add mamba installation to docs #141
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CChahrour
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CChahrour
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* bug fixes for conda release * remove duplicates from hub (#140) * add mamba installation to docs (#141) * Remove wrappers from rules (#144) * remove wrapper from fastqc * fix multiqc rule * Fix chip rx (#145) * remove old util functions from chip-rx * fix fastqscreen for inputs * make fastqscreen an option outside of chiprx * add fastqscreen conf to tests
alsmith151
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Mar 25, 2024
* bug fixes for conda release * remove duplicates from hub (#140) * add mamba installation to docs (#141) * Remove wrappers from rules (#144) * remove wrapper from fastqc * fix multiqc rule * Fix chip rx (#145) * remove old util functions from chip-rx * fix fastqscreen for inputs * make fastqscreen an option outside of chiprx * add fastqscreen conf to tests * pinned snakemake to v7.32.4 * unpin snakemake * less specific snakemake pin * fix typo * add time for alignment * Feat upgrade snakemake version (#154) * fix(deps): cleaned dependencies * feat: updated profiles * Update snakemake version in environment files and pyproject.toml * Update conda-incubator/setup-miniconda version to v3 * Update Python version to 3.12 and add Python dependency for 3.11 * Feat split utils into separate modules (#156) * Add NormDesign class to utils.py * Refactor normalisation workflow and add new rules for scaling factors and bigwig normalisation * Add script to calculate scaling factors * Add script to calculate scaling normalization factors * Update normalization and scaling factors in deeptools_make_bigwigs * Add spikein and scale normalization output files * Refactor NormDesign to use NormGroup * Refactor NormGroups class in utils.py * Add get_group_for_sample function to normalisation.smk * Add sample_groups and group_samples properties to NormGroups class * Add get_group_for_sample function to utils.py * Add pileup_normalisation.smk and related functions * Add normalization factors output to resources folder * Refactor get_group method and add new methods for retrieving sample group and grouped samples * Add spike-in normalization and output size factors * Refactor design export in seqnado/cli.py * Add pileup_normalisation rule to snakefiles * fix: fastq screen rule failing RNA even when not active * Update pileup_normalisation.smk file * fix: design missing from function * Remove 'assay' parameter from NormGroup class * Remove unused 'assay' parameter in NormGroups.from_design() method * Refactor get_group_for_sample to use get_sample_group * Update file paths and remove spaces in scaling factors * Fix spikein factor file path in pileup_normalisation.smk * Fix conditional statement for scale argument in define_output_files function * Update align_paired rule resources in align_rna.smk * add scale to config for rna * update config scale * feat: enable rules to run using snakemake 8+ * feat: split utils into helpers and design * feat: updated snakefiles * Add symlink functions for fastq files * chore: removed symlink fastq * Refactor imports in seqnado/cli.py * Update import statements and function calls * typo misisng "=" * additional typos * Fix formatting issues in design.py and snakefiles * Update paths for unscaled bigwig files * Update files property in NonRNAOutput class * add test data for chip-rx and rna-rx * feat: split utils into helpers and design * feat: updated snakefiles * Add symlink functions for fastq files * chore: removed symlink fastq * Refactor imports in seqnado/cli.py * Update import statements and function calls * typo misisng "=" * additional typos * Fix formatting issues in design.py and snakefiles * Update paths for unscaled bigwig files * Update files property in NonRNAOutput class * Add NormGroup and NormGroups classes for handling normalization groups * Add pileup_grouping and peak_call_grouped rules * Refactor file handling in Output classes * Update atac rule order * Add logger to stderr and fix bug in peaks method * Update pileup_grouping.smk to pileup_grouped.smk * Update snakefile_chip with new rules and output files * Refactor ANALYSIS_OUTPUT variable in snakefile_rna * Update heatmap and pileup rules * Add spikein option to user_inputs function * Update typing in design.py * Refactor output variables in snakefiles * Update input paths in validate_peaks and generate_hub rules * Fix conditional statement