merge master into chip branch #115
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…ipeline (#107) * remove large file from tests * publish only on push to master * add singularity path to tests * Feat split fastq files (#65) * feat: add fastq_split option * add fastq_split option to atac chip and rna & test * add num of parts to split fastq to config * update test for snp with split and call snps * feat: Added chip-rx assay (#68) * feat: Added chip-rx assay * Added rule to align spike-in reads to spike-in reference * Added script and rule to count spike-in reads * Script also calculates normalization factor * Added rules to generate normalised bigwigs * feat: completed v1 of chip-rx * fix: Added hub.smk rules to add output design rule * commented out snps * fix: removed seqnado import. Not in container. (#73) * fix: Enable profile to work on new JADE cluster (#70) * feat: added new slurm profile * fix: updated all memory values for cluster usage * fix: "false" missing from is_off function. (#72) * fix: ChIP-rx pipeline when duplicate samples present (#71) * fix: deduplicated normalisation * feat: added check for presence of spikein index * fix: typo in deseq2 key * fix blacklist populating from cookiecutter * Fix profile for jade cluster (#83) * fix blacklist populating from cookiecutter (#81) * fix profile for jade * fix bugs in deseq2 report (#87) * make raw bams temp (#97) * Fix rna pipeline (#98) * small fixes for deseq2 * fix deseq2 report minimal design sample and deseq2 * add docs for minimal deseq2 * Feat add attempts for potential oom jobs (#101) * Create dependabot.yml (#93) * Update dependabot.yml (#94) * Update dependabot.yml (#95) * feat: added attempts to multiqc * feat: attempts added to alignment counts * feat: attempts added to multiqc * feat: added attempts to heatmap * feat: enabled snakefmt precommit * fix: typo in heatmap.smk * fix: typo in alignment_counts --------- Co-authored-by: Alastair Smith <[email protected]> Co-authored-by: alsmith <[email protected]> * add attempts to sorting (#102) * Fix snp pipeline (#103) * rule all in snp called twice * update default config to shared resources * make deseq2 optional * fix split fastq * test snps * fix snp tests and config * fix snp test and configs * remove resources from plot heatmap * add hub info to snp test * increase resources * fix call snps * make snp raw bams temp * resolve conflicts * feat: added consensus peak calling (#90) Performs merging of bam files and re-calls peaks using lancotron. Provides increased accuracy for quantitative differences in peaks * Add new test files and update .gitignore * Refactor code and update experiment design * Update DesignIP class to use 'assays' instead of 'experiments' * Refactor align_single rule in align.smk * Update fastq_trim.smk workflow rules * Update paths for control files in peak_call.smk * Add query method to Design and DesignIP classes * Refactor fastqc rule and add wrapper for fastqc_trimmed * Refactor QC rules in seqnado workflow * Add QC reports for different stages of the pipeline * Add pydantic to dependencies * Remove unnecessary code and update pipeline config * Fix fastq file symlinking and include qc rules * Fix file path and symlink issues * Add dependencies and update file paths for seqnado workflow * Fix fastqc_dir path in qc.smk * Refactor get_fastqc_files function signature * Refactor design generation and add error handling for missing fastq files * Refactor fastq file handling in cli_design function * Refactor DesignIP instantiation in cli.py * Refactor symlink_files function and update DesignIP class * Update RNA workflow and experiment configuration * Update requires-python and snakemake version * fix(deps): fix pulp version * Update dependencies in pyproject.toml * Refactor test_snp.py file * Remove wildcard constraints from snakefile_atac * Feature/chip spikein (#108) * add chip ref norm with concat genome * add split_bam.py * split with samtools * amended norm to orlando method * add rx to chip as an option * fix fastqscreen to run * fix scaling factors for deeptools * change heatmap to scale regions and add metaplot * changed config to jinja2 * add deseq2 template * change config file ext to yml * fix indentation in too options * update chiprx in snakefile * fix typos for rna config * add preset genomes to config * fix for genome other * made jinja env work in other dir * updated chip test for jinja config * debug tests * remove --no-input from testpipeline * fix rna test * fix type in orlando spike in py * remove config test from test_pipeline.yml * tweek heatmap time limit * Add QC reports for different stages of the pipeline * Refactor symlink_files function and update DesignIP class * Refactor test_snp.py file --------- Co-authored-by: CChahrour <[email protected]> Co-authored-by: Catherine Chahrour <[email protected]>
* feat: add fastq_split option * add fastq_split option to atac chip and rna & test * add num of parts to split fastq to config * update test for snp with split and call snps
* feat: Added chip-rx assay * Added rule to align spike-in reads to spike-in reference * Added script and rule to count spike-in reads * Script also calculates normalization factor * Added rules to generate normalised bigwigs * feat: completed v1 of chip-rx * fix: Added hub.smk rules to add output design rule * commented out snps
* fix: deduplicated normalisation * feat: added check for presence of spikein index
* Create dependabot.yml (#93) * Update dependabot.yml (#94) * Update dependabot.yml (#95) * feat: added attempts to multiqc * feat: attempts added to alignment counts * feat: attempts added to multiqc * feat: added attempts to heatmap * feat: enabled snakefmt precommit * fix: typo in heatmap.smk * fix: typo in alignment_counