Code

PR for first release#54

Code

Merged

kbestak merged 183 commits intomasternf-core/molkart:masterfrom devnf-core/molkart:devCopy head branch name to clipboardFeb 12, 2024

+4,469-1,372

Commits

Commits on Jun 30, 2023

• Template update for nf-core/tools version 2.9

  nf-core-bot

  committed
  349aa30

Commits on Jul 13, 2023

• Updated README to include note about development phase.

  FloWuenne

  committed
  78c9c51

• Merge pull request #1 from nf-core/nf-core-template-merge-2.9

  Show description for 0510805
  FloWuenne

  authored
  0510805

Commits on Aug 10, 2023

• Installed first batch of nf-core modules.

  FloWuenne

  committed
  f2be8fc

• Automatic nextflow.config update.

  FloWuenne

  committed
  2f1e800

Commits on Sep 19, 2023

• Started removing genome specific parameters from template.

  FloWuenne

  committed
  111658f

• Prettier modification.

  FloWuenne

  committed
  a2b153c

• Added mindagap and project spots to pipeline.

  FloWuenne

  committed
  de52076

• Added local modules

  FloWuenne

  committed
  f3e4de9

Commits on Sep 20, 2023

• Modified main workflow.

  FloWuenne

  committed
  4235a64

• Removed Fastqc module. Added parametre for project_spots.

  FloWuenne

  committed
  9cc6e15

• Fully working minimal pipeline.

  FloWuenne

  committed
  b585509

• Added version parsing for modules.

  FloWuenne

  committed
  f67dd2b

• Minimal pipeline completely working.

  FloWuenne

  committed
  75aff27

Commits on Sep 25, 2023

• Template update for nf-core/tools version 2.10

  nf-core-bot

  committed
  3a1dcd8

Commits on Sep 27, 2023

• Merge pull request #2 from FloWuenne/minimal_pipeline

  Show description for cd6ed39
  FloWuenne

  authored
  cd6ed39

• Resolving conflicts with new template

  kbestak

  committed
  ba4ab94

• Ran Python linting (black)

  kbestak

  committed
  f47b8d1

• Indentation fix in modules.config

  kbestak

  committed
  155caf8

• Merge pull request #3 from nf-core/nf-core-template-merge-2.10

  Show description for 49d9e97
  FloWuenne

  authored
  49d9e97

• Removed igenome from main.nf

  kbestak

  committed
  c9742be

Commits on Oct 6, 2023

• Reformatted channel handling for parallelisability

  kbestak

  committed
  8478b82

Commits on Oct 10, 2023

• Added channel stacking and optional membrane handling - not yet with Cellpose

  kbestak

  committed
  170cbab

Commits on Oct 11, 2023

• Added parameters, Cellpose external model, rewrote channel processing

  kbestak

  committed
  67467a7

Commits on Oct 12, 2023

• Started work on create training subset functionality

  kbestak

  committed
  f8470c9

• Updated changelog

  kbestak

  committed
  1fd16d0

• Create training subset functional

  kbestak

  committed
  c9d58ed

• Merge pull request #1 from kbestak/TODO_0

  Show description for 457328d
  kbestak

  authored
  457328d

• Fixed container registry for 2 modules and added flows for cellpose.

  FloWuenne

  committed
  40fc2bd

• Fixed container repo for 2 modules. Added cellpose flow fields parameter.

  FloWuenne

  committed
  6695106

Commits on Oct 16, 2023

• Ran Python Black to reformat code

  kbestak

  committed
  2da3f69

Commits on Oct 17, 2023

• Added ilastik segmentation with custom project files

  kbestak

  committed
  cfbcc8e

• Merge pull request #4 from kbestak/Initial_setup

  Show description for 60439b4
  FloWuenne

  authored
  60439b4

Commits on Oct 18, 2023

• Added MultiQC processing - first version

  kbestak

  committed
  ff75e56

• Added MultiQC processing - CHANGELOG

  kbestak

  committed
  e2315f6

Commits on Oct 23, 2023

• Fixed URL in multiqc and spacing in createtraining.tiff.nf

  FloWuenne

  committed
  c659d39

• Replaced clahe param with skip_clahe

  kbestak

  committed
  2cb3705

• Reverting multiqc report_comment link fix.

  FloWuenne

  committed
  d568505

• Merge pull request #10 from nf-core/multiqc

  Show description for a2499bb
  FloWuenne

  authored
  a2499bb

• Merge branch 'dev' into clahe_param_to_skip_clahe

  FloWuenne

  authored
  1f775c4

• Prettier linting fix for changelog.md.

  FloWuenne

  committed
  f348642

• Fixed random text in nextflow.config.

