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Merge dev third rev #20

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merged 630 commits into from
Dec 4, 2024
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6ddd824
write only relevant fields in `.nf-core.yml`
mashehu Oct 16, 2024
313a4d1
switch from docstrings to Field descsriptions
mashehu Oct 16, 2024
16e6ff2
[automated] Update CHANGELOG.md
nf-core-bot Oct 16, 2024
4225001
Merge pull request #3225 from nf-core/maxulysse-patch-7
mashehu Oct 16, 2024
87ab7ee
update test to new error
mashehu Oct 16, 2024
612570f
Merge branch 'fix-pydantic-dump' of github.com:mashehu/tools into fix…
mashehu Oct 16, 2024
6645e4c
second attempt to add ro crates
mashehu Jan 16, 2024
553135a
fix import
mashehu Jan 16, 2024
bf30f0d
first running version
mashehu Jan 23, 2024
9ed053a
restructure code and add tests
mashehu Jan 24, 2024
56a170c
add missing dep
mashehu Jan 24, 2024
8419e9f
add recommendations from comments
mashehu Jan 25, 2024
bdbc045
add git contributors
mashehu Jan 25, 2024
3ba54c4
fix filename for CI
mashehu Jan 25, 2024
9a66883
better help hint message
mashehu Jan 25, 2024
a656617
fix class name
mashehu Jan 25, 2024
fb0d091
add correct parent directory to faked crate
mashehu Jan 25, 2024
2469697
add empty ro-crate after sync
mashehu Jan 25, 2024
f521fa3
fix tests
mashehu Jul 31, 2024
797fefb
fix ci test
mashehu Jul 31, 2024
9d5251f
use github to guess author name, set names as ids if no orcid
mashehu Jul 31, 2024
a605ae6
add bioschemas, datecreated and datemodified (only set to current tim…
mashehu Jul 31, 2024
6c6b8c9
follow `ComputationalWorkflow` schema for main entitty.
mashehu Aug 5, 2024
c2f837c
fix date created field
mashehu Aug 5, 2024
0778b2a
add "about" field to workflow diagram
mashehu Aug 5, 2024
ccfd6d9
add input as separate entity
mashehu Aug 5, 2024
776c6cc
add version to main entity
mashehu Aug 5, 2024
a50f12f
fix incorrect type
mashehu Aug 16, 2024
49592cb
switch to add_workflow method to add main entity and add components a…
mashehu Aug 16, 2024
c1d08d7
ro_crate -> rocrate
mashehu Aug 27, 2024
5bc36e4
allow mixed list and dict in lint config
mashehu Oct 17, 2024
81bdb3b
nested too deeply
mashehu Oct 17, 2024
3d8d4b7
[automated] Update CHANGELOG.md
nf-core-bot Oct 17, 2024
5e4b4f3
use repo2crate to generate the main structure of the crate
mashehu Oct 17, 2024
4616629
Merge branch 'add-rocreate' of github.com:mashehu/tools into add-rocr…
mashehu Oct 17, 2024
ff32ff1
chore(deps): update dependency prompt_toolkit to <=3.0.48
renovate[bot] Oct 18, 2024
5d56b43
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0
renovate[bot] Oct 18, 2024
09181a7
chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0
renovate[bot] Oct 18, 2024
09a4732
[automated] Update CHANGELOG.md
nf-core-bot Oct 18, 2024
f62edb0
[automated] Update CHANGELOG.md
nf-core-bot Oct 18, 2024
fa3ba47
Merge pull request #3229 from nf-core/renovate/astral-sh-ruff-pre-com…
mashehu Oct 18, 2024
deab2db
Merge pull request #3121 from nf-core/renovate/prompt_toolkit-3.x
mashehu Oct 18, 2024
3d41820
Merge branch 'dev' into renovate/pre-commit-mirrors-mypy-1.x
mashehu Oct 18, 2024
250e63b
Fix typos
mribeirodantas Oct 19, 2024
9b078db
Fix typos (second round)
mribeirodantas Oct 19, 2024
f82a7bf
Merge branch 'dev' into fix-typos
mribeirodantas Oct 19, 2024
5fea053
Undo accidental typos fixes
mribeirodantas Oct 19, 2024
08c43f5
Fix typos (third round)
mribeirodantas Oct 19, 2024
d5fb5f8
Update textual snapshots
