Code

Merge Haploflow into master#1015

Code

Draft

Donaim wants to merge 68 commits intomastercfe-lab/MiCall:masterfrom Haploflow-test1cfe-lab/MiCall:Haploflow-test1Copy head branch name to clipboard

+111-161

Commits

Commits on Jul 23, 2021

• Use Haploflow instead of IVA

  CBeelen

  committed
  18dcfe3

Commits on Jul 30, 2021

• Merge branch 'master' into Haploflow to prevent splitting contigs matches into pieces on the coverage map

  CBeelen

  committed
  4d505d5

Commits on Aug 4, 2021

• Read in Haploflow's input arguments

  CBeelen

  committed
  8eb81be

• Add debug mode to generate graphs

  CBeelen

  committed
  550bb55

• Correct default error rate

  CBeelen

  committed
  b0a7e0a

Commits on Aug 9, 2021

• Trim and merge contigs after assembly using IVA's tools

  CBeelen

  committed
  7960ef9

Commits on Aug 11, 2021

• Add optional scaffolding and patching

  CBeelen

  committed
  8a36f33

• Correct contig paths

  CBeelen

  committed
  d8b1e46

• Handle unsuccessful scaffolding or patching

  CBeelen

  committed
  06c043f

• Better handle unsuccessful scaffolding or patching

  CBeelen

  committed
  75cb275

Commits on Aug 12, 2021

• Correct nucmer options

  CBeelen

  committed
  bdf5704

• Add option for a second try at assembly with filtered reads

  CBeelen

  committed
  89d5c2e

Commits on Aug 18, 2021

• Merge newest changes in master, and resolve conflicts

  CBeelen

  committed
  30e34a5

Commits on Aug 19, 2021

• Use information from remap.csv to separate reads

  CBeelen

  committed
  7b75e64

• Correct filename

  CBeelen

  committed
  cb5949b

Commits on Sep 1, 2021

• Add option for IVA assembly and modify scaffolding parameters

  CBeelen

  committed
  adf13f5

Commits on Sep 27, 2021

• Merge branch 'whole-genome-consensus' into Haploflow to create whole-genome consensus for result

