/nf-core/rnafusion into gener…
nschcolnicov Nov 28, 2024
704d23d
Updated ci.yml and nftests
nschcolnicov Nov 28, 2024
56ea6b4
Pulled from optional_cosmic branch
nschcolnicov Nov 28, 2024
fa4f771
Update tests
nschcolnicov Nov 28, 2024
460b645
add parameter interpretation in modules.config
rannick Nov 29, 2024
0c90acb
Merge branch 'dev' into refactor-references
rannick Nov 29, 2024
96184d4
Merge branch 'dev' into flexible_fq_names
rannick Nov 29, 2024
f35833b
Merge pull request #548 from nf-core/flexible_fq_names
rannick Nov 29, 2024
098a92d
add skip_vcf param
rannick Nov 29, 2024
7e1fa66
changelog
rannick Nov 29, 2024
3d9dce5
Merge branch 'dev' into stringtie_workflow_test
atrigila Nov 29, 2024
228f5f4
Merge pull request #554 from nf-core/vcf_optional
rannick Nov 29, 2024
b82235e
Merge branch 'dev' into stringtie_workflow_test
atrigila Nov 29, 2024
c5ed11b
Merge branch 'dev' into fusion_report_optional_cosmic
rannick Nov 29, 2024
6bbef42
Merge pull request #547 from nf-core/fusion_report_optional_cosmic
rannick Nov 29, 2024
b921165
Merge branch 'dev' into stringtie_workflow_test
atrigila Nov 29, 2024
345a562
fix: fix bug in `fusionreport_download` when building references
atrigila Nov 29, 2024
b3d0f94
docs: update changelog
atrigila Nov 29, 2024
88deea5
ci: add `--no_cosmic` flag for tests in CI
atrigila Nov 29, 2024
90d309d
Update test_build test and add it to ci
nschcolnicov Nov 29, 2024
9b4180a
Pulled from dev
nschcolnicov Nov 29, 2024
ff75e38
Merge pull request #558 from atrigila/build_references_no_cosmic
atrigila Nov 29, 2024
914ec5e
Merge branch 'dev' into stringtie_workflow_test
atrigila Nov 29, 2024
18bf7c0
Update test_build_stub
nschcolnicov Nov 29, 2024
d7f791f
Pulled from dev
nschcolnicov Nov 29, 2024
6e4f519
refactor: `FUSIONREPORT_DOWNLOAD` accepts cosmic credentials via `ext…
atrigila Nov 29, 2024
1649e77
docs: update changelog
atrigila Nov 29, 2024
dea4f09
Merge pull request #559 from atrigila/fusionreport_no_cosmic
atrigila Dec 2, 2024
703b57e
test: add nf-test to `FUSIONREPORT_DOWNLOAD`
atrigila Dec 2, 2024
9e7fe54
refactor: emit outputs separately
atrigila Dec 2, 2024
8d0e6f7
docs: update changelog
atrigila Dec 2, 2024
5b74d37
fix: use wildcard to get rrna gtf
atrigila Dec 2, 2024
a211077
docs: update changelog
atrigila Dec 2, 2024
52108b6
fix: add gffread config
atrigila Dec 2, 2024
4b19e5a
docs: update changelog
atrigila Dec 2, 2024
96f6f9f
fix: update fix from nf-core/modules
atrigila Dec 2, 2024
d026414
Merge branch 'dev' of https://github.com/nf-core/rnafusion into gener…
nschcolnicov Dec 2, 2024
5361818
Merge pull request #543 from atrigila/stringtie_workflow_test
atrigila Dec 3, 2024
132b79a
Merge branch 'dev' into fix_rrnatranscript_bug
atrigila Dec 3, 2024
a56eb97
test: add config to fusionreport nf-test
atrigila Dec 3, 2024
26b8c54
Merge branch 'dev' into fusionreport_download_test
atrigila Dec 3, 2024
2be6ceb
Added test_build test
nschcolnicov Dec 3, 2024
d379b8f
Pulled from dev
nschcolnicov Dec 3, 2024
144c780
Update snaps
nschcolnicov Dec 3, 2024
b06bc4e
Updated rrnatranscripts
nschcolnicov Dec 3, 2024
2519d66
Use latest-stable instead of latest-everything in CI
nschcolnicov Dec 3, 2024
b4ff921
test: add latest-stable to fix issues in ci
atrigila Dec 3, 2024
5557d17
Merge pull request #567 from atrigila/fix_gffread_bug
atrigila Dec 3, 2024
837507d
Merge branch 'dev' into fix_rrnatranscript_bug
atrigila Dec 3, 2024
d742f87
Merge pull request #562 from atrigila/fusionreport_download_test
atrigila Dec 3, 2024
9602378
Merge branch 'dev' into fix_rrnatranscript_bug
atrigila Dec 3, 2024
489161e
Merge pull request #564 from atrigila/fix_rrnatranscript_bug
atrigila Dec 3, 2024
bd419d4
Addressing PR comments
nschcolnicov Dec 3, 2024
0f88731
Updated snaps
nschcolnicov Dec 3, 2024
4b607dd
change module structure
alanmmobbs93 Dec 3, 2024
0a3f3e2
update modules
alanmmobbs93 Dec 3, 2024
e63d5a9
run test and update workflow
alanmmobbs93 Dec 3, 2024
4c68f9a
Pulled from dev
nschcolnicov Dec 3, 2024
474a89e
add missing conda lines
nschcolnicov Dec 3, 2024
7c942d8
update test to constant poprtion
alanmmobbs93 Dec 3, 2024
63d84df
Merge branch 'dev' into qc_subworkflow_test
alanmmobbs93 Dec 4, 2024
4d08dfd
update changelog
alanmmobbs93 Dec 4, 2024
13588e4
Remove line from changelog
alanmmobbs93 Dec 4, 2024
be02390
Update snaps and profile resources
nschcolnicov Dec 4, 2024
9683f58
Add salmon index skip parameter
nschcolnicov Dec 4, 2024
a8f9bc4
add md5 to snaps
alanmmobbs93 Dec 4, 2024
40e30a3
Update comments on the subworkflow
alanmmobbs93 Dec 4, 2024
3c630e9
remove commented lines
alanmmobbs93 Dec 4, 2024
c8247c8
update test snaps
alanmmobbs93 Dec 4, 2024
fa2c71d
Merge pull request #568 from alanmmobbs93/qc_subworkflow_test
alanmmobbs93 Dec 4, 2024
d8bfba2
change module structure and test
alanmmobbs93 Dec 5, 2024
06ba247
create snap
alanmmobbs93 Dec 5, 2024
ea4487f
fix folder name
alanmmobbs93 Dec 5, 2024
e033e94
update test for skipping fastp
alanmmobbs93 Dec 5, 2024
8f3c70e
update changelog
alanmmobbs93 Dec 5, 2024
cc916e6
fix: change hardcoded container for seqera container, mv conda to env…
atrigila Dec 5, 2024
2010578
docs: update changelog
atrigila Dec 5, 2024
ca0870b
fix: specify version 1.33 in bioconda and seqera container
atrigila Dec 5, 2024
90aced2
add new test
alanmmobbs93 Dec 5, 2024
e2a255b
Merge pull request #572 from alanmmobbs93/trim_workflow_test
alanmmobbs93 Dec 5, 2024
8e1aa7e
Merge pull request #550 from nf-core/general_fixes
nschcolnicov Dec 5, 2024
6189acf
refactor: emit a directory and add meta
atrigila Dec 5, 2024
2620dcf
test: add fusionreport nf-test
atrigila Dec 5, 2024
9673b85
update module
alanmmobbs93 Dec 5, 2024
275889e
update subworkflow
alanmmobbs93 Dec 5, 2024
a7e1b53
Merge pull request #574 from alanmmobbs93/update_arriba-arriba_module
apeltzer Dec 5, 2024
d290fcd
update fusioncatcher container
rannick Dec 6, 2024
19757b6
Merge branch 'refactor-references' of https://github.com/nf-core/rnaf…
rannick Dec 6, 2024
75b65f7
test: add test to `FUSIONREPORT_DETECT`
atrigila Dec 6, 2024
2c860bb
docs: update changelog
atrigila Dec 6, 2024
e80fd83
change module structure and first test attempt
alanmmobbs93 Dec 6, 2024
a6c082e
update test and generate first snap
alanmmobbs93 Dec 6, 2024
1a1314e
fix merge conflicts
rannick Dec 9, 2024
be6e102
fix linting issues
rannick Dec 9, 2024
41523f9
prettier
rannick Dec 9, 2024
55b0562
update tests after fixing fasta in github
alanmmobbs93 Dec 9, 2024
55db5b5
update changelog
alanmmobbs93 Dec 9, 2024
739c482
Merge pull request #573 from atrigila/fusioncatcher_download
atrigila Dec 9, 2024
ce331dc
docs: udpdate changelog
atrigila Dec 9, 2024
54b1932
Merge branch 'dev' into fusionreport_detect
atrigila Dec 9, 2024
d7a06ea
test: update nf-test
atrigila Dec 9, 2024
df269a9
update test excluding samtools
alanmmobbs93 Dec 9, 2024
715be91