mribeirodantas Oct 19, 2024
76c7969
Merge pull request #3231 from nf-core/fix-typos
mribeirodantas Oct 19, 2024
e8dff3f
chore(deps): update python:3.12-slim docker digest to 032c526
renovate[bot] Oct 19, 2024
9ba36f3
[automated] Update CHANGELOG.md
nf-core-bot Oct 20, 2024
2b4029b
handle new nf-core.yml structure
mashehu Oct 21, 2024
3a55f36
update documentation for `multiqc_config` linting
mashehu Oct 21, 2024
fcc442a
parse yaml correctly
mashehu Oct 21, 2024
482f9f9
found a better way to handle the ignore file being None
mashehu Oct 21, 2024
663a932
handle new lint config structure
mashehu Oct 21, 2024
15c23fb
Merge pull request #3230 from nf-core/renovate/pre-commit-mirrors-myp…
mashehu Oct 21, 2024
53ae873
add tests with different valid yaml structures
mashehu Oct 21, 2024
b5a546c
Merge branch 'fix-yml-config-type' of github.com:mashehu/tools into f…
mashehu Oct 21, 2024
00db9c7
use correct profile options for sfw test command
mashehu Oct 21, 2024
ea03ff2
[automated] Update CHANGELOG.md
nf-core-bot Oct 21, 2024
57f7ca8
remove last traces of LintConfigType
mashehu Oct 21, 2024
e743185
fix incorrect type
mashehu Oct 21, 2024
58869a1
more type fixes
mashehu Oct 21, 2024
2ba0d30
Update CHANGELOG.md
mashehu Oct 22, 2024
170623f
Merge pull request #3233 from mashehu/fix-swf-test-profile
mashehu Oct 22, 2024
afbd51b
add all lint tests to config
mashehu Oct 22, 2024
9bf91f5
switch all defaults to None and drop them on dump
mashehu Oct 22, 2024
4abbc4a
Update nf_core/utils.py
mashehu Oct 22, 2024
ff27b29
Update nf_core/utils.py
mashehu Oct 22, 2024
61bb733
drop None values when checking for test names
mashehu Oct 22, 2024
d3453aa
Merge branch 'dev' into fix-pydantic-dump
mashehu Oct 22, 2024
fdef700
[automated] Fix code linting
nf-core-bot Oct 22, 2024
bc37fb0
no need for Field value
mashehu Oct 22, 2024
930b170
Merge branch 'fix-pydantic-dump' of github.com:mashehu/tools into fix…
mashehu Oct 22, 2024
e2ac2b5
fix test_lint tests
mashehu Oct 22, 2024
02259f9
Merge pull request #3227 from mashehu/fix-pydantic-dump
mashehu Oct 22, 2024
e7e21f2
fix worklfow_dispatch trigger and parse more review comments
mashehu Oct 23, 2024
4c744e5
[automated] Update CHANGELOG.md
nf-core-bot Oct 23, 2024
befd38e
Merge branch 'dev' of github.com:nf-core/tools into fix-yml-config-type
mashehu Oct 23, 2024
b7d52a9
Merge branch 'fix-yml-config-type' of github.com:mashehu/tools into f…
mashehu Oct 23, 2024
1911888
Merge pull request #3235 from mashehu/fix-awsfulltest
mashehu Oct 23, 2024
2674f5f
Update pre-commit hook pre-commit/mirrors-mypy to v1.13.0
renovate[bot] Oct 23, 2024
b87106d
Merge pull request #3236 from nf-core/renovate/pre-commit-mirrors-myp…
mashehu Oct 23, 2024
ad37735
chore(deps): update github actions
renovate[bot] Oct 23, 2024
1ef9134
[automated] Update CHANGELOG.md
nf-core-bot Oct 23, 2024
2993fbb
Merge branch 'dev' of github.com:nf-core/tools into add-rocreate
mashehu Oct 23, 2024
ad7b895
remove outdated file
mashehu Oct 23, 2024
796c219
Merge pull request #2680 from mashehu/add-rocreate
mashehu Oct 23, 2024
76bb9b5
Revert "Add new command `nf-core rocrate` to create a Research Object…
mashehu Oct 23, 2024
3bc6453
Merge pull request #3238 from nf-core/revert-2680-add-rocreate
mashehu Oct 23, 2024
78e8264
move test in correct directory
mashehu Oct 23, 2024
b74319d
fix tests
mashehu Oct 23, 2024
bc0ba13
Add seqera containers example
pinin4fjords Oct 23, 2024
993031c
bump ci
pinin4fjords Oct 23, 2024
32f1b22
Modify test_find_container_images_modules() for Seqera Containers.
