Code

Refactor design. #182

Code

Merged

alsmith151 merged 47 commits intomasteralsmith151/SeqNado:masterfrom fix-refactor-designipalsmith151/SeqNado:fix-refactor-designipCopy head branch name to clipboardApr 23, 2024

+681-522

Commits

Commits on Apr 8, 2024

• Refactor hub.smk and create_hub.py to use "method" instead of "pileup_method"

  alsmith151

  committed
  779330d

  Copy full SHA for 779330d

Commits on Apr 13, 2024

• Fix control not found issues and fix --preset ls

  alsmith151

  committed
  2f321bc

  Copy full SHA for 2f321bc

• Fix control duplication issue in DesignIP class

  alsmith151

  committed
  5e9d7d6

  Copy full SHA for 5e9d7d6

• Fix sample name assignment in DesignIP class

  alsmith151

  committed
  7b9b5bf

  Copy full SHA for 7b9b5bf

• Refactor DesignIP class to include from_directory method

  alsmith151

  committed
  cbccad8

  Copy full SHA for cbccad8

• Fix control file naming issue in peak_call_chip.smk

  alsmith151

  committed
  b5e01cf

  Copy full SHA for b5e01cf

• Fix control file naming issue in DesignIP class

  alsmith151

  committed
  738ee43

  Copy full SHA for 738ee43

• Fix control file naming issue in DesignIP class

  alsmith151

  committed
  10c4459

  Copy full SHA for 10c4459

Commits on Apr 16, 2024

• Add pandera to dependencies in pyproject.toml

  alsmith151

  committed
  96f63bc

  Copy full SHA for 96f63bc

• Refactor alignment_post_processing.smk and pileup_grouped.smk rules

  alsmith151

  committed
  a87e523

  Copy full SHA for a87e523

• Refactor DesignIP class to handle different types of designs

  alsmith151

  committed
  795d87c

  Copy full SHA for 795d87c

Commits on Apr 17, 2024

• fix: corrects always adding unscaled to bigwigs

  alsmith151

  committed
  43aedb8

  Copy full SHA for 43aedb8

• Refactor get_group_for_sample function in helpers.py to handle missing samples in normalisation groups

  alsmith151

  committed
  d21ecfd

  Copy full SHA for d21ecfd

• Refactor peak_call_chip.smk to format MACS options and handle control file naming issue

  alsmith151

  committed
  138432c

  Copy full SHA for 138432c

• Fix control file naming issue in test_pipelines.py

  alsmith151

  committed
  e41948d

  Copy full SHA for e41948d

• Refactor exogenous_norm.smk and pileup_norm.smk rules to remove unused imports and update sample selection

  alsmith151

  committed
  35a84fc

  Copy full SHA for 35a84fc

• Add NormGroups class to handle normalization scaling and merging in snakefile_chip

  alsmith151

  committed
  f77ec2e

  Copy full SHA for f77ec2e

• Fix bowtie2 options in config_yaml_for_testing function

  alsmith151

  committed
  dd7adbf

  Copy full SHA for dd7adbf

• Fix condition for checking number of peak lines in validate_peaks rule

  alsmith151

  committed
  38a27f6

  Copy full SHA for 38a27f6

Commits on Apr 21, 2024

• Fix condition for checking number of peak lines in validate_peaks rule

  alsmith151

  committed
  73fe17a

  Copy full SHA for 73fe17a

• Refactor pileup_norm.smk to use NORMALISATION_SCALING instead of NORM_GROUPS

  alsmith151

  committed
  21e8a42

  Copy full SHA for 21e8a42

• fix: add sample groups to snakefiles

  alsmith151

  committed
  60280b2

  Copy full SHA for 60280b2

• fix: correct NormGroup from design

  alsmith151

  committed
  14c1787

  Copy full SHA for 14c1787

• fix: updated chip test files

  alsmith151

  committed
  ad2f08a

  Copy full SHA for ad2f08a

• Fix SEACR command in peak_call_chip.smk to handle failure gracefully

  alsmith151

  committed
  7c28520

  Copy full SHA for 7c28520

• Refactor pileup_norm.smk to remove extendReads and -e options for unpaired samples

