nf-core/molkart issues and pull requests

#54 - PR for first release

Pull Request - State: open - Opened by kbestak 8 months ago - 1 comment

#53 - updated mesmer to exlude leftover todo

Pull Request - State: closed - Opened by kbestak 8 months ago - 1 comment

#52 - Module update + CI

Pull Request - State: closed - Opened by kbestak 9 months ago - 3 comments

#51 - Molkartqc hotfix

Pull Request - State: closed - Opened by FloWuenne 9 months ago - 1 comment

#50 - Molkart local fix

Pull Request - State: closed - Opened by FloWuenne 9 months ago - 1 comment

#49 - Added anndata as an output format

Pull Request - State: closed - Opened by FloWuenne 9 months ago - 1 comment

#48 - Template update for nf-core/tools version 2.11.1

Pull Request - State: closed - Opened by kbestak 9 months ago - 1 comment

#47 - Merge template update for nf-core/tools v2.11

Issue - State: closed - Opened by kbestak 9 months ago

#46 - Important! Template update for nf-core/tools v2.11

Pull Request - State: closed - Opened by nf-core-bot 10 months ago

#45 - Fixed bug in Maskfilter config.

Pull Request - State: closed - Opened by FloWuenne 10 months ago - 1 comment

#44 - Process resources

Pull Request - State: closed - Opened by FloWuenne 10 months ago - 1 comment

#43 - Mesmer randomly fails on HPC using singularity due to model loading

Issue - State: closed - Opened by FloWuenne 10 months ago - 1 comment
Labels: bug

#42 - Clahe prefix fix

Pull Request - State: closed - Opened by FloWuenne 10 months ago - 1 comment

#41 - Go over remaining TODOs

Issue - State: closed - Opened by kbestak 10 months ago

#40 - Speedup mask filter.

Pull Request - State: closed - Opened by FloWuenne 10 months ago - 3 comments
Labels: enhancement

#39 - Added full test config file.

Pull Request - State: closed - Opened by FloWuenne 10 months ago - 1 comment

#38 - Maskfilter too slow

Issue - State: closed - Opened by kbestak 10 months ago - 1 comment
Labels: enhancement

#37 - Update tower.yml to include all qc metrics

Issue - State: open - Opened by kbestak 10 months ago - 1 comment
Labels: enhancement, help wanted

#36 - Crop overview multiqc

Pull Request - State: closed - Opened by kbestak 10 months ago - 3 comments

#35 - Local module revamp

Pull Request - State: closed - Opened by kbestak 10 months ago - 3 comments
Labels: enhancement

#34 - Reduce image size for local modules.

Issue - State: closed - Opened by kbestak 10 months ago - 1 comment

#33 - maskfilter added, molkartqc update, prefix fix, versions

Pull Request - State: closed - Opened by kbestak 10 months ago - 1 comment

#32 - Replaced local mindagap/duplicatefinder with nf-core module.

Pull Request - State: closed - Opened by FloWuenne 10 months ago - 1 comment

#31 - CLAHE changes

Pull Request - State: closed - Opened by kbestak 10 months ago - 1 comment

#30 - Mindagap outputs

Pull Request - State: closed - Opened by kbestak 10 months ago - 2 comments

#29 - If create training subset is run, pass crop overview to MultiQC.

Issue - State: closed - Opened by kbestak 10 months ago - 1 comment
Labels: enhancement

#28 - Molcart_QC --> Molkart_QC

Issue - State: closed - Opened by kbestak 10 months ago - 1 comment

#27 - Clahe optimization

Issue - State: closed - Opened by kbestak 10 months ago - 2 comments
Labels: enhancement

#26 - Add anndata container as an output format

Issue - State: closed - Opened by FloWuenne 10 months ago - 1 comment
Labels: enhancement

#25 - Added nf-test for pipeline main.nf

Pull Request - State: closed - Opened by kbestak 10 months ago - 1 comment

#24 - Documentation update

Issue - State: closed - Opened by kbestak 10 months ago - 1 comment
Labels: documentation

#23 - Added HOME mounting for mesmer singularity.

Pull Request - State: closed - Opened by FloWuenne 10 months ago - 2 comments

#22 - Mesmer does not require stack

Issue - State: closed - Opened by kbestak 10 months ago
Labels: enhancement

#21 - Mindagap - multiple samples with same input name

Issue - State: closed - Opened by kbestak 10 months ago
Labels: bug

#20 - Cellpose fix - custom model and multiple samples

Pull Request - State: closed - Opened by kbestak 11 months ago - 3 comments

#19 - Documentation

Pull Request - State: closed - Opened by kbestak 11 months ago - 3 comments

#18 - Added tilesize parameter for mindagap and mindagap_duplicatefinder

Pull Request - State: closed - Opened by kbestak 11 months ago - 2 comments

#17 - Additional parameters for Mindagap_mindagap and Mindagap_duplicatefinder

Issue - State: closed - Opened by kbestak 11 months ago - 2 comments
Labels: enhancement

#16 - Add tag to project_spots container / spot2cell container

Issue - State: closed - Opened by kbestak 11 months ago - 2 comments
Labels: enhancement

#15 - Replacing PROJECT_SPOTS and MCQUANT by more optimized method

Pull Request - State: closed - Opened by FloWuenne 11 months ago - 4 comments

#14 - Replaced clahe param with the skip_clahe param

Pull Request - State: closed - Opened by kbestak 12 months ago - 2 comments

#13 - Replace clahe parameter to skip_clahe so that the default is set to False, not True

Issue - State: closed - Opened by kbestak 12 months ago - 1 comment
Labels: enhancement

#12 - Add testing using nf-test

Issue - State: closed - Opened by FloWuenne 12 months ago - 4 comments
Labels: enhancement

#11 - Replace project spots and mcquant with faster method

Issue - State: closed - Opened by FloWuenne 12 months ago - 1 comment
Labels: WIP, enhancement

#10 - Initial MultiQC parsing

Pull Request - State: closed - Opened by kbestak 12 months ago - 2 comments

#9 - Add QC parsing with MultiQC

Issue - State: closed - Opened by kbestak 12 months ago - 2 comments
Labels: enhancement

#8 - Add option to filter masks and exclude mean intensities

Issue - State: closed - Opened by kbestak 12 months ago - 7 comments
Labels: enhancement, feature-request

#7 - #molkart QC parsing with MultiQC

Issue - State: closed - Opened by kbestak 12 months ago

#6 - Add ilastik pixel classifier and multicut as segmentation options

Issue - State: closed - Opened by kbestak 12 months ago - 1 comment
Labels: enhancement

#5 - Documentation update: add documentation

Issue - State: closed - Opened by kbestak 12 months ago - 1 comment
Labels: documentation

#4 - Initial setup

Pull Request - State: closed - Opened by kbestak 12 months ago - 1 comment

#3 - Important! Template update for nf-core/tools v2.10

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 2 comments

#2 - First minimal working version of pipeline

Pull Request - State: closed - Opened by FloWuenne about 1 year ago - 2 comments

#1 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago

GitHub / nf-core/molkart issues and pull requests