MatthiasZepper Oct 23, 2024
c1f2172
Enable Seqera Containers download.
MatthiasZepper Oct 23, 2024
78c2d60
Merge branch 'dev' of github.com:nf-core/tools into add-rocreate
mashehu Oct 24, 2024
406bdf8
run tests without commiting ro-crate
mashehu Oct 24, 2024
94bddc2
add ro-crate creation to pipelines create command
mashehu Oct 24, 2024
5c4a5e6
fix command import
mashehu Oct 24, 2024
a679a14
add rocrate to skip features
mashehu Oct 24, 2024
d79ba10
remove schema loading, because it is not needed anymore
mashehu Oct 24, 2024
dfb9283
update snapshots
mashehu Oct 24, 2024
4b705b8
`modules update`: add a panel around diffs
mashehu Oct 24, 2024
6d3a306
add `--dir/-d` option to schema commands
mashehu Oct 24, 2024
6782bf7
[automated] Update CHANGELOG.md
nf-core-bot Oct 24, 2024
63153cf
[automated] Update CHANGELOG.md
nf-core-bot Oct 24, 2024
2696940
try to fix coverage report generation
mashehu Oct 24, 2024
fdb511a
Merge branch 'add-rocreate' of github.com:mashehu/tools into add-rocr…
mashehu Oct 24, 2024
5099313
fix test_cli
mashehu Oct 24, 2024
6729d0a
Merge branch 'add-dir-to-schema-commands' of github.com:mashehu/tools…
mashehu Oct 24, 2024
b79525b
nf-core download: Fix forgotten symlinks in cache.
MatthiasZepper Oct 24, 2024
884cafd
try specifying the coverage output file
mashehu Oct 24, 2024
0cb8f49
try naming the files directly
mashehu Oct 24, 2024
103a196
fix variable name
mashehu Oct 24, 2024
f49e9cf
add hiddnen files for upload-artifact action v4
mashehu Oct 24, 2024
d59ac3f
Merge pull request #3247 from mashehu/add-dir-to-schema-commands
mashehu Oct 24, 2024
0ebc779
Merge branch 'dev' into add-diff-seperator
mashehu Oct 24, 2024
221030a
group diffs by module
mashehu Oct 24, 2024
4660d89
Merge branch 'add-diff-seperator' of github.com:mashehu/tools into ad…
mashehu Oct 24, 2024
79b9b44
Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1
renovate[bot] Oct 24, 2024
718f585
[automated] Update CHANGELOG.md
nf-core-bot Oct 24, 2024
b11b3fb
Merge pull request #3250 from nf-core/renovate/astral-sh-ruff-pre-com…
mashehu Oct 24, 2024
354311d
Update GitHub Actions
renovate[bot] Oct 24, 2024
fec9929
Ensure that prioritize_direct_download() retains Seqera Singularity C…
MatthiasZepper Oct 24, 2024
3d953fe
Merge branch 'dev' into seqera_containers_example_mod
MatthiasZepper Oct 24, 2024
76d399d
make group border blue
mashehu Oct 24, 2024
29f6765
make module names white
mashehu Oct 25, 2024
32a7e6b
Apply suggestions from code review
MatthiasZepper Oct 25, 2024
eb4c237
Merge pull request #3246 from mashehu/add-diff-seperator
mashehu Oct 25, 2024
65db460
Merge pull request #3244 from MatthiasZepper/seqera_containers_exampl…
MatthiasZepper Oct 25, 2024
ab93287
Add resource limits to Gitpod profile
mahesh-panchal Oct 28, 2024
fc778f3
Update changelog
mahesh-panchal Oct 29, 2024
566d579
I fix typos for infrastickers
jfy133 Oct 31, 2024
dc9c1d1
Merge pull request #3267 from nf-core/fix-logo-typo
mashehu Oct 31, 2024
04bbf4a
Merge pull request #3255 from mahesh-panchal/add_gitpod_resource_limits
