Code

Kmer count + Dimensionality reduction#40

Code

Merged

DLBPointon merged 97 commits intodevsanger-tol/ascc:devfrom kmer_countsanger-tol/ascc:kmer_countCopy head branch name to clipboardApr 4, 2024

+954-133

Commits

Commits on Oct 16, 2023

• Add kmer count modules

  weaglesBio

  committed
  25d5d64

Commits on Oct 17, 2023

• Add to main workflow

  weaglesBio

  committed
  f3bedf9

• Add kmer count modules

  weaglesBio

  committed
  a311d1e

• Add to main workflow

  weaglesBio

  committed
  af871fe

Commits on Oct 25, 2023

• Add parameters

  weaglesBio

  committed
  1b51964

• Merge changes

  weaglesBio

  committed
  e29612f

Commits on Oct 30, 2023

• Handle one line csv

  weaglesBio

  committed
  3e67c80

• Add kmer count modules

  weaglesBio

  committed
  aacc15c

Commits on Nov 6, 2023

• Combine embeddings csv

  weaglesBio

  committed
  ca54275

Commits on Nov 17, 2023

• Fix combine

  weaglesBio

  committed
  1e9852b

• Adding organellar blast subworkflow

  

  DLBPointon

  authored and

  weaglesBio

  committed
  927b1a3

• Updates

  

  DLBPointon

  authored and

  weaglesBio

  committed
  0e7850a

• Completing organelle blast, modified python script to accept arrayList and parse inside script

  

  DLBPointon

  authored and

  weaglesBio

  committed
  5c6b6db

• Black linting

  

  DLBPointon

  authored and

  weaglesBio

  committed
  fb15428

• Uncommenting BLAST for testing

  

  DLBPointon

  authored and

  weaglesBio

  committed
  e5526fd

• Updates

  

  DLBPointon

  authored and

  weaglesBio

  committed
  bac7913

• Updates for Organella Blast output checking

  

  DLBPointon

  authored and

  weaglesBio

  committed
  b36c554

• Local update for diamond blast

  

  DLBPointon

  authored and

  weaglesBio

  committed
  c7da079

• Updated to filter out empties

  

  DLBPointon

  authored and

  weaglesBio

  committed
  b2e23a2

• Fixes for blast subworkflows

  

  DLBPointon

  authored and

  weaglesBio

  committed
  5bc2f95

• Added a blast module that does not rely on makeblastdb

  

  DLBPointon

  authored and

  weaglesBio

  committed
  a761e62

• Fixes to better allow running on github

  

  DLBPointon

  authored and

  weaglesBio

  committed
  65614f3

• Updating modules

  

  DLBPointon

  authored and

  weaglesBio

  committed
  c60721d

• Updating modules and patches

  

  DLBPointon

  authored and

  weaglesBio

  committed
  f9e65d2

• Updating pipeline to reflect changes

  

  DLBPointon

  authored and

  weaglesBio

  committed
  154b185

• Generalising the Blast module for FULL databases as well as local makeblastdb ones

  

  DLBPointon

  authored and

  weaglesBio

  committed
  009f1e3

• Prettier linting

  

  DLBPointon

  authored and

  weaglesBio

  committed
  8c57157

• Adding tracedir to schema

  

  DLBPointon

  authored and

  weaglesBio

  committed
  193f480

• Update script based on recomendation

  

  DLBPointon

  authored and

  weaglesBio

  committed
  05e25b5

• Black Linting

  

  DLBPointon

  authored and

  weaglesBio

  committed
  79305c5

• testing

  

  DLBPointon

  authored and

  weaglesBio

  committed
  99a7aa5

• Updating

  

  DLBPointon

  authored and

  weaglesBio

  committed
  1654931

• add coverage

  

  yumisims

  authored and

  weaglesBio

  committed
  8925cac

• add samtools merge

  

  yumisims

  authored and

  weaglesBio

  committed
  e49331f

• add merged

  

  yumisims

  authored and

  weaglesBio

  committed
  b2ed42d

• put in condition for different read type

  

  yumisims

  authored and

  weaglesBio

  committed
  bbb05d9

• re-written samtools_depth_average_coverage.py

  

  yumisims

  authored and

  weaglesBio

  committed
  a784236

• re-written samtools_depth_average_coverage.py

  

  yumisims

  authored and

  weaglesBio

  committed
  4e71157

• re-written samtools_depth_average_coverage.py

  

  yumisims

  authored and

  weaglesBio

  committed
  fb7bf44

• amended gc_content.py to comprehension form

  

  yumisims

  authored and

  weaglesBio

  committed
  6f0c412

• added change to samtools_depth_average_coverage.nf

  

  yumisims

  authored and

  weaglesBio

  committed
  5e2ad8e

• black

  

  yumisims

  authored and

  weaglesBio

  committed
  d39d99d

• change main workflow

  

  yumisims

  authored and

  weaglesBio

  committed
  033043f

• remove space

  

  yumisims

  authored and

  weaglesBio

  committed
  f1025fb

• changed github test yaml

  

