Code

v3.0.0 release#404

Code

Merged

apeltzer merged 168 commits intomasternf-core/scrnaseq:masterfrom devnf-core/scrnaseq:devCopy head branch name to clipboardDec 10, 2024

+3,088-2,704

Commits

Commits on Aug 15, 2024

• bump version to v2.8dev

  grst

  committed
  4c27011

• update changelog

  grst

  committed
  3aaf168

• Merge pull request #362 from nf-core/bump-version

  Show description for 783510f
  grst

  authored
  783510f

Commits on Aug 19, 2024

• comment out for development

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  52fa9ca

• refact modules for STAR aligner

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  bbf299c

• directly pass txp2gene

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  c3eb5ea

• simplify module lines

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  4771ed1

• emit h5ad on starsolo

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  af85f87

• add versions emition

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  d2a5386

• update module to use templates and cleanup way of priting versions

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  0e55051

Commits on Aug 20, 2024

• fix h5ad generator script

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  994d5a5

• simplify check

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  b317165

Commits on Aug 21, 2024

• Fix h5ad structure

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  72e9d50

Commits on Aug 30, 2024

• updated concat module

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  8829080

• workflow misses emptydrops and seurat & mtx conversion modules

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  9fc75b4

Commits on Sep 12, 2024

• start emptydrops cellbender subworkflow

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  dc69f47

Commits on Sep 13, 2024

• fix paths

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  9c20420

• started the anndatar standardization module

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  6831195

• concat h5ad with anndatar h5ad

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  237d1ca

• update tag information

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  f5fb4a2

• update tags

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  752666b

• module is only to convert to rds

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  d0ad7f6

• update directives

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  20ac4ae

• update comments

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  da5b036

• add cellbender to workflow

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  b90f388

• start organisation of files

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  7c304cc

Commits on Sep 16, 2024

• update doc related to alevin-fry, simpleaf and salmon

  an-altosian

  committed
  012f608

• update simpleaf reference

  an-altosian

  committed
  c02a054

• change aligner name back to alevin

  an-altosian

  committed
  f2c1a24

• change aligner name back to alevin

  an-altosian

  committed
  77f91f7

• make prettier happy

  an-altosian

  committed
  973508b

Commits on Sep 24, 2024

• Merge pull request #368 from an-altosian/dev

  Show description for 3e2412d
  DongzeHE

  authored
  3e2412d

Commits on Sep 26, 2024

• fix file naming

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  8320431

• resolve emptydrops naming

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  1c95e85

• also convert emptydrops filter matrices

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  e6fff34

• move files to BKP since they will be replaced

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  e9c88e8

• add conversion for alevin

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  f7f5fa5

• re-organise star modules

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  73c91c2

Commits on Sep 27, 2024

• fixed publishDir directives

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  417bf69

Commits on Sep 30, 2024

• add h5ad conversion module

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  94bf9c1

• integrate to mtx_conversion module

  Show description for 43a29c2
  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  43a29c2

• reorganize module levels and fix docker image

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  7fc32f0

• reorganize star modules

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  e366396

Commits on Oct 4, 2024

• re-structure and include cellranger

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  76f126e

• add alevin to new structure

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  b92af8b

• add star to new structure

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  c57b09f

• Add kallisto standard workflow to structure

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  d0d1f81

• Account for non-standard kallisto workflows

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  aa99cd1

• Simplify alevin template

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  0ca1161

Commits on Oct 7, 2024

• reorganise star template

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  28251b0

Commits on Oct 8, 2024

• Template update for nf-core/tools version 3.0.0

  nf-core-bot

  committed
  c785b97

Commits on Oct 9, 2024

• Template update for nf-core/tools version 3.0.1

  nf-core-bot

  committed
  3958cc2

Commits on Oct 11, 2024

• Template update for nf-core/tools version 3.0.2

  nf-core-bot

  committed
  d88d669

• Fix #380

  esrice

  committed
  81ba001

• Fix same error as last commit, but for alevin

  Show description for 017e0d3
  esrice

  committed
  017e0d3

Commits on Oct 17, 2024

• Merge branch 'dev' into nf-core-template-merge-3.0.2

  nictru

  committed
  623e02d

• Update fastqc and multiqc

  nictru

  committed
  6f9dc79

• Remove check_max usages

  nictru

  committed
  2ed44fe

• Remove old resource limits from tests

  nictru

  committed
  ecba92d

• Set global resource limits

  nictru

  committed
  42c5aa3

• Align test resource limits with previous implementation

  nictru

  committed
  a6ed155

Commits on Oct 18, 2024

• Remove problematic workflow snapshotting

  nictru

  committed
  4a71603

• Merge pull request #381 from nf-core/nf-core-template-merge-3.0.2

  Show description for 44c9360
  nictru

  authored
  44c9360

Commits on Oct 28, 2024

• Fix potential filename conflict

  Show description for 9d13a7e
  esrice

  committed
  9d13a7e

• Merge pull request #382 from esrice/fix-star-gzip-error

  Show description for eaa74dd
  grst

  authored
  eaa74dd

Commits on Oct 29, 2024

• feat(cellranger count and multi): Add create-bam option to cellranger count and multi pipelines

  kopichris

  committed
  0098906

• chore: Update changelog

  kopichris

  committed
  c749bf2

Commits on Oct 30, 2024

• write uncompressed

  Show description for c1e8357
  

  fmalmeida

  and

  grst

  authored
  c1e8357

• use .astype(str)

  Show description for ae85710
  

  fmalmeida

  and

  grst

  authored
  ae85710

• simplify iteration

  Show description for ae8809a
  

  fmalmeida

  and

  grst

  authored
  ae8809a

• perform join left operation

  Show description for 68464de
  

  fmalmeida

  and

  grst

  authored
  68464de

• do not compress output h5ad

  Show description for fdedc4d
  

  fmalmeida

  and

  grst

  authored
  fdedc4d

• perform join left operation

  Show description for 187dbf6
  

  fmalmeida

  and

  grst

  authored
  187dbf6

• not compress h5ad output

  fmalmeida

  committed
  98af608

• simplify iteration

  fmalmeida

  committed
  efd6299

• simplify index iteration

  fmalmeida

  committed
  f357fd7

• fix unmatched parenthesis

  fmalmeida

  committed
  bd1a74c

• fix use of igenomes ... pipeline was not properly selecting igenomes options

  fmalmeida

  committed
  4731e00

• correct values parsing

  fmalmeida

  committed
  a71348f

• fix container registry

  fmalmeida

  committed
  d2f9cfd

• do not save versions files

  fmalmeida

  committed
  5c31226

• also convert concat h5ads

  fmalmeida

  committed
  8278429

• manage subdirectory in publishDir

  fmalmeida

  committed
  2b199d0

• match template scripts with new publishDir

  fmalmeida

  committed
  cb67797

• have outputs separated

  fmalmeida

  committed
  7230095

• make parsing inside sub-workflow

  fmalmeida

  committed
  206a7c1

• added kallisto to correct structure

  fmalmeida

  committed
  c4a09e0

• correct mix of channels

  fmalmeida

  committed
  971667b

• correct for cellranger multi

  fmalmeida

  committed
  8122113

• correct stub

  fmalmeida

  committed
  44d1cb7

• remove glob in txp2gene

  fmalmeida

  committed
  18cfdd7

• added small comment to local modules

  fmalmeida

  committed
  079bb7e

Commits on Nov 1, 2024

• feat: Create single boolean parameter allowing users to control how alignment files are saved for CellRanger and STAR

  kopichris

  committed
  36eeee3

Commits on Nov 2, 2024

• Add pre-built cellranger, cellranger-arc simpleaf

  FelixKrueger

  committed
  128b183

• Added pre-build iundex support to Changelog

  FelixKrueger

  committed
  dd566c9

• better comment

  FelixKrueger

  committed
  952a24c

Commits on Nov 4, 2024

• make cellranger arc index conditional

  FelixKrueger

  committed
  d2478c1

Commits on Nov 5, 2024

• Merge remote-tracking branch 'upstream/dev' into feature/create-bam-parameter

  kopichris

  committed
  2a89724

• cleaner cellranger index declaration

  FelixKrueger

  committed
  613a4c5

• removed trailing whitespace

  FelixKrueger

  committed
  8c43909

• fixed space

  FelixKrueger

  committed
  d68c883

Commits on Nov 6, 2024

• Merge pull request #390 from nf-core/use_indices

  Show description for b5b061e
  grst

  authored
  b5b061e

• Remove check_max function in cellranger_count block

  Show description for bf1a9df
  

  kopichris

  and

  grst

  authored
  bf1a9df

Commits on Nov 8, 2024

• chore: remove string from time property in cellranger count module

  kopichris

  committed
  2cfe0df

Commits on Nov 15, 2024

• split mtx to h5ad conversion and general conversion, so h5ad is generated separately for all aligners, and then passed for format conversion, custom filter and concat.