  FloWuenne

  committed
  8153591

• Merge pull request #14 from nf-core/clahe_param_to_skip_clahe

  Show description for 8313bf2
  FloWuenne

  authored
  8313bf2

• Replace project spots and mcquant with spots2cell.

  FloWuenne

  committed
  f6cba52

• Added process labels to modules missing it.

  FloWuenne

  committed
  b7b6444

Commits on Oct 24, 2023

• MolcartQC working with spots2cell.

  FloWuenne

  committed
  8e540c0

• Added meta map to MOLCART_QC.

  FloWuenne

  committed
  de1389a

• Python black fixes.

  FloWuenne

  committed
  a4d7461

• Fixed multiqc break, removed Project_spots and MCQuant, added Duplicated spot count to QC

  kbestak

  committed
  58ec42f

• Updated CHANGELOG.md

  kbestak

  committed
  9123124

• Updated scripts with Python Black

  kbestak

  committed
  1cd329a

Commits on Oct 25, 2023

• Added tilesize parameter for mindagap and mindagap_duplicatefinder

  kbestak

  committed
  73f8ec1

• Updated CHANGELOG.md

  kbestak

  committed
  e9ca17a

• Removed mcquant completely.

  FloWuenne

  committed
  91d31bd

• Merge pull request #15 from nf-core/spot2cell

  Show description for 1822788
  FloWuenne

  authored
  1822788

• Merge branch 'dev' into mindagap_tilesize

  FloWuenne

  authored
  ac6b1ff

• Prettier fixing of Changeleg.

  FloWuenne

  committed
  df32423

• Merge pull request #18 from nf-core/mindagap_tilesize

  Show description for f6c535d
  FloWuenne

  authored
  f6c535d

Commits on Nov 10, 2023

• Added output.md and updated modules to include environment.yml to pass lint warning

  kbestak

  committed
  f726d69

• removed fastqc plots as they are not releveant for this pipeline

  kbestak

  committed
  3b138c6

• Specified usage

  kbestak

  committed
  b7971d6

• Updated usage

  kbestak

  committed
  d8068fb

• Updated changelog, added segmentation overhead folder

  kbestak

  committed
  0635f33

• Added optional params to documentation

  kbestak

  committed
  28dbee7

Commits on Nov 13, 2023

• Updated CHANGELOG, README, CITATIONS

  kbestak

  committed
  4ab90b6

• Updated date in changelog

  kbestak

  committed
  9f2e1ea

Commits on Nov 14, 2023

• Fixed WorkflowMolkart.groovy

  kbestak

  committed
  0e5e4a2

• Added metromap png

  kbestak

  committed
  4b77047

• Removed workflow TODO

  kbestak

  committed
  241354d

• Prettier changes.

  FloWuenne

  committed
  e88a4c3

• Merge pull request #19 from nf-core/Documentation

  Show description for 3c46f9d
  FloWuenne

  authored
  3c46f9d

Commits on Nov 15, 2023

• Fixed Cellpose custom model multisample, added clahe_skip_pyramid

  kbestak

  committed
  6b152d7

• Added usage for clahe_skip_pyramid

  kbestak

  committed
  15de9b0

• Ran black on apply_clahe.dask.py

  kbestak

  committed
  a74f794

Commits on Nov 16, 2023

• Moved docker entrypoint fix from process to docker scope.

  FloWuenne

  committed
  3c5b0fe

Commits on Nov 20, 2023

• Updated cellpose and fixed singularity error.

  FloWuenne

  committed
  07d1b30

• Merge pull request #20 from nf-core/Cellpose_fix

  Show description for 2da1dd5
  FloWuenne

  authored
  2da1dd5

Commits on Nov 24, 2023

• Added nf-test for pipeline main.nf

  kbestak

  committed
  bebee88

• Updated CHANGELOG

  kbestak

  committed
  350d73c

• Added test.config specifications

  kbestak

  committed
  e961077

• Updated tests

  kbestak

  committed
  6becbbd

• Removed hardcoded memory requirements

  kbestak

  committed
  9d4ead6

Commits on Nov 27, 2023

• Merge pull request #25 from nf-core/nf_test

  Show description for bc6f446
  FloWuenne

  authored
  bc6f446

Commits on Nov 28, 2023

• Filename overwrites for mindagap and spot2cell fixed

  kbestak

  committed
  12fd24b

• Mesmer does not require stacks

  kbestak

  committed
  007afe4

Commits on Nov 29, 2023

• Ran Python black on spot2cell.py

  kbestak

  committed
  d9b8149

• Merge pull request #30 from nf-core/mindagap_outputs

  Show description for 3d80a6e
  FloWuenne

  authored
  3d80a6e

Commits on Nov 30, 2023

• CLAHE changes

  kbestak

  committed
  1fa06a9

• updated test.config

  kbestak

  committed
  c39ee20

• updated usage.md

  kbestak

  committed
  3cd81c6

• updated output.md

  kbestak

  committed
  4e63f0f

Commits on Dec 2, 2023

• Merge pull request #31 from nf-core/clahe_and_filter

  Show description for 09918f0
  FloWuenne

  authored
  09918f0

• Replaced local mindagap/duplicatefinder with nf-core module.