  yumisims

  authored and

  weaglesBio

  committed
  d62859e

• add barcode to ci

  

  yumisims

  authored and

  weaglesBio

  committed
  5343545

• change in se mapping

  

  yumisims

  authored and

  weaglesBio

  committed
  b95e351

• change config

  

  yumisims

  authored and

  weaglesBio

  committed
  42c49a0

• change config

  

  yumisims

  authored and

  weaglesBio

  committed
  5208ab1

• changed bedtool

  

  yumisims

  authored and

  weaglesBio

  committed
  c0a5a03

• changed grabfile wildcard

  

  yumisims

  authored and

  weaglesBio

  committed
  6baec5c

• changed grabfile wildcard

  

  yumisims

  authored and

  weaglesBio

  committed
  3b8d867

• changed grabfile wildcard

  

  yumisims

  authored and

  weaglesBio

  committed
  84b50c3

• done

  

  yumisims

  authored and

  weaglesBio

  committed
  e754440

• done

  

  yumisims

  authored and

  weaglesBio

  committed
  a386866

• added ncbi id

  

  yumisims

  authored and

  weaglesBio

  committed
  4600cdc

• change software version'

  

  yumisims

  authored and

  weaglesBio

  committed
  af67f69

• refine bedtools and other scripts

  

  yumisims

  authored and

  weaglesBio

  committed
  029f1f6

• Replacing grep with awk, grep caused errors with empty products

  

  DLBPointon

  authored and

  weaglesBio

  committed
  2808cba

• Updating organellar blast based on discussion with Eerik and @yumisims

  

  DLBPointon

  authored and

  weaglesBio

  committed
  036c014

• Updated container from @yumisims and tested

  

  DLBPointon

  authored and

  weaglesBio

  committed
  f05f05b

• Black formatting

  

  DLBPointon

  authored and

  weaglesBio

  committed
  3b50c01

• Black Formatting

  

  DLBPointon

  authored and

  weaglesBio

  committed
  b61cadf

• Updates based on comments from @Ea10

  

  DLBPointon

  authored and

  weaglesBio

  committed
  4401fb6

• Correction and removal of view statement

  

  DLBPointon

  authored and

  weaglesBio

  committed
  efdc828

• Black linting for python script

  

  DLBPointon

  authored and

  weaglesBio

  committed
  65e87c8

• Add parameters

  weaglesBio

  committed
  1a8b635

• Add kmer count modules

  weaglesBio

  committed
  2958627

• Add to main workflow

  weaglesBio

  committed
  0bee610

• Handle one line csv

  weaglesBio

  committed
  e40e4ce

• Merge branch 'dev' into kmer_count

  weaglesBio

  authored
  40ce6a4

Commits on Nov 27, 2023

• dp24 suggested changes

  weaglesBio

  committed
  34385bb

Commits on Feb 23, 2024

• Updates to fix bugs, add params and get kmer analysis running

  DLBPointon

  committed
  5cfe9ad

• Merge branch 'dev' into kmer_count

  DLBPointon

  authored
  0fdc0f3

Commits on Feb 27, 2024

• linting fixes

  DLBPointon

  committed
  891964e

• fixes

  DLBPointon

  committed
  336a6c8

• linting

  DLBPointon

  committed
  aeeabb0

• linting

  DLBPointon

  committed
  63f3c34

• linting

  DLBPointon

  committed
  e37baa4

• barcode was wrong in test

  DLBPointon

  committed
  5f5ccf0

Commits on Feb 29, 2024

• Fixed container import, added conda recipe and corrected version output

  DLBPointon

  committed
  ebc1d5a

• Updated container, added custom version information for the umap moddule

  DLBPointon

  committed
  87e8b8d

• /tmp/ was being used, changed to custom cache dirs to script

  DLBPointon

  committed
  25bb22b

• updating the main script, minor stuff

  DLBPointon

  committed
  e75d030

Commits on Mar 1, 2024

• Changes for testing

  DLBPointon

  committed
  4978ec2

• Updating the vecscreen value, apparently changed from correct value in past

  DLBPointon

  committed
  affd380

Commits on Apr 4, 2024

• Updating data

  DLBPointon

  committed
  e6550bf

• Updating test files, test data, formatting and logic change

  DLBPointon

  committed
  4e8d53d

• Add pre-fetch for the containers in ascc with nf-download

  DLBPointon

  committed
  f36ed3f

• Fix CI and Black formatting

  DLBPointon

  committed
  77e08e6

• Black Formatting

  DLBPointon

  committed
  858fefb

• CI fix

  DLBPointon

  committed
  74a74f6

• CI fix add aptainer

  DLBPointon

  committed
  b9745c7

• kill lint for file exist

  DLBPointon

  committed
  d31813c

• Lint fix

  DLBPointon

  committed
  a9fe2c8

• Update resources

  DLBPointon

  committed
  f2c8e71

• Merge branch 'kmer_count' of https://github.com/sanger-tol/ascc into kmer_count

  DLBPointon

  committed
  b43f082