Merge branch 'dev' into add_test_arriba_workflow
alanmmobbs93 Dec 9, 2024
cc5d4b9
Merge pull request #577 from atrigila/fusionreport_detect
atrigila Dec 9, 2024
86c299d
update comments
rannick Dec 9, 2024
4c3bc68
Merge branch 'dev' into refactor-references
rannick Dec 9, 2024
aecc7ef
update test to include cram files
alanmmobbs93 Dec 9, 2024
743113a
Merge branch 'dev' into add_test_arriba_workflow
alanmmobbs93 Dec 9, 2024
9d87a37
remove original script
alanmmobbs93 Dec 9, 2024
3a45cbb
fix changelog
alanmmobbs93 Dec 9, 2024
032583a
fix: fix container versions
atrigila Dec 10, 2024
6dcac4f
test: add nf-test initial draft
atrigila Dec 10, 2024
35b5d9c
fix i/o in channels
rannick Dec 10, 2024
cdea091
Merge branch 'refactor-references' of https://github.com/nf-core/rnaf…
rannick Dec 10, 2024
24a4610
test build removed from ci as build_references happens before the run
rannick Dec 10, 2024
94fe609
remove double nested folder
rannick Dec 10, 2024
e522449
update changelog
rannick Dec 10, 2024
18ab239
update changelog
rannick Dec 10, 2024
76cf2aa
update snapshots, add meta
rannick Dec 10, 2024
56ed001
remove trash files
rannick Dec 10, 2024
2e928ed
update test
rannick Dec 10, 2024
82c1fc0
update download snapshot
rannick Dec 10, 2024
87f5ff8
update detect snapshot
rannick Dec 10, 2024
23c4014
use stubs
rannick Dec 10, 2024
d52f0a0
update changelog, first step
rannick Dec 10, 2024
5409f8c
update GTF_TO_REFFLAT options, update snapshots
rannick Dec 10, 2024
ef5ab96
update star in snapshot
rannick Dec 10, 2024
1ae795e
Merge pull request #581 from nf-core/fix_fusionreport
rannick Dec 10, 2024
58aab76
fix: simplify starfusion module
atrigila Dec 10, 2024
7ff8be1
tests: update nf-test starfusion
atrigila Dec 10, 2024
0770939
refactor: add stubs and ext.args
atrigila Dec 10, 2024
5b0b9e1
docs: update meta.yml
atrigila Dec 10, 2024
572e8df
test: update snapshots
atrigila Dec 10, 2024
5f6857e
refactor: revert add nf-test initial draft
atrigila Dec 10, 2024
117884c
add human_gencode_filter to starfusion build
rannick Dec 11, 2024
4fab8b6
Merge branch 'dev' into refactor-references
rannick Dec 11, 2024
3788788
remove test.xml
rannick Dec 11, 2024
dcd9e21
Merge branch 'refactor-references' of https://github.com/nf-core/rnaf…
rannick Dec 11, 2024
8e9be7c
update snap
rannick Dec 11, 2024
5cdf95a
try updating snapshot again
rannick Dec 11, 2024
c257c62
fix: add versions to dependencies
atrigila Dec 11, 2024
f2df932
feat: add fusion annot lib as an external param
atrigila Dec 11, 2024
9dc94cb
docs: add param type and where to get it
atrigila Dec 11, 2024
d2a7bd4
test: run starfusion in test_build
atrigila Dec 11, 2024
cf71e62
refactor: add metamap to output
atrigila Dec 11, 2024
ef36aed
test: update tests
atrigila Dec 11, 2024
1b649b4
test: add fusion_annot_lib so that stub does not fail
atrigila Dec 11, 2024
4fd46f4
PR changes
alanmmobbs93 Dec 11, 2024
d9cedb1
Merge branch 'dev' into add_test_arriba_workflow
alanmmobbs93 Dec 11, 2024
077eb17
Merge pull request #578 from alanmmobbs93/add_test_arriba_workflow
alanmmobbs93 Dec 11, 2024
ec373b3
fix: add dependencies versions and update container
atrigila Dec 12, 2024
99033b5
refactor: add readlength as ext.args
atrigila Dec 12, 2024
17dd8b4
test: update stub structure
atrigila Dec 12, 2024
4f078b5
test: add nf-test to `starfusion`
atrigila Dec 16, 2024
9f3a0d6
docs: update changelog
atrigila Dec 16, 2024
a2217fd