  FloWuenne

  committed
  68bd97a

Commits on Dec 3, 2023

• Delete null/pipeline_info/execution_trace_2023-12-02_12-23-56.txt

  Show description for 610b1c8
  FloWuenne

  authored
  610b1c8

Commits on Dec 4, 2023

• Moved duplicatefinder to nf-core modules section

  kbestak

  authored
  cdabd16

• Merge pull request #32 from nf-core/duplicatefinder_patch

  Show description for 4acfb71
  kbestak

  authored
  4acfb71

Commits on Dec 5, 2023

• maskfilter added, molkartqc update, prefix fix, versions

  kbestak

  committed
  788c3c6

• Updated documentation

  kbestak

  committed
  1e779bc

• lint_fix

  kbestak

  committed
  db0df33

Commits on Dec 6, 2023

• Merge pull request #33 from nf-core/maskfilter

  Show description for f9a8aa5
  FloWuenne

  authored
  f9a8aa5

Commits on Dec 7, 2023

• local_module_revamp first

  kbestak

  committed
  307e1e6

• adapted clahe and stack

  kbestak

  committed
  b07a389

• added versions for stack

  kbestak

  committed
  c4ebc3d

• stack version emitted

  kbestak

  committed
  137f2df

• Ran Python black

  kbestak

  committed
  a49d2e0

• Removed trailing whitespace...

  kbestak

  committed
  50bf72c

• publish dir mode change

  kbestak

  committed
  20bb42b

• Updated license

  kbestak

  committed
  c05c6ae

Commits on Dec 8, 2023

• Update CHANGELOG.md

  Show description for 346e6b8
  

  kbestak

  and

  FloWuenne

  authored
  346e6b8

• Merge pull request #35 from nf-core/local_module_revamp

  Show description for 68a2028
  FloWuenne

  authored
  68a2028

• mulitqc parses crop overview

  kbestak

  committed
  6b92202

Commits on Dec 9, 2023

• Updated modules

  kbestak

  committed
  db5f385

Commits on Dec 11, 2023

• crop_overview_checkup

  kbestak

  committed
  ca2e30f

• Added molkartqcpng process

  kbestak

  committed
  282362c

• black on collect_QC.py

  kbestak

  committed
  baa87db

Commits on Dec 14, 2023

• Publish cropsummary in multiqc folder

  kbestak

  committed
  86a3286

Commits on Dec 15, 2023

• Removed leftover line

  kbestak

  committed
  8bd15fd

• Merge pull request #36 from nf-core/crop_overview_multiqc

  Show description for 3a0b2ef
  FloWuenne

  authored
  3a0b2ef

• Added full test config file.

  FloWuenne

  committed
  e437bb6

• Updated changelog.

  FloWuenne

  committed
  5b53fb3

• Speedup mask filter.

  FloWuenne

  committed
  43e231e

• Prettier fix.

  FloWuenne

  committed
  cb44f93

Commits on Dec 16, 2023

• Fixed formatting.

  FloWuenne

  committed
  f4c22fe

• reverted nfcore gitpod to latest

  kbestak

  committed
  3b654a3

• Merge pull request #39 from nf-core/full_test

  Show description for 9776860
  kbestak

  authored
  9776860

• Update bin/maskfilter.py

  Show description for 1d68330
  

  FloWuenne

  and

  kbestak

  authored
  1d68330

• Merge pull request #40 from nf-core/speedup_maskfilter

  Show description for eecf921
  kbestak

  authored
  eecf921

Commits on Dec 18, 2023

• Changed prefix naming for CLAHE to prevent file overlap.

  FloWuenne

  committed
  b36db58

• Updated Changelog.

  FloWuenne

  committed
  5ae7dd6

• Delete null/pipeline_info/execution_trace_2023-12-18_13-37-29.txt

  FloWuenne

  authored
  15a6152

• Update conf/modules.config

  Show description for 6967c92
  

  FloWuenne

  and

  kbestak

  authored
  6967c92

• Merge pull request #42 from nf-core/clahe_prefix_fix

  Show description for 6c1eef8
  FloWuenne

  authored
  6c1eef8

• Increased label to process_medium for clahe and maskfilter.

  FloWuenne

  committed
  48f76a4

• Updated Changelog.

  FloWuenne

  committed
  d12c4a2

Commits on Dec 19, 2023

• Fixed bug in Maskfilter config.

  FloWuenne

  committed
  a7fbd6e

• Merge pull request #45 from nf-core/hotfix_maskfilter

  Show description for 7bff06d
  kbestak

  authored
  7bff06d

• Added first version of formatting spot2cell as anndata.

  FloWuenne

  committed
  cccd7b9

• Black reformatting.

  FloWuenne

  committed
  2d0b476

• Template update for nf-core/tools version 2.11

  nf-core-bot

  committed
  fd736f1

Commits on Dec 20, 2023

• Template update for nf-core/tools version 2.11.1

  nf-core-bot

  committed
  45a4ca9

Commits on Jan 2, 2024

• Merge pull request #44 from nf-core/process_resources

  Show description for 1f6ec81
  kbestak

  authored
  1f6ec81

Commits on Jan 3, 2024

• Merged changes from nf-core template

  kbestak

  committed
  661c53a

Commits on Jan 4, 2024

• Merge pull request #48 from kbestak/merging-template-updates2.11.1

  Show description for 13fbef4
  kbestak

  authored
  13fbef4

• Merge remote-tracking branch 'origin/dev' into anndata_output

  FloWuenne

  committed
  87a1cbf

• Added createanndata process after spot2cell.

  FloWuenne

  committed
  6223d0d

• Updated molkart-local version to v0.0.3 for all local modules.

  FloWuenne

  committed
  ce431c6

• Modified create anndata code to add regionprops to adata.obs.

  FloWuenne

  committed
  a2444c3

• Prettier fix.

  FloWuenne

  committed
  0f6bc16

• Changelog update.

  FloWuenne

  committed
  b2db2eb

• Added anndata to output.md

  FloWuenne

  committed
  9f2c81f

• Added anndata to CITATIONS.md

  FloWuenne

  committed
  01ff5c9

Commits on Jan 5, 2024

• minor_fixes

  kbestak

  committed
  e095a69

• Merge pull request #49 from nf-core/anndata_output

  Show description for 252f68d
  FloWuenne

  authored
  252f68d

• Updated molkart-local container version.

  FloWuenne

  committed
  d245f99

Commits on Jan 6, 2024

• Added changes to changelog.

  FloWuenne

  committed
  f5abf0d

• Merge pull request #50 from nf-core/molkart_local_fix

  Show description for 7aa97ec
  FloWuenne

  authored
  7aa97ec

Commits on Jan 8, 2024

• Fixed maskfilter bug.

  FloWuenne

  committed
  6ab6e27

• Fixed Changelog typo.

  FloWuenne

  committed
  c0a4b43

• Merge pull request #51 from nf-core/molkartqc_hotfix

  Show description for 81eafe9
  kbestak

  authored
  81eafe9

Commits on Jan 16, 2024

• updated modules

  kbestak

  committed
  a535b30

• Adapted pipeline to new mindagap version

  kbestak

  committed
  0660f03

• removed mindagap todo

  kbestak

  committed
  2de50b4

• updated changelog

  kbestak

  committed
  a6fcde6

• fixed test.config

  kbestak

  committed
  8307d1f

• updated usage

  kbestak

  committed
  829503b

• update ci.yml

  kbestak

  committed
  155d9c2

• attempt at better ci

  kbestak

  committed
  1aaaf42

• attempt at ci

  kbestak

  committed
  e7bce41

• ci attempt

  kbestak

  committed
  68d0b15

• ci attempt

  kbestak

  committed
  950ab23

• ci attempt

  kbestak

  committed
  be09362

• ci attempt

  kbestak

  committed
  b8e7530

• removed singularity from ci test

  kbestak

  committed
  c33fdc6

• updated base.config

  kbestak

  committed
  59c7ece

Commits on Jan 19, 2024

• metromap and logo update

  kbestak

  committed
  181c2ac

• Revert "metromap and logo update"

  Show description for f37b992
  kbestak

  committed
  f37b992

• reverted previous commit and updated metromap

  kbestak

  committed
  a81bb19

• [automated] Fix linting with Prettier

  nf-core-bot

  committed
  6d5f606

Commits on Jan 24, 2024

• Update test_full.config

  Show description for ae4c361
  FloWuenne

  authored
  ae4c361

• Merge pull request #52 from kbestak/todo_module_update

  Show description for a729ac4
  kbestak

  authored
  a729ac4

• updated mesmer to exlude leftover todo

  kbestak

  committed
  7496468

• Merge pull request #53 from nf-core/version_bump

  Show description for cb9e81f
  kbestak

  authored
  cb9e81f

• version bump 1.0.0

  kbestak

  committed
  14841ae