Added spots counts and spots intensities steps #6

cgoina · 2025-05-14T18:21:07Z

PR checklist

…t-rs-fish

… warped spots from moving rounds

…e which prevents further joins downstream

…and now it defaults to false

github-actions · 2025-05-14T18:21:17Z

This PR is against the `master` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @cgoina,

It looks like this pull-request is has been made against the JaneliaSciComp/easifish main branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the JaneliaSciComp/easifish dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2025-05-15T21:36:40Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 0b48e75

+| ✅ 222 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗  24 tests had warnings |!
-| ❌  40 tests failed       |-

Details

❌ Test failures:

files_exist - File not found: assets/nf-core-easifish_logo_light.png
files_exist - File not found: docs/images/nf-core-easifish_logo_light.png
files_exist - File not found: docs/images/nf-core-easifish_logo_dark.png
files_exist - File must be removed: lib/NfcoreTemplate.groovy
files_exist - File must be removed: lib/Utils.groovy
files_exist - File must be removed: lib/WorkflowMain.groovy
files_exist - File must be removed: lib/nfcore_external_java_deps.jar
nextflow_config - Plugin 'nf-validation' does not have a pinned version
nextflow_config - Config variable (incorrectly) found: params.max_cpus
nextflow_config - Config variable (incorrectly) found: params.max_memory
nextflow_config - Config variable (incorrectly) found: params.max_time
nextflow_config - Config default value incorrect: params.bigstream_config is set as ${projectDir}/conf/bigstream_config.yml in nextflow_schema.json but is /home/runner/work/easifish/easifish/conf/bigstream_config.yml in nextflow.config.
nextflow_config - Config default value incorrect: params.dask_config is set as ${projectDir}/conf/dask_config.yml in nextflow_schema.json but is /home/runner/work/easifish/easifish/conf/dask_config.yml in nextflow.config.
nextflow_config - Config default value incorrect: params.local_align_worker_cpus is set as 3 in nextflow_schema.json but is 1 in nextflow.config.
nextflow_config - Config default value incorrect: params.bigstream_inv_use_root is set as true in nextflow_schema.json but is false in nextflow.config.
nextflow_config - Config default value incorrect: params.multiscale_spark_workers is set as 1 in nextflow_schema.json but is 0 in nextflow.config.
nextflow_config - Config default value incorrect: params.multiscale_spark_worker_cores is set as 3 in nextflow_schema.json but is 0 in nextflow.config.
nextflow_config - Config default value incorrect: params.multiscale_spark_driver_mem_gb is set as 1 in nextflow_schema.json but is 0 in nextflow.config.
nextflow_config - Config default value incorrect: params.seg_channels is set as c1 in nextflow_schema.json but is `` in nextflow.config.
nextflow_config - Config default value incorrect: params.cellpose_log_config is set as ${projectDir}/conf/cellpose_logging_config.ini in nextflow_schema.json but is /home/runner/work/easifish/easifish/conf/cellpose_logging_config.ini in nextflow.config.
nextflow_config - Config default value incorrect: params.cellpose_dask_config is set as ${projectDir}/conf/dask_config.yml in nextflow_schema.json but is /home/runner/work/easifish/easifish/conf/dask_config.yml in nextflow.config.
nextflow_config - Config default value incorrect: params.cellpose_dask_workers is set as 10 in nextflow_schema.json but is 8 in nextflow.config.
nextflow_config - Config default value incorrect: params.user_id is set as 0 in nextflow_schema.json but is 1001 in nextflow.config.
nextflow_config - Config default value incorrect: params.group_id is set as 0 in nextflow_schema.json but is 118 in nextflow.config.
nextflow_config - Config default value incorrect: params.singularity_cache_dir is set as $HOME/.singularity_cache in nextflow_schema.json but is /home/runner/.singularity_cache in nextflow.config.
files_unchanged - .github/CONTRIBUTING.md does not match the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
files_unchanged - .github/workflows/branch.yml does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template
actions_ci - Minimum pipeline NF version '23.04.0' is not tested in '.github/workflows/ci.yml'
schema_params - Param distributed_spot_extraction from nextflow config not found in nextflow_schema.json
schema_params - Param skip_warp_spots from nextflow config not found in nextflow_schema.json
schema_params - Param warped_spots_subdir from nextflow config not found in nextflow_schema.json
schema_params - Param warp_spots_cpus from nextflow config not found in nextflow_schema.json
schema_params - Param warp_spots_mem_in_gb from nextflow config not found in nextflow_schema.json
schema_params - Param bleeding_channel from nextflow config not found in nextflow_schema.json
schema_params - Default value for param bigstream_inv_use_root invalid: Schema default (True) does not match the config default (false)
schema_params - Default value for param bleed_channel invalid: Not in pipeline parameters. Check nextflow.config.
modules_json - Your modules.json file is outdated. It will be automatically generated by running any module command.
multiqc_config - assets/multiqc_config.yml not found.