Merge branch 'dev' into starfusion_detect
atrigila Dec 16, 2024
dbb45c9
fix test config resources
nvnieuwk Dec 17, 2024
4245c54
add ctatsplicing module
nvnieuwk Dec 17, 2024
fa128b6
avoid using meta for remapping
rannick Dec 17, 2024
f025945
implement ctatsplicing
nvnieuwk Dec 17, 2024
f2bc314
fix merge conflicts
rannick Dec 17, 2024
3268a45
fix pre-commit
nvnieuwk Dec 17, 2024
a84033b
Update nextflow.config
nvnieuwk Dec 17, 2024
4247b12
update changelog
nvnieuwk Dec 17, 2024
af80d58
Merge branch 'new-module-ctat-splicing' of github.com:nf-core/rnafusi…
nvnieuwk Dec 17, 2024
5e58fbf
use docker containers for fusioninspector, fusioncatcher and starfusion
rannick Dec 17, 2024
081249a
update changelog
rannick Dec 17, 2024
33f4b57
revert change
rannick Dec 17, 2024
ff69a60
revert change
rannick Dec 17, 2024
0db19d9
make ctatsplicing possible with arriba input
nvnieuwk Dec 17, 2024
b7383eb
test to see if dependencies are working with starfusion1.14 onluy
rannick Dec 17, 2024
17ef233
use custom container for fusioncatcher, fix typo
rannick Dec 17, 2024
a67cc0f
add dependencies explicitly
rannick Dec 18, 2024
bf05cb7
update bin path
rannick Dec 18, 2024
b6db271
Merge branch 'dev' into fusioninspector
rannick Dec 18, 2024
235a752
bin path to prep_genome_lib not working with singularity wave contain…
rannick Dec 18, 2024
a0698b1
propagate container of starfusion to fusioninspector
rannick Dec 18, 2024
b2a075b
update star
rannick Dec 18, 2024
853e48d
update changelog
rannick Dec 18, 2024
9cad032
update changelog
rannick Dec 18, 2024
f2b5ed5
fix: update starfusion container declaration to latest nf-core standards
atrigila Dec 18, 2024
350de1b
add some views to debug the full run
nvnieuwk Dec 19, 2024
a08c02f
update dependencies
rannick Dec 19, 2024
34109cd
update path again
rannick Dec 19, 2024
0ea316e
add minimap
rannick Dec 19, 2024
27b3f8b
propagate container/env change
rannick Dec 19, 2024
1ede9b4
Merge pull request #588 from nf-core/add_singularity_containers
rannick Dec 19, 2024
0596694
Merge branch 'dev' into fusioninspector
rannick Dec 19, 2024
b8bae77
try to fix issue with arriba output
nvnieuwk Dec 19, 2024
00673c6
Update conf/modules.config
atrigila Dec 19, 2024
0006394
remove views
nvnieuwk Dec 19, 2024
f3f5714
fix merge conflicts
rannick Dec 19, 2024
05e0e61
remove breaking ifEmpties
nvnieuwk Dec 19, 2024
f8dd516
update changelog
rannick Dec 19, 2024
62fdf33
remove def
nvnieuwk Dec 19, 2024
d62c4b5
update changelog, retrofit trim_workflowo
rannick Dec 19, 2024
8155168
redo star changes
nvnieuwk Dec 19, 2024
e386c81
use bam from starfusion
nvnieuwk Dec 19, 2024
2c01b3c
use placeholder and add TODO for update
rannick Dec 19, 2024
62ee76f
create junctions with arriba for ctatsplicing
nvnieuwk Dec 19, 2024
612723f
Merge branch 'dev' into starfusion_detect
rannick Dec 19, 2024
19d1cc1
do not create an index in ctat splicing
nvnieuwk Dec 19, 2024
1237fef
fix: add full path to module to avoid changing nf-tests
atrigila Dec 19, 2024
89b2649
feat: use previous `.dat.gz` file as default
atrigila Dec 19, 2024
4d9b7c8
Merge branch 'fusioninspector' of https://github.com/atrigila/rnafusi…
atrigila Dec 19, 2024
fb64ca6
test: update snapshot
atrigila Dec 19, 2024
34121d1
Merge pull request #583 from atrigila/fusioninspector
atrigila Dec 19, 2024
d08b0b2
Merge branch 'dev' into starfusion_detect
atrigila Dec 19, 2024
dea8445
feat: allow to use either reads or junction files