  CBeelen

  committed
  667255d

Commits on Sep 28, 2021

• Merge branch 'whole-genome-consensus' into Haploflow

  CBeelen

  committed
  199e98c

Commits on Sep 29, 2021

• Merge branch 'whole-genome-consensus' into Haploflow

  CBeelen

  committed
  5e34e3e

• Merge branch 'whole-genome-consensus' into Haploflow

  CBeelen

  committed
  e5b50ee

Commits on Oct 14, 2021

• Merge branch 'whole-genome-consensus' into Haploflow

  CBeelen

  committed
  789cd9c

Commits on Oct 20, 2021

• Merge branch 'master' into Haploflow

  CBeelen

  committed
  79ccbfd

Commits on Nov 1, 2021

• Merge branch 'master' into Haploflow

  CBeelen

  committed
  b0e53d5

Commits on Nov 3, 2021

• Merge branch 'master' into Haploflow

  CBeelen

  committed
  4951a05

Commits on Nov 18, 2021

• Merge branch 'Consensus_insertions' into Haploflow

  CBeelen

  committed
  d36d3bd

Commits on Nov 19, 2021

• Merge branch 'Consensus_insertions' into Haploflow

  CBeelen

  committed
  cdbfc3e

Commits on Nov 20, 2021

• Merge branch 'Consensus_insertions' into Haploflow

  CBeelen

  committed
  c076787

Commits on Dec 2, 2021

• Merge branch 'Consensus_insertions' into Haploflow

  CBeelen

  committed
  11a7f50

Commits on Dec 3, 2021

• Merge branch 'Consensus_insertions' into Haploflow

  CBeelen

  committed
  47613a9

Commits on Dec 9, 2021

• Merge branch 'Consensus_insertions' into Haploflow

  CBeelen

  committed
  e70d131

Commits on Dec 10, 2021

• Merge branch 'Consensus_insertions' into Haploflow

  CBeelen

  committed
  d34852e

Commits on Jan 15, 2022

• Merge branch 'master' into Haploflow

  CBeelen

  committed
  94e4ce5

Commits on Feb 4, 2022

• Merge branch 'master' into Haploflow

  CBeelen

  committed
  2dd8e78

Commits on Mar 17, 2022

• Merge branch 'master' into Haploflow

  CBeelen

  committed
  2dfc1dd

Commits on Jun 7, 2022

• Merge branch 'master' into Haploflow

  CBeelen

  committed
  bcbcc70

Commits on Sep 15, 2023

• Merge branch 'master' into Haploflow

  Donaim

  committed
  d5ac6b2

Commits on Sep 19, 2023

• Install Haploflow during docker initialization

  Donaim

  committed
  138dcb2

• Install Haploflow on CI

  Donaim

  committed
  c621522

• Pin exact Haploflow version

  Show description for 272635d
  Donaim

  committed
  272635d

Commits on Sep 20, 2023

• Switch to Debian in Singularity image

  Donaim

  committed
  5ecb109

Commits on Sep 25, 2023

• Merge branch 'master' into Haploflow-test1

  Donaim

  committed
  d0407a8

Commits on Nov 6, 2024

• Reset to 'master' branch

  Donaim

  committed
  c958723

• Merge branch 'master' into Haploflow-test1

  Donaim

  committed
  d3139ae

• Replace IVA by Haploflow

  Show description for e229317
  Donaim

  committed
  e229317

• Update comment that mentions dropped IVA

  Donaim

  committed
  7f0e351

• Do not mention IVA in pyproject.toml

  Donaim

  committed
  e03ab97

Commits on Nov 7, 2024

• Ensure that output file is created in denovo.py

  Donaim

  committed
  f6e6ec2

Commits on Dec 4, 2024

• Fix a file system error in denovo

  Donaim

  committed
  c8a23ee

• Do not needlessly suppress Haploflow logs

  Donaim

  committed
  6191099

• Reduce the size of a minimal contig output by Haploflow

  Donaim

  committed
  644aad0

• Improve Haploflow code

  Donaim

  committed
  2316ae4

• Further improve typing in denovo.py

  Donaim

  committed
  f37027d

• Merge remote-tracking branch 'origin/master' into Haploflow-test1

  Donaim

  committed
  1bc101b

• Fix type error in sample.py

  Donaim

  committed
  22cd569

• Reduce k-mer size for Haploflow

  Donaim

  committed
  4077ca3

Commits on Dec 6, 2024

• Fix blast installation on CI

  Donaim

  committed
  9810504

• Remove unnecessary apt-update on CI

  Donaim

  committed
  76f9e38

• Remove unnecessary apt-update in Dockerfile

  Donaim

  committed
  dcb8220

• Fix Dockerfile build

  Donaim

  committed
  8dc4a23

• Fix apt command in CI

  Donaim

  committed
  740c11a

• Fix type error in test_denovo.py

  Donaim

  committed
  4ae5283

• [DEVELOPMENT] Silence some errors caused by Haploflow

  Donaim

  committed
  064d895

• Remove obsolete IVA marker from test_denovo.py

  Donaim

  committed
  19f2c27

Commits on Dec 7, 2024

• Merge remote-tracking branch 'origin/master' into Haploflow-test1

  Donaim

  committed
  847a5ea

Commits on Dec 9, 2024

• Merge remote-tracking branch 'origin/master' into Haploflow-test1

  Donaim

  committed
  48d1af7

Commits on Dec 10, 2024

• Merge remote-tracking branch 'origin/master' into Haploflow-test1

  Donaim

  committed
  222bab7

Commits on Dec 23, 2024

• Merge remote-tracking branch 'origin/master' into Haploflow-test1

  Donaim

  committed
  0777234

Commits on Jan 2, 2025

• Merge remote-tracking branch 'origin/master' into Haploflow-test1

  Donaim

  committed
  646ebf6