Code

Fix issue 81, "call empty droplets"#301

Code

Merged

fmalmeida merged 34 commits intodevnf-core/scrnaseq:devfrom 81-call-empty-dropletsnf-core/scrnaseq:81-call-empty-dropletsCopy head branch name to clipboardMar 18, 2024

+682-174

Commits

Commits on Jan 31, 2024

• minimum inclusion for module

  Show description for 6d81894
  

  fmalmeida

  committed
  6d81894

Commits on Feb 1, 2024

• update input_type labels

  

  fmalmeida

  committed
  afe4904

Commits on Feb 2, 2024

• fixed workflow conversions to work with star align results

  

  fmalmeida

  committed
  d03d81f

Commits on Feb 5, 2024

• include modifications for working with cellranger

  

  fmalmeida

  committed
  796afba

Commits on Feb 7, 2024

• fix the path of matrices when running non-standard kallisto workflow (tested with lamanno)

  

  fmalmeida

  committed
  c9c38ea

• fix spliced/unspliced empty_drops conversion

  

  fmalmeida

  committed
  a9ee3f1

• solve number of list levels when having spliced / unspliced

  

  fmalmeida

  committed
  0cb2a2f

Commits on Feb 14, 2024

• Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 81-call-empty-droplets

  

  fmalmeida

  committed
  8a2e818

• update shared nf-test config

  

  fmalmeida

  committed
  6458e2d

• update alevin file names

  

  fmalmeida

  committed
  c5cc1ca

• update alevin tests to also include the .rds files

  fmalmeida

  committed
  c539399

• update the number of tasks that are executed, and include raw/filtered in the testings (cellranger)

  fmalmeida

  committed
  2d7c90e

• fix naming of generated files (kallisto)

  fmalmeida

  committed
  c72c8f2

• update the amount of tasks and generated file names raw/filtered (star)

  fmalmeida

  committed
  5d1d783

• update gitignore

  fmalmeida

  committed
  4095c3d

Commits on Feb 15, 2024

• add new params to schema

  fmalmeida

  committed
  6981c44

Commits on Mar 7, 2024

• Merge branch 'dev' into 81-call-empty-droplets

  grst

  authored
  030322a

Commits on Mar 8, 2024

• Update bin/emptydrops_cell_calling.R

  Show description for e350399
  

  fmalmeida

  and

  grst

  authored
  e350399

Commits on Mar 11, 2024

• fixing stub snippet

  

  fmalmeida

  committed
  7daa310

• fix transposition snippet in new module

  

  fmalmeida

  committed
  c24a05d

• Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 81-call-empty-droplets

  

  fmalmeida

  committed
  618c721

Commits on Mar 12, 2024

• fixed problem on loading fasta&gtf from params.genome

  

  fmalmeida

  committed
  492598b

• fixed transposition

  

  fmalmeida

  committed
  6207655

• fixed file used

  

  fmalmeida

  committed
  8c5702b

Commits on Mar 13, 2024

• Merge branch 'dev' into 81-call-empty-droplets

  grst

  authored
  7c8ed95

• updating documentation

  

  fmalmeida

  committed
  3adeb65

• remove unused parameter

  

  fmalmeida

  committed
  48dd996

• adjust modules to handle kallisto outputs form non-standard (lamanno & nac) workflows

  

  fmalmeida

  committed
  9cd8edd

• when running kallisto non-standard workflow store emptydrops in subdirs to avoid file collision

  

  fmalmeida

  committed
  d77eda8

Commits on Mar 18, 2024

• update modules to get them from nf-core/modules

  

  fmalmeida

  committed
  c460f28

• prettier fix

  fmalmeida

  committed
  1c1f1ac

• small update as file names changed

  fmalmeida

  committed
  6351f76

• add ending line

  fmalmeida

  committed
  9734ace

• update changelog

  fmalmeida

  committed
  2406600