atrigila Dec 19, 2024
9aff4ea
test: update snaps
atrigila Dec 19, 2024
a369518
docs: update changelog
atrigila Dec 19, 2024
6f2a382
fix: add junction if provided
atrigila Dec 19, 2024
9dc352f
readd indexing to ctat & sort arriba bam
nvnieuwk Dec 20, 2024
45e4879
Merge branch 'dev' into new-module-ctat-splicing
nvnieuwk Dec 20, 2024
38de48b
fix merge conflicts
rannick Dec 20, 2024
de5d6d5
add species as parameter
rannick Dec 20, 2024
9ea1f3b
remove ctatsplicing check from starfusion
nvnieuwk Dec 20, 2024
1c98fc7
clarify changelog
nvnieuwk Dec 20, 2024
74d4534
update docs
nvnieuwk Dec 20, 2024
a209fea
prettyyy
nvnieuwk Dec 20, 2024
bdae293
fix some issues with channels
rannick Dec 20, 2024
509a792
add species to schema
rannick Dec 20, 2024
8776835
fix erroneous addition of meta
rannick Dec 20, 2024
3f4406a
Merge pull request #587 from nf-core/new-module-ctat-splicing
nvnieuwk Dec 20, 2024
60f0da6
Merge branch 'dev' into refactor-references
rannick Dec 20, 2024
ab65540
fixes
rannick Dec 20, 2024
ed4855e
Update modules/local/starfusion/detect/main.nf
atrigila Dec 20, 2024
f42d9dc
Update modules/local/starfusion/detect/main.nf
atrigila Dec 20, 2024
945bf0f
Merge branch 'dev' into starfusion_detect
atrigila Dec 20, 2024
a815895
Merge pull request #586 from atrigila/starfusion_detect
atrigila Dec 20, 2024
31b400a
Merge branch 'dev' into refactor-references
rannick Dec 20, 2024
31d29aa
Merge pull request #505 from nf-core/refactor-references
rannick Dec 20, 2024
910cf8d
test: add nf-test for starfusion subworkflow
atrigila Dec 23, 2024
e23ff39
chore: add todo message
atrigila Dec 23, 2024
d5ce9dc
fix: remove commited debug view
atrigila Dec 23, 2024
ef88977
docs: update changelog
atrigila Dec 23, 2024
dba1d63
Merge pull request #597 from atrigila/sbwf_starfusion
atrigila Dec 23, 2024
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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"]
}
}
}
33 changes: 33 additions & 0 deletions .editorconfig
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
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
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
128 changes: 103 additions & 25 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -1,47 +1,125 @@
# nf-core/rnafusion: Contributing Guidelines

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

We try to manage the required tasks for nf-core/rnafusion 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/rnafusion then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
We try to manage the required tasks for nf-core/rnafusion 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 ;)

> [!NOTE]
> If you need help using or modifying nf-core/rnafusion then the best place to ask is on the nf-core Slack [#rnafusion](https://nfcore.slack.com/channels/rnafusion) channel ([join our Slack here](https://nf-co.re/join/slack)).

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

1. Check that there isn't already an issue about your idea in the
[nf-core/rnafusion issues](https://github.com/nf-core/rnafusion/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 the [nf-core/rnafusion repository](https://github.com/nf-core/rnafusion) 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.
If you'd like to write some code for nf-core/rnafusion, the standard workflow is as follows:

If you're not used to this workflow with git, you can start with some [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/) or even their [excellent interactive tutorial](https://try.github.io/).
1. Check that there isn't already an issue about your idea in the [nf-core/rnafusion issues](https://github.com/nf-core/rnafusion/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/rnafusion repository](https://github.com/nf-core/rnafusion) 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
When you create a pull request with changes, [Travis CI](https://travis-ci.org/) will run automatic 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, BUT DON'T FORGET TO ADD THE PARAMETERS cosmic_username AND cosmic_passwd in tests/main.nf.test.

```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
The nf-core has a [set of guidelines](http://nf-co.re/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.
### 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 pipelines lint <pipeline-directory>` command.

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

### Pipeline Tests
Each nf-core pipeline should be set up with a minimal set of test-data.
Travis CI then runs the pipeline on this data to ensure that it exists successfully.
### 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.
If there are any failures then the automated tests fail.
These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.
These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.

## Patch

: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.

## Getting help
For further information/help, please consult the [nf-core/rnafusion documentation](https://github.com/nf-core/rnafusion#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).

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

## Pipeline contribution conventions

To make the nf-core/rnafusion 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 in `nextflow.config` under the `params` scope.

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/rnafusion/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/rnafusion pipeline documentation](https://nf-co.re/rnafusion/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/rnafusion _(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 #rnafusion channel"
url: https://nfcore.slack.com/channels/rnafusion
about: Discussion about the nf-core/rnafusion pipeline
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name: Feature request
description: Suggest an idea for the nf-core/rnafusion 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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Many thanks to contributing to nf-core/rnafusion!
<!--
# nf-core/rnafusion pull request

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
Many thanks for contributing to nf-core/rnafusion!

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/rnafusion/tree/master/.github/CONTRIBUTING.md)
-->

## PR checklist
- [ ] 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/rnafusion branch on the nf-core/test-datasets repo]( https://github.com/nf-core/test-datasets/pull/new/nf-core/rnafusion)
- [ ] 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:** https://github.com/nf-core/rnafusion/tree/master/.github/CONTRIBUTING.md

- [ ] 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/rnafusion/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/rnafusion _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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