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
files_exist - File not found: ro-crate-metadata.json
nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
schema_params - Schema param bleed_channel not found from nextflow config
schema_description - No description provided in schema for parameter: stitching_result_container
schema_description - No description provided in schema for parameter: sample_anisotropy
schema_description - No description provided in schema for parameter: sample_expansion_factor
schema_description - No description provided in schema for parameter: sample_voxel_spacing
schema_description - No description provided in schema for parameter: sample_z_axis
schema_description - No description provided in schema for parameter: cellpose_verbose
schema_description - No description provided in schema for parameter: cellpose_preprocessing_steps
schema_description - No description provided in schema for parameter: cellpose_preprocessing_params_file
schema_description - No description provided in schema for parameter: cellpose_worker_runtime_opts
schema_description - No description provided in schema for parameter: cellpose_worker_lsf_opts
local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - multiscale.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - stitching.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - cellpose_segmentation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: assets/nf-core-easifish_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-easifish_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-easifish_logo_dark.png
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/easifish/easifish/.github/workflows/awstest.yml

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-easifish_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowEasifish.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-validation plugin
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.resolution= 0.23,0.23,0.42
nextflow_config - Config default value correct: params.stitching_result_container= stitched.n5
nextflow_config - Config default value correct: params.stitching_channel= all
nextflow_config - Config default value correct: params.axis_mapping= -x,y,z
nextflow_config - Config default value correct: params.stitching_block_size= 128,128,64
nextflow_config - Config default value correct: params.final_block_size_xy= 512
nextflow_config - Config default value correct: params.stitching_mode= incremental
nextflow_config - Config default value correct: params.stitching_padding= 0,0,0
nextflow_config - Config default value correct: params.stitching_blur_sigma= 2
nextflow_config - Config default value correct: params.spark_cluster= true
nextflow_config - Config default value correct: params.spark_workers= 10
nextflow_config - Config default value correct: params.min_spark_workers= 5
nextflow_config - Config default value correct: params.spark_worker_cores= 1
nextflow_config - Config default value correct: params.spark_gb_per_core= 15
nextflow_config - Config default value correct: params.spark_driver_cores= 1
nextflow_config - Config default value correct: params.spark_driver_mem_gb= 12
nextflow_config - Config default value correct: params.reuse_global_affine= true
nextflow_config - Config default value correct: params.global_steps= affine
nextflow_config - Config default value correct: params.global_scale= s3
nextflow_config - Config default value correct: params.local_inverse_cpus= 1
nextflow_config - Config default value correct: params.local_inverse_mem_gb= 0
nextflow_config - Config default value correct: params.local_deform_cpus= 1
nextflow_config - Config default value correct: params.local_deform_mem_gb= 0
nextflow_config - Config default value correct: params.local_steps= affine,deform
nextflow_config - Config default value correct: params.local_scale= s2
nextflow_config - Config default value correct: params.local_transform_name= deform.n5
nextflow_config - Config default value correct: params.local_inv_transform_name= inv-deform.n5
nextflow_config - Config default value correct: params.with_dask_cluster= true
nextflow_config - Config default value correct: params.warped_scales= s0
nextflow_config - Config default value correct: params.global_align_cpus= 3
nextflow_config - Config default value correct: params.global_align_mem_gb= 0
nextflow_config - Config default value correct: params.local_align_cpus= 1
nextflow_config - Config default value correct: params.local_align_mem_gb= 0
nextflow_config - Config default value correct: params.local_align_workers= 10
nextflow_config - Config default value correct: params.local_align_min_workers= 1
nextflow_config - Config default value correct: params.local_align_worker_mem_gb= 0
nextflow_config - Config default value correct: params.bigstream_local_overlap_factor= 0.125
nextflow_config - Config default value correct: params.bigstream_inv_step= 1.0
nextflow_config - Config default value correct: params.bigstream_inv_iterations= 20
nextflow_config - Config default value correct: params.bigstream_inv_shrink_spacings=
nextflow_config - Config default value correct: params.bigstream_inv_smooth_sigmas= 0.
nextflow_config - Config default value correct: params.bigstream_inv_step_cut_factor= 0.5
nextflow_config - Config default value correct: params.bigstream_inv_pad= 0.1
nextflow_config - Config default value correct: params.bigstream_dashboard_port= 0
nextflow_config - Config default value correct: params.bigstream_scheduler_port= 0
nextflow_config - Config default value correct: params.global_registration_container= global-registration.n5
nextflow_config - Config default value correct: params.local_registration_container= registration.n5
nextflow_config - Config default value correct: params.registration_subdir= registration
nextflow_config - Config default value correct: params.rsfish_spark_workers= 2
nextflow_config - Config default value correct: params.rsfish_min_spark_workers= 1
nextflow_config - Config default value correct: params.rsfish_spark_worker_cores= 5
nextflow_config - Config default value correct: params.rsfish_spark_gb_per_core= 5
nextflow_config - Config default value correct: params.rsfish_spark_driver_cores= 1
nextflow_config - Config default value correct: params.rsfish_spark_driver_mem_gb= 4
nextflow_config - Config default value correct: params.spots_counts_cores= 1
nextflow_config - Config default value correct: params.spots_counts_mem_gb= 2
nextflow_config - Config default value correct: params.spots_props_cores= 1
nextflow_config - Config default value correct: params.spots_props_mem_gb= 2
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.lsf_queue_size= 500
nextflow_config - Config default value correct: params.default_mem_gb_per_cpu= 15
nextflow_config - Config default value correct: params.max_cpus= 500
nextflow_config - Config default value correct: params.max_memory= 1024.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.multiscale_with_spark_cluster= true
nextflow_config - Config default value correct: params.multiscale_min_spark_workers= 1
nextflow_config - Config default value correct: params.multiscale_spark_gb_per_core= 15
nextflow_config - Config default value correct: params.multiscale_spark_driver_cores= 1
nextflow_config - Config default value correct: params.multiscale_resolution= 0.23,0.23,0.42
nextflow_config - Config default value correct: params.segmentation_ids= t1
nextflow_config - Config default value correct: params.seg_scales= s2
nextflow_config - Config default value correct: params.segmentation_subdir= segmentation
nextflow_config - Config default value correct: params.segmentation_imgname= segmentation.n5
nextflow_config - Config default value correct: params.sample_anisotropy= 1.0
nextflow_config - Config default value correct: params.sample_expansion_factor= 1.0
nextflow_config - Config default value correct: params.sample_z_axis= 0
nextflow_config - Config default value correct: params.distributed_cellpose= true
nextflow_config - Config default value correct: params.cellpose_model= cyto3
nextflow_config - Config default value correct: params.distributed_cellpose_blocksize= 128,128,128
nextflow_config - Config default value correct: params.cellpose_use_gpu= true
nextflow_config - Config default value correct: params.cellpose_device= 0
nextflow_config - Config default value correct: params.cellpose_diameter= 30
nextflow_config - Config default value correct: params.cellpose_eval_channels= 0,0
nextflow_config - Config default value correct: params.cellpose_min_size= 5
nextflow_config - Config default value correct: params.cellprob_threshold= 1.0
nextflow_config - Config default value correct: params.cellpose_iou_threshold= 0.05
nextflow_config - Config default value correct: params.cellpose_labels_distance_th= 1.0
nextflow_config - Config default value correct: params.cellpose_save_intermediate_labels= true
nextflow_config - Config default value correct: params.cellpose_merge_iou_depth= 1
nextflow_config - Config default value correct: params.cellpose_segmentation_cpus= 1
nextflow_config - Config default value correct: params.cellpose_segmentation_mem_gb= 0
nextflow_config - Config default value correct: params.cellpose_dask_min_workers= 1
nextflow_config - Config default value correct: params.cellpose_dask_worker_cpus= 1
nextflow_config - Config default value correct: params.cellpose_dask_worker_mem_gb= 0
nextflow_config - Config default value correct: params.cellpose_scheduler_port= 0
nextflow_config - Config default value correct: params.cellpose_dashboard_port= 0
nextflow_config - Config default value correct: params.cellpose_worker_lsf_opts= -q gpu_l4 -gpu "num=1
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.workdir= work
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.2.0

Run details

nf-core/tools version 3.2.0
Run at 2025-05-15 21:36:26

cgoina added 30 commits April 21, 2025 15:34

modules for assign and measure spots; changed spots container for pos…

10eecf1

…t-rs-fish

changed warp_spots to return both fixed round spots - unchanged - and…

1c5a32d

… warped spots from moving rounds

added some comments

4877fa6

fixed typo

278f9be

changed result returned when skipping segmentation

279eabf

removed fixme comment

14dadeb

fixed post-rs-fish container

99069dd

renamed var

06dead7

changed log messages

4f60794

update cellpose to include dataset in the results

2730bf9

added step to extract spots features

b25b48e

fixed var name

1904007

use the same meta for segmentation instead of creating a different on…

bfaf949

…e which prevents further joins downstream

missed return

d74ddea

logging

c26d909

fixed the channel passed in the tuple

f14c5e3

rs-fish return real input image path

698d6ea

fixed log call

7388bdf

stage paths to avoid conflict

8d9cd6c

fixed syntax error - extra comma

e70def4

concat fixed and warped spots instead of mix

63df28d

logging - the output from warp spots is not as I expected

de64e9f

more logging; changed some cellpose params

f55a813

changed how I get the fixed spots

8a00651

fixed unique call

6a8e0ba

combine warped spots with segmentaton results

17dab80

changed how results are combined

4d929fa

eliminate seg meta from combined results

ceaa214

fixed the pattern; display command

e1bc1a9

pass different output dir for spot features

0f73426

cgoina and others added 23 commits April 30, 2025 18:41

check if spots file exist - bug fix

ec087fc

only test with -f

d8d1f97

fixed var

2979054

filter empty spots

791825e

bug fix - explicit return from filter

750a7e7

changed log level

8eefa62

use dapi channel for segmentation

db95429

renamed spots_counts module

32e5857

renamed spots counts

b5070a1

renamed measure spots wf

c2089c5

logging

ce6c87f

combine transform with all spots

3c1acc2

logging to track why not cell props are processed

c19b51c

combine all spot channels to extract region properties

eee0185

fixed syntax error

da2ae4a

missed include

1e4e050

use the proper round id to create the dataset

7b7c90f

renamed vars

c17581d

renamed spots props module

95b3b03

enable all steps

700d40e

changed cellpose_use_model_and_size to cellpose_eval_with_model_only …

866c842

…and now it defaults to false

change log level

8224020

changelog update

433b84e

cgoina assigned krokicki May 14, 2025

cgoina added 2 commits May 14, 2025 15:58

added missing params

6d87dee

Merge branch 'main' into spot-intensities

0b48e75

cgoina merged commit 22c17b4 into main May 15, 2025
0 of 9 checks passed

cgoina deleted the spot-intensities branch May 15, 2025 21:36

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Added spots counts and spots intensities steps #6

Added spots counts and spots intensities steps #6

Uh oh!

cgoina commented May 14, 2025

Uh oh!

github-actions bot commented May 14, 2025

Uh oh!

Uh oh!

github-actions bot commented May 15, 2025 •

edited

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Added spots counts and spots intensities steps #6

Added spots counts and spots intensities steps #6

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cgoina commented May 14, 2025

PR checklist

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github-actions bot commented May 14, 2025

This PR is against the master branch ❌

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github-actions bot commented May 15, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Failed ❌

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This PR is against the `master` branch ❌

github-actions bot commented May 15, 2025 •

edited

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`nf-core pipelines lint` overall result: Failed ❌