mashehu Oct 31, 2024
d95b628
Fix typo
SPPearce Oct 31, 2024
9412504
Merge remote-tracking branch 'origin/dev' into fix_typo
SPPearce Oct 31, 2024
b7bb2b0
Update changelog
SPPearce Oct 31, 2024
3081f83
Merge pull request #3268 from nf-core/fix_typo
mashehu Oct 31, 2024
14c3e03
Update Gitpod to use Miniforge instead of Miniconda
mahesh-panchal Nov 8, 2024
f410310
Update Changelog
mahesh-panchal Nov 8, 2024
eda7208
Merge pull request #3274 from mahesh-panchal/gitpod_miniforge
mahesh-panchal Nov 8, 2024
5f900fd
Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3
renovate[bot] Nov 8, 2024
ab2fbed
[automated] Update CHANGELOG.md
nf-core-bot Nov 8, 2024
27659c5
Merge pull request #3275 from nf-core/renovate/astral-sh-ruff-pre-com…
mashehu Nov 8, 2024
335b7e1
handle new schema structure in create-params-file
mashehu Nov 11, 2024
f3a92f0
add tests
mashehu Nov 11, 2024
049990b
[automated] Update CHANGELOG.md
nf-core-bot Nov 11, 2024
e57a096
Merge branch 'dev' into fix-create-params
mashehu Nov 11, 2024
24e2dc2
Merge pull request #3276 from mashehu/fix-create-params
mashehu Nov 12, 2024
8f93842
add hint to solve git errors with a synced repo
mirpedrol Nov 14, 2024
a974b6a
run pre-commit when testing linting the template pipeline
mirpedrol Nov 14, 2024
0396f40
[automated] Update CHANGELOG.md
nf-core-bot Nov 14, 2024
555d88e
[automated] Update CHANGELOG.md
nf-core-bot Nov 14, 2024
269af7d
fix template trailing spaces
mirpedrol Nov 14, 2024
bdce677
write proper path and raise a UserWarning to avoid printing the error…
mirpedrol Nov 14, 2024
30c3745
Apply suggestions from code review
mirpedrol Nov 14, 2024
db11da5
remove logging git error from wrong place
mirpedrol Nov 14, 2024
0848508
Merge pull request #3279 from mirpedrol/fix_3263
mirpedrol Nov 14, 2024
d26c3e9
Merge pull request #3280 from mirpedrol/run-pre-commit-with-lint-tests
mirpedrol Nov 14, 2024
48fa28f
add option to skip .vscode from the template
mirpedrol Nov 15, 2024
18b3df7
Merge branch 'dev' of https://github.com/nf-core/tools into vscode-se…
mirpedrol Nov 15, 2024
9321971
update textual snapshots
mirpedrol Nov 15, 2024
7f40b3a
Merge branch 'dev' of https://github.com/nf-core/tools
mirpedrol Nov 15, 2024
c5cd95c
Merge pull request #3192 from ewels/vscode-settings
ewels Nov 15, 2024
7cd3dea
update and fix swf patch tests
mirpedrol Nov 15, 2024
e6da4e6
Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.4
renovate[bot] Nov 16, 2024
882ba78
[automated] Update CHANGELOG.md
nf-core-bot Nov 16, 2024
01e85dd
Update codecov/codecov-action action to v5 (#3283)
renovate[bot] Nov 17, 2024
89a9c9f
Merge branch 'dev' into renovate/astral-sh-ruff-pre-commit-0.x
mashehu Nov 17, 2024
207129d
Merge pull request #3282 from nf-core/renovate/astral-sh-ruff-pre-com…
mashehu Nov 17, 2024
41b4516
Update python:3.12-slim Docker digest to 2a6386a (#3284)
renovate[bot] Nov 18, 2024
424bbae
Merge branch 'dev' into master
ewels Nov 21, 2024
25940f7
apply patch reverse when linting a patched subworkflow
mirpedrol Nov 22, 2024
