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Pseudo-review: first release - #88

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ewels wants to merge 382 commits into

pesudo-review-template-4.3.0from

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Commits on Jul 6, 2026

run commit fix
antoniasaracco
committed
f70feec
update nextflow version
antoniasaracco
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5513e64
Merge branch 'nf-core:implement_rclone' into implement_rclone
antoniasaracco
authored
70f8209
move rclone to local folder
antoniasaracco
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3a98fc6
run fix lint
antoniasaracco
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80b09ca
fix
antoniasaracco
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03a79a3

Commits on Jul 7, 2026

Update CHANGELOG with new features and fixes
antoniasaracco
authored
db581e8
Merge pull request #38 from antoniasaracco/implement_rclone
antoniasaracco
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dad2dc2
Merge remote-tracking branch 'upstream/dev' into report
delfiterradas
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4968204
Do not expert plots for multiqc and update snapshots
delfiterradas
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7da1d5a
Ignore linting for multiqc_config file
delfiterradas
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b550108
Remove notes from report
delfiterradas
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018e1af
Update multiqc module
delfiterradas
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c889174
Update citations
delfiterradas
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a7d6b58

Commits on Jul 8, 2026

Update CHANGELOG
delfiterradas
authored
27c8a9e
Merge pull request #41 from delfiterradas/report
delfiterradas
authored
9fee02b

Commits on Jul 14, 2026

import rclone_copy from nf core
antoniasaracco
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4553595
update changelog
antoniasaracco
committed
23d9d02

Commits on Jul 15, 2026

Commits on Jul 16, 2026

improve samplesheet parsing
zxBIB
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6d6f22d
Install `rclone` modules from nf-core
delfiterradas
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c244677
Revert changes made to conf containers
delfiterradas
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6b2e34b
Remove whitespace
delfiterradas
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1e0b28d
update snapshots
antoniasaracco
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e9456f2
update rclone copy
antoniasaracco
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9ad475c
update containers files
antoniasaracco
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f3a4727
remove withespace
antoniasaracco
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e294dee
Update CHANGELOG.md
delfiterradas
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684bdfd
Merge pull request #46 from antoniasaracco/import_rclone_copy
delfiterradas
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5d1da84
Update snapshots
delfiterradas
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27eed24
Merge remote-tracking branch 'upstream/dev' into rclone_check
delfiterradas
committed
55ac0bc
Fix container config files
delfiterradas
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ce56247
Update CHANGELOG.md
delfiterradas
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6624c41
Update CHANGELOG.md
delfiterradas
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36491b2
Make report descriptions clearer
delfiterradas
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a185ae8
Update methods description
delfiterradas
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97909c7
Create helper function to parse rclone output
delfiterradas
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5981d68
Fix typo
delfiterradas
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4b960ac

Commits on Jul 17, 2026

Merge pull request #49 from delfiterradas/rclone_check
atrigila
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e91d1f9
add color to multiqc report
atrigila
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25c08ec
Merge pull request #54 from atrigila/multiqc_report
atrigila
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656582d
update multiqc report
atrigila
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f678fee
docs: document datasync pipeline
antoniasaracco
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1fa3a48
docs: expand rclone remote configuration guidance
antoniasaracco
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447fa14
Merge pull request #55 from atrigila/multiqc_report
delfiterradas
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ce6bd4a

Commits on Jul 20, 2026

add edge test cases
atrigila
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0506dc7
update changelog
atrigila
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4b9c262
Merge pull request #57 from atrigila/add_nf-tests
atrigila
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b1120ce

Commits on Jul 21, 2026

Commits on Jul 22, 2026

Update README.md
antoniasaracco
authored
be56cb8
Update usage.md
antoniasaracco
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ca5f192
Update CHANGELOG.md
antoniasaracco
authored
ceb7d63
Update README.md
antoniasaracco
authored
f10bc2c
Update CHANGELOG.md
antoniasaracco
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c0cb403
Update README.md
antoniasaracco
authored
7dea7d8
Update output.md
antoniasaracco
authored
6ff8774
Update rclone modules and inputs in workflow
delfiterradas
committed
790a648
Update README.md
antoniasaracco
authored
eb934c8
Add files via upload
antoniasaracco
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4f16da8
Update README.md
antoniasaracco
authored
40af01f
Update README.md

antoniasaracco
and
atrigila
authored
fdb0a8d
Update README.md
antoniasaracco
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51b9fdf
Update README.md
antoniasaracco
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b558b3c
Update README.md

antoniasaracco
and
atrigila
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c3c93c9
Update snapshots
delfiterradas
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c6d12e3
Update README.md
antoniasaracco
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fd9b00c
Update docs/usage.md

antoniasaracco
and
atrigila
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110eaf8
Update docs/usage.md

antoniasaracco
and
atrigila
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cfd37ed

Commits on Jul 23, 2026

Apply suggestion
delfiterradas
committed
fa3c7e8
Merge pull request #61 from delfiterradas/update_rclone
delfiterradas
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fbf1c85
Update usage.md
antoniasaracco
authored
65d43d6
Update usage.md
antoniasaracco
authored
673cd47
Update usage.md
antoniasaracco
authored
f59d297
Update usage.md
antoniasaracco
authored
13c6314
Update usage.md
antoniasaracco
authored
e4b7ddd
Add files via upload
antoniasaracco
authored
90155e6
Delete docs/images/metromap_style_pipeline_workflow_components.drawio.png
antoniasaracco
authored
dd4a552
Update README.md
antoniasaracco
authored
64a41d6
Update output.md
antoniasaracco
authored
3baecb6

Commits on Jul 24, 2026

Update usage.md
antoniasaracco
authored
18e1b6b
Add files via upload
antoniasaracco
authored
98c775e
Update output.md
antoniasaracco
authored
331046b
Update output.md
antoniasaracco
authored
c184be4
Update usage.md
antoniasaracco
authored
10631f6
Update docs/output.md

antoniasaracco
and
atrigila
authored
d5daf90
Update docs/output.md

antoniasaracco
and
atrigila
authored
db62912
Update docs/output.md

antoniasaracco
and
atrigila
authored
01f6cda
Update docs/usage.md

antoniasaracco
and
atrigila
authored
679d210
Update docs/output.md

antoniasaracco
and
atrigila
authored
083f023
Update docs/output.md

antoniasaracco
and
atrigila
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70519cc
Update docs/output.md

antoniasaracco
and
atrigila
authored
1983a4f
Update docs/usage.md

antoniasaracco
and
atrigila
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e9a292a
Delete docs/images/datasync-metromap.drawio.png
antoniasaracco
authored
e5dd017
Add files via upload
antoniasaracco
authored
359a1b0
Delete docs/images/datasync-metromap.drawio.png
antoniasaracco
authored
2b553c3
Add files via upload
antoniasaracco
authored
c6dcf3d
Delete docs/images/datasync-metromap.drawio.png
antoniasaracco
authored
2ff8c91
Add files via upload
antoniasaracco
authored
d11002a
Delete docs/images/datasync-metromap.drawio.png
antoniasaracco
authored
a720a7b
Add files via upload
antoniasaracco
authored
c38ce42
Delete docs/images/datasync-metromap.drawio.png
antoniasaracco
authored
316efd3
Add files via upload
antoniasaracco
authored
1a69b5e
Update README.md
antoniasaracco
authored
589fb05
Update output.md
antoniasaracco
authored
3fe2a48
Update output.md
antoniasaracco
authored
1da035b

Commits on Jul 27, 2026

Commits on Jul 28, 2026

Remove vulnerable PR-comment artifact pattern
nf-core-bot
committed
556e2ba
Merge pull request #68 from nf-core/patch
mashehu
authored
8f34b11
Apply suggestions from code review

apeltzer
and
atrigila
authored
426b319
Merge branch 'nf-core:dev' into create_documentation
antoniasaracco
authored
06a59a6
Update README.md
antoniasaracco
authored
35778f5
Update README.md
antoniasaracco
authored
3c365be
Update usage.md
antoniasaracco
authored
71318c9
Add test scenario copying only matching files
delfiterradas
committed
f892c20
Remove vulnerable PR-comment artifact pattern

nf-core-bot
authored and
delfiterradas
committed
fe97a5c
Update changelog.md
delfiterradas
committed
cac46dd
Merge pull request #59 from antoniasaracco/create_documentation
apeltzer
authored
71a8dc6

Commits on Jul 29, 2026

Update rclone_copy
delfiterradas
committed
6cb7cac
Merge pull request #67 from delfiterradas/only_copy_validated
delfiterradas
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ff96d7d

Commits on Jul 30, 2026

Merge dev into nf-core-template-merge-4.0.3
apeltzer
committed
e1d29fa
Fix linting
apeltzer
committed
371ae90
Create temp file avoiding errors with write permissions in workdir
delfiterradas
committed
65b7dfe
Update CHANGELOG
delfiterradas
committed
790b8fe
Fix linting
delfiterradas
committed
05b139e
Merge pull request #73 from delfiterradas/only_copy_validated
delfiterradas
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54b293e
Add download parameter when using shasums
delfiterradas
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4a705aa
Add validation when using shasums
delfiterradas
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fa6dd32
Checksums cannot be csvs and accept additional formats
delfiterradas
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0ed68fc
Update tests and snapshots
delfiterradas
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447fc7b
Update CHANGELOG
delfiterradas
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7261126

Commits on Jul 31, 2026

Merge remote-tracking branch 'upstream/dev' into shasum_handling
delfiterradas
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caad856
Update usage documentation
delfiterradas
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e3e47d2
Update checksum verification documentation to SHA256
delfiterradas
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97e6f57
Update docs/usage.md

delfiterradas
and
atrigila
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3621357
Update workflows/datasync.nf

delfiterradas
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atrigila
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b91df99
Update CHANGELOG.md

delfiterradas
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atrigila
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0bb34e3
Update workflows/datasync.nf

delfiterradas
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atrigila
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fff74fc
Update nextflow_schema.json

delfiterradas
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atrigila
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a7c7f08
Update nextflow_schema.json

delfiterradas
and
atrigila
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d5b06b4
Add failing test scenario
delfiterradas
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8cbd838
Clean up edge.nf.test by removing unused variables
delfiterradas
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c802695
Merge pull request #74 from delfiterradas/shasum_handling
delfiterradas
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d29ad7e

Commits on Aug 3, 2026

fix linting
atrigila
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c6ea9c6
fix container config linting
atrigila
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39eb943
Revert linting fixes and container issues
atrigila
committed
6949fb1
fix pull request template
atrigila
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080bef8
Merge pull request #66 from nf-core/nf-core-template-merge-4.0.3
atrigila
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03e0139

Commits on Aug 4, 2026

remove todos
atrigila
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66f5df3
add missing subworkflow meta.yml
atrigila
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292d673
fix nextflow lint issues
atrigila
committed
fd4e5a2
fix linting warnings
atrigila
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ff429db
remove todos
atrigila
committed
4cb4feb
update subworkflows to latest versions
atrigila
committed
b2b267b
fix rocrate
atrigila
committed
91d2264
fix nextflow lint
atrigila
committed
f03a010
delete unused modules
atrigila
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3110f6a
update rclone modules
atrigila
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fffea3c
update snapshots
atrigila
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6fb5387
update changelog
atrigila
committed
ef3f45f

Commits on Aug 5, 2026

Commits on Aug 6, 2026

Commits on Aug 7, 2026

Add exit code summary to report
delfiterradas
committed
800f6d4
Update snapshots
delfiterradas
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ad82719
Fix minor format issues in readme file
delfiterradas
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4e15bfe
Update changlelog
delfiterradas
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17d50d8
Add module name to prefix and update tests
delfiterradas
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b41718e
Bugfix: Add hash to module name in exit code summary
delfiterradas
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442e237
Update snapshots
delfiterradas
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16eade4
Add validation summary section to output documentation
delfiterradas
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7d1f26d
Merge pull request #79 from delfiterradas/dev
delfiterradas
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5ce0a10

Commits on Aug 18, 2026

Bump version
delfiterradas
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296469f
Fix linting
delfiterradas
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b17c85c
Add release dat to changlelog
delfiterradas
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220c860
Update tests
delfiterradas
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bdf1f34
Fix linting
delfiterradas
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23ae865
Update PR template links to use master branch
delfiterradas
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3d99943

Commits on Aug 19, 2026

Merge pull request #81 from delfiterradas/dev
delfiterradas
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54988aa

Commits on Aug 20, 2026

Add apptainer version to avoid error in CI test
delfiterradas
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fb32bbf
Update CHANGELOG.md
delfiterradas
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7bc7797
Merge pull request #83 from delfiterradas/dev
delfiterradas
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d2d46b6

Commits on Aug 25, 2026

Make sample column a unique entry
delfiterradas
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6711148
Avoid silenlty dropping samples
delfiterradas
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229af6b
Move samplesheet validation to utils subworkflow and get a single warning instead of one per row
delfiterradas
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c14cd93
Skip RCLONE_COPY if there are no files in common in files_to_copy
delfiterradas
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26f7d59
Modify regex to capture inputs with ":"
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2194875
Capture 0 exit code status
delfiterradas
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cb6bd9f

Commits on Aug 31, 2026

Update rclone_copy version
delfiterradas
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1720b85

Commits on Sep 1, 2026

Template update for nf-core/tools version 4.1.0
nf-core-bot
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dc2ee38
Apply literal match for rclone_coopy whn requested
delfiterradas
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2b98f35
Touch all output files to avoid losing error code
delfiterradas
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50b86cb
Raise clear error message
delfiterradas
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2a50d9b
Add local module to generate files_to_copy for rclone_copy
delfiterradas
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31cb76f
Update docs to accept only local and URI paths
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18d85ed

Commits on Sep 2, 2026

Commits on Sep 3, 2026

Update rclone modules
delfiterradas
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9178433
Run prek
delfiterradas
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29f8ee9
Update CHANGELOG
delfiterradas
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46d4636
Merge pull request #84 from delfiterradas/review_dev
delfiterradas
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23f779f

Commits on Sep 4, 2026

Add local test profile
delfiterradas
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412a67d
Fix linting
delfiterradas
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4cf6105
Update CHANGELOG.md
delfiterradas
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d68d8bf
Addexplanation for real data test profile
delfiterradas
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23161e1

Commits on Sep 7, 2026

Merge pull request #87 from delfiterradas/review_dev
delfiterradas
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366487c

Commits on Sep 8, 2026

Implement review suggestions
delfiterradas
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5cd483d
Template update for nf-core/tools version 4.1.0
delfiterradas
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e4372d9
Merge branch 'TEMPLATE' into dev
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5619860
Change default branch and update rclone checksum
delfiterradas
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a3bfda8
Fix linting
delfiterradas
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5117470
Skip linting for PULL_REQUEST_TEMPLATE.md
delfiterradas
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ba00df5
Merge pull request #90 from delfiterradas/dev
delfiterradas
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0bdf8b9
Update changelog for first release
delfiterradas
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bcfdc6a
Merge remote-tracking branch 'upstream/dev' into review_dev
delfiterradas
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69ad859
Add nf-metro plot
delfiterradas
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4cbf146
Fix linting
delfiterradas
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c43ec12

Commits on Sep 23, 2026

Implement suggestions to documentation and minor changes in outputs
delfiterradas
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4af74f2

Commits on Sep 24, 2026

Add documentation to create md5 and shasums
delfiterradas
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fc37342
Create prepareSamplesheet function
delfiterradas
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3024ac0
Add test assertions
delfiterradas
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520599b

Commits on Sep 25, 2026

Move warning checks to edge test
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b3b9581
Fix linting
delfiterradas
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e713808
Fix linting
delfiterradas
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29a2987
Update release date
delfiterradas
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fc53e82
Use nft-csv for assertion of line counts for rclone output files
delfiterradas
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b6a189d
Add back md5 snapshots
delfiterradas
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bd709bf

Commits on Sep 28, 2026