  alsmith151

  committed
  22060e1

  Copy full SHA for 22060e1

• Update deeptools threads to 8 in seqnado/config.py

  alsmith151

  committed
  cbd6ba5

  Copy full SHA for cbd6ba5

• Fix scale_method assignment in BigWigFiles model

  alsmith151

  committed
  1c046d5

  Copy full SHA for 1c046d5

• Refactor snakefiles to use remove_unwanted_run_files function for cleanup

  alsmith151

  committed
  ca9d893

  Copy full SHA for ca9d893

• Refactor dplyr select and setNames in deseq2.qmd.jinja to use sample_info.sample_name instead of sample_info.sample

  alsmith151

  committed
  875c6f2

  Copy full SHA for 875c6f2

• Refactor get_group_for_sample function in helpers.py to include an optional strip parameter

  alsmith151

  committed
  5b482a6

  Copy full SHA for 5b482a6

• Refactor calculate_spikein_norm_factors.r to suppress package startup messages and update column names

  alsmith151

  committed
  1a167df

  Copy full SHA for 1a167df

• Refactor deseq2_rna.smk to remove size_factors output

  alsmith151

  committed
  9579c0e

  Copy full SHA for 9579c0e

• Add rule calculate_scaling_factors_spikein to pileup_norm.smk

  alsmith151

  committed
  37f012c

  Copy full SHA for 37f012c

• Refactor calculate_spikein_norm_factors.r to use relative path for script execution

  alsmith151

  committed
  a72b3a2

  Copy full SHA for a72b3a2

• Refactor spike-in normalization check in snakefile_rna

  alsmith151

  committed
  64de2ed

  Copy full SHA for 64de2ed

• Refactor file names and update read_table to read_delim in calculate_scaling_factors.R

  alsmith151

  committed
  a1c23e4

  Copy full SHA for a1c23e4

• Refactor dplyr select and setNames in deseq2.qmd.jinja to use sample_info.sample_name instead of sample_info.sample

  alsmith151

  committed
  2fa2a30

  Copy full SHA for 2fa2a30

• Refactor pileup_norm.smk to use input.chromsizes and params.tile_size in tile_regions rule

  alsmith151

  committed
  62b4af1

  Copy full SHA for 62b4af1

• fix left_join in deseq2.qmd.jinja to use sample_info.sample_name instead of sample_info.sample

  alsmith151

  committed
  ad0da6d

  Copy full SHA for ad0da6d

• Fix left_join in deseq2.qmd.jinja to use sample_info.sample_name instead of sample_info.sample

  alsmith151

  committed
  25f859b

  Copy full SHA for 25f859b

• Fix left_join in deseq2.qmd.jinja to use sample_info.sample_name instead of sample_info.sample

  alsmith151

  committed
  7610f61

  Copy full SHA for 7610f61

• Refactor snakefile_chip to import remove_unwanted_run_files from seqnado.helpers

  alsmith151

  committed
  ef48a19

  Copy full SHA for ef48a19

Commits on Apr 22, 2024

• Merge branch 'fix-hub-supertracks' into fix-refactor-designip

  alsmith151

  committed
  86978ba

  Copy full SHA for 86978ba

• Fix supergroup_by parameter in hub.smk to use None as default value

  alsmith151

  committed
  6d65aaa

  Copy full SHA for 6d65aaa

Commits on Apr 23, 2024

• Refactor create_hub.py to use "method" instead of "pileup_method" for ChIP assay

  alsmith151

  committed
  25c15af

  Copy full SHA for 25c15af

• Refactor symlink_file function in helpers.py to remove debug logging statements

  alsmith151

  committed
  9ac2503

  Copy full SHA for 9ac2503