b2cfd01
update get_patch_fn to work with subworkflows
mirpedrol Nov 22, 2024
6ec2dcd
move modules_differ.py to components_differ.py
mirpedrol Nov 22, 2024
27582f9
add subworkflows patch missing tests
mirpedrol Nov 25, 2024
4f93d57
fix subworkflows update test
mirpedrol Nov 25, 2024
5ad4570
update changelog
mirpedrol Nov 25, 2024
37ca244
add help text for --remove flag
mirpedrol Nov 25, 2024
805ba91
apply code review suggestions to patch tests
mirpedrol Nov 25, 2024
84cec26
Update tests/modules/test_patch.py
mirpedrol Nov 25, 2024
8b2bec4
apply suggestions by @mashehu
mirpedrol Nov 25, 2024
4e4bbaa
Merge pull request #2861 from ctuni/master
mirpedrol Nov 25, 2024
9e9d930
remove def from nextflow.config and add trace_report_suffix param
mirpedrol Nov 25, 2024
225699c
[automated] Update CHANGELOG.md
nf-core-bot Nov 25, 2024
9f5a95c
Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0
renovate[bot] Nov 26, 2024
5965621
[automated] Update CHANGELOG.md
nf-core-bot Nov 26, 2024
f903ce1
add validation.monochromeLogs to config
mirpedrol Nov 26, 2024
d56c87c
ignore trace_report_suffix default check
mirpedrol Nov 26, 2024
6a6de1d
Merge pull request #3296 from mirpedrol/fix-nextflow-language-server-…
mirpedrol Nov 26, 2024
ba332b6
Merge pull request #3299 from nf-core/renovate/astral-sh-ruff-pre-com…
mashehu Nov 26, 2024
b2e1192
Merge branch 'dev' of github.com:nf-core/tools into add-rocreate
mashehu Nov 27, 2024
af1a1be
update snapshots
mashehu Nov 27, 2024
d48b300
add more tests
mashehu Nov 27, 2024
84da138
Merge branch 'add-rocreate' of github.com:mashehu/tools into add-rocr…
mashehu Nov 27, 2024
65d74d5
enable zip output
mashehu Nov 27, 2024
0d33739
Move modules config import after base.config
LouisLeNezet Nov 28, 2024
85338c9
Merge branch 'dev' into LouisLeNezet-config
LouisLeNezet Nov 28, 2024
43287c6
Update nf_core/pipelines/create/template_features.yml
mirpedrol Nov 28, 2024
7284262
Merge pull request #3240 from mashehu/add-rocreate
mashehu Nov 28, 2024
2eec420
Update documentation
LouisLeNezet Nov 28, 2024
b12459a
Update CHANGELOG
LouisLeNezet Nov 28, 2024
c8f22cf
Update CHANGELOG.md
LouisLeNezet Nov 28, 2024
aacc24d
Merge branch 'dev' into LouisLeNezet-config
LouisLeNezet Nov 28, 2024
1dd8ea0
Merge pull request #3301 from LouisLeNezet/LouisLeNezet-config
LouisLeNezet Nov 28, 2024
859acdd
Merge branch 'dev' into documentation
LouisLeNezet Nov 28, 2024
07984be
Fix linting
Nov 28, 2024
82d6797
Update CHANGELOG
Nov 28, 2024
ac3fbc6
Download: Need to deduplicate Seqera Container matches as well, other…
MatthiasZepper Nov 19, 2024
a5b0e86
Add new function to handle Seqera Container Oras URIs.
MatthiasZepper Nov 19, 2024
838286b
Ensure, that oras:// containers are correctly handled.
MatthiasZepper Nov 19, 2024
c2f9056
Download: Add test data for oras:// modules.
MatthiasZepper Nov 19, 2024
50896ea
Test the new container elimination routine.
MatthiasZepper Nov 21, 2024
7ef1cfb
Download: Update the tests.
MatthiasZepper Nov 21, 2024
335c48d
Add dedicated ORAS image format error.
MatthiasZepper Nov 22, 2024
0d0fe6b
Include oras:// regex in download to recognize the paths.
MatthiasZepper Nov 22, 2024
66ffaf1
Changelog.
MatthiasZepper Nov 22, 2024
8c28530
Update dawidd6/action-download-artifact action to v7 (#3306)
renovate[bot] Nov 30, 2024
d7f1df2
Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.1
renovate[bot] Nov 30, 2024
a61abdd
Merge pull request #3305 from nf-core/renovate/astral-sh-ruff-pre-com…
mashehu Nov 30, 2024
800fd8d
Update gitpod/workspace-base Docker digest to 12853f7 (#3309)
renovate[bot] Dec 2, 2024
acb9103
update modules and subworkflows
mirpedrol Dec 2, 2024
8800b71
[automated] Update CHANGELOG.md
nf-core-bot Dec 2, 2024
86a0daa
Merge branch 'dev' into template-monochrome-logs
mirpedrol Dec 2, 2024
22ff44b
also add monochrome_logs if nf-schema is used
mirpedrol Dec 2, 2024
ed04e1f
Merge branch 'dev' into seqera_containers_patch2
mashehu Dec 2, 2024
dabf1ef
Merge pull request #3310 from mirpedrol/template-monochrome-logs
mirpedrol Dec 2, 2024
c63f3be
Merge branch 'dev' of github.com:nf-core/tools into fix-yml-config-type
mashehu Dec 2, 2024
b91bd77
add manifest.contributors to nextflow.config
mirpedrol Dec 2, 2024
da021fe
[automated] Update CHANGELOG.md
nf-core-bot Dec 2, 2024
9c8d50f
fix contributors map
mirpedrol Dec 2, 2024
df3d25d
Update nf_core/pipeline-template/.github/CONTRIBUTING.md
LouisLeNezet Dec 2, 2024
a683b97
Merge branch 'dev' into documentation
LouisLeNezet Dec 2, 2024
d72667c
Typo in error message.
MatthiasZepper Dec 2, 2024
3c17e81
Merge pull request #3293 from MatthiasZepper/seqera_containers_patch2
MatthiasZepper Dec 2, 2024
86b926b
test also the main sync function itsel
mashehu Dec 2, 2024
ee86c15
combine json parsing code
mashehu Dec 2, 2024
538893c
loop over list of authors to supply contributors
mirpedrol Dec 2, 2024
10e691b
remove broken test
mashehu Dec 2, 2024
11f7f42
fix type error
mashehu Dec 2, 2024
be5f2e2
Merge pull request #3311 from mirpedrol/manifest_contributors
mirpedrol Dec 3, 2024
ac5497a
Merge branch 'dev' into documentation
mashehu Dec 3, 2024
9d3d074
Merge pull request #3302 from LouisLeNezet/documentation
mashehu Dec 3, 2024
eed0598
Apply suggestions from code review
mashehu Dec 3, 2024
a7351a2
Merge pull request #3228 from mashehu/fix-yml-config-type
mashehu Dec 3, 2024
9c9c66a
Merge branch 'dev' into merge-dev-third-rev
jvfe Dec 4, 2024
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remove def from nextflow.config and add trace_report_suffix param
  • Loading branch information
mirpedrol committed Nov 25, 2024
commit 9e9d930ebbb16f717e8d3e51849cb9e7f41c0488
10 changes: 5 additions & 5 deletions nf_core/pipeline-template/nextflow.config
Original file line number Diff line number Diff line change
@@ -52,6 +52,7 @@ params {
version = false
{%- if test_config %}
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

{%- if nf_core_configs -%}
// Config options
@@ -249,22 +250,21 @@ set -C # No clobber - prevent output redirection from overwriting files.
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}

manifest {
8 changes: 7 additions & 1 deletion nf_core/pipeline-template/nextflow_schema.json
Original file line number Diff line number Diff line change
@@ -229,7 +229,13 @@
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
}{% endif %}
}{% endif %},
"trace_report_suffix": {
"type": "string",
"fa_icon": "far calendar",
"description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
"hidden": true
}
}
}
},