in generate_hub rule * Add --cores 4 option to pytest command * fix: missing qc files from output * Update output file paths in utils.py * Remove unused code in seqnado/utils.py * Add test_rna_size_factors.ipynb to .gitignore * Add is_path function to check if a path is valid * Remove "consensus-peaks" option from method argument in cli_design function * Add data.json file to config directory * Add Optional import to helpers.py * Add test_pipelines.py for unit testing * Update treatment paths in peak_call_chip and peak_call_other rules * Remove unused test files and fixtures * Refactor Output class to include a new property for bigbed files * Refactor hub.smk and remove unused function * Refactor test_pipelines.py to download and extract genome indices and additional files * Add is_paired property to AssayIP and ExperimentIP classes, and update DesignIP query method to handle IP and control names properly * Refactor symlink_fastq_files function and format_deeptools_options * Remove commented out code in hub.smk * Refactor deeptools options formatting * Add genome test data and remove unnecessary lines in snakefiles * Refactor snakefile_atac and snakefile_chip * Add NormGroups initialization from design * Add NormGroups and update normalization factors * Add get_scale_method to ChIPOutput initialization * Add scale_group column to design dataframe * Add debug option to create_config function and update helpers.py * Add pepe_silvia function and get_scale_method to helpers.py * Update fastq files * Remove unnecessary print statement in snakefile_chip * Refactor NormGroups class to handle subset columns in design * Update file paths in pileup_norm.smk * Fix wildcard constraints in snakefile_chip * Fix indentation in get_scale_method function * Update test_pipelines.py with new config options * Add pyranges as a dependency * Update paths and download files in test_pipelines.py * Update .gitignore to exclude tests/data/ directory * Update STAR options in config.py * Remove unnecessary option for star command * Add spikein scaling option to RNAOutput * Update size factors file in deseq2_rna.smk * Update spikein normalization factors in deeptools_make_bigwigs_rna_spikein_plus and deeptools_make_bigwigs_rna_spikein_minus rules * feat: pipeline exits if run deseq and no column * Add options to STAR command for RNA assay * Delete fastq files * Add deseq2 column to design file * Add conditional check for vst function * Update DESeq2 configuration file to include rjson package and output size factors * Add logging to deeptools_make_bigwigs_rna_spikein_plus and deeptools_make_bigwigs_rna_spikein_minus rules * Update file path for writing normalization factors * heatmaps should use normalised bigwigs if present * Add full QC report to seqnado_output * Fix typo in get_scale_method parameter name * Update heatmap.smk to handle unscaled bigwigs * set apptainer prefix for snakemake * Update default values for remove_pcr_duplicates and make_heatmaps * Fix pipeline command in test_pipelines.py * Add full QC report to QCFiles class * add get_fastqc_files. corrects single vs paired * Fix logic in get_fastqc_files function * peak_call_method can be False * Add 'False' as an option for peak_calling_method * Update symlink_file function to print a message instead of using logger * Add "scale" parameter to user_inputs function * Increased default thread number * Update logger level to WARNING * Commented out code for RNA assay in test_pipelines.py * fix: inputs not being properly paired * Update data loading in snakefiles * Fix r2 FastqFile initialization in Design class * Fix symlink issue in helpers.py * Add profile_test configuration file * fix: issue with apptainer args * Fix is_paired method to check if r2 path is a file * Add new functions for extracting cores and apptainer arguments from Snakemake options * Add imports and extract cores from options * Fix control variable initialization in peak_call_chip.smk * Update rule order in peak_call_chip.smk * fixed: symlinks not working for input samples * Refactor control variables in peak_call_chip.smk * Refactor name comparison in DesignIP class * Refactor control variables to use "UNDEFINED" instead of empty lists * Update rule macs2_no_input to handle undefined control bam * Commented out apptainer-args in config.yaml --------- Co-authored-by: CChahrour <[email protected]> --------- Co-authored-by: CChahrour <[email protected]> Co-authored-by: Catherine Chahrour <[email protected]>
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