  fmalmeida

  committed
  a0bf7ab

Commits on Nov 18, 2024

• [automated] Fix code linting

  nf-core-bot

  committed
  1a18dc8

• Merge branch 'dev' into feature/create-bam-parameter

  grst

  authored
  750e644

Commits on Nov 22, 2024

• Merge pull request #387 from kopichris/feature/create-bam-parameter

  Show description for 2d0015e
  grst

  authored
  2d0015e

Commits on Nov 25, 2024

• fix star index channel generation

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  2fd1d41

• fixed tuple size

  fmalmeida

  committed
  b615e01

• Update kallisto script

  grst

  committed
  ae74481

• update alevin nf-test and snaps

  fmalmeida

  committed
  bf78578

• Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow

  fmalmeida

  committed
  e8e5094

• added singlecellobject export

  fmalmeida

  committed
  8f3f187

• include singlecellexperiment object in nf-test and update namings

  fmalmeida

  committed
  fae2099

• avoind assessing params from modules

  fmalmeida

  committed
  9d8577b

• add snippet to make values unique

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  705df81

• Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  e1a8844

• fix star channel parsing

  fmalmeida

  committed
  804d5cd

• Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow

  fmalmeida

  committed
  916ddb6

• simplified kallisto so non-standardo workflow have spliced and unspliced as layers in the same object

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  41731ac

• Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  4a03b7f

• update star nf-test, snaps and file namings

  fmalmeida

  committed
  298c491

• Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow

  fmalmeida

  committed
  c4eda69

Commits on Nov 26, 2024

• fix channel size

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  208c11b

• Fix kallisto mtx script

  grst

  committed
  f120824

• add a little comment line

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  8e88384

• updated cellranger nf-test sizes, namings and snaps

  fmalmeida

  committed
  a15a28b

• Update kallisto script (again)

  grst

  committed
  245ae5b

• update kallisto nf-test size, namings and snaps

  fmalmeida

  committed
  bee74f6

• adding versions.yml output for modules CONCAT_H5AD, MTX_TO_H5AD and ANNDATAR_CONVERT

  fmalmeida

  committed
  dfb439a

• correct ifelse order for file renames

  fmalmeida

  committed
  eed41c0

Commits on Nov 28, 2024

• Merge branch 'dev' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  c001a0f

• re-add missing star_align ext.args

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  b245be2

• correct the parsing of getGenomeAttribute as a nextflow variable, since it is not possible to overwrite params. in the workflow scope

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  80e7850

• current version of star is incompatible with the star index available in igenomes

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  395a3e8

• add checkIfExists: true to file loading calls

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  6ddcf15

• remove old conversion scripts

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  72c2242

Commits on Nov 29, 2024

• update changelog

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  dd41a8b

• add TODO

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  9c6d405

• update emptydrops documentation

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  f07cac6

• update cellranger snaps

  fmalmeida

  committed
  d12f64d

• Merge branch 'standardize-conversion-workflow' of https://github.com/nf-core/scrnaseq into standardize-conversion-workflow

  fmalmeida

  committed
  595be8b

• update kallisto snaps

  fmalmeida

  committed
  a6f47f5

• update alevin snaps

  fmalmeida

  committed
  a2c1a11

• Update modules/local/templates/barcodes.py

  Show description for d106e6e
  

  fmalmeida

  and

  grst

  authored
  d106e6e

• fix anndatar to nf-core container

  fmalmeida

  committed
  b84770e

• add resources control to cellrangermulti testing profile

  fmalmeida

  committed
  a2fc476

• add metadata

  fmalmeida

  committed
  d194bfa

• allow regex to also find cellrangermulti results

  fmalmeida

  committed
  e9836fd

• update cellranger multi nf-test snaps

  fmalmeida

  committed
  3e3608c

• update star nf-test snaps

  fmalmeida

  committed
  2830093

• prettier fix

  fmalmeida

  committed
  fae53a2

• avoid fetching star index from iGenomes due version incompatibility

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  84a83c2

Commits on Dec 2, 2024

• add .var_names_make_unique() to star code which was missing

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  b498ddc

• Merge pull request #369 from nf-core/standardize-conversion-workflow

  Show description for d3d8a6f
  grst

  authored
  d3d8a6f

Commits on Dec 3, 2024

• update changelog

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  ba38a9c

• remove all universc things

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  0a48157

• update images

  fmalmeida

  committed
  8a98f31

Commits on Dec 4, 2024

• use correct java version in ci

  fmalmeida

  committed
  5aa3068

Commits on Dec 9, 2024

• Merge pull request #396 from nf-core/289-update-or-remove-universc

  Show description for c336812
  grst

  authored
  c336812

• bump version and update changelog

  grst

  committed
  6878b6b

• enable custom pipeline config

  grst

  committed
  eaca45a

• Merge pull request #403 from nf-core/bump-version

  Show description for 1a84433
  grst

  authored
  1a84433

• Improved statement regarding 10X container(s)

  apeltzer

  committed
  ffe4ae2

• Merge pull request #405 from nf-core/licence-readme

  Show description for 5209fe4
  apeltzer

  authored
  5209fe4

Commits on Dec 10, 2024

• include nac conversion workflow

  

  zxBIB Almeida,Felipe (GCBDS) EXTERNAL

  committed
  e00f98c

• Merge pull request #406 from nf-core/fix-kallisto-nac-in-v300

  Show description for 68d2811
  fmalmeida

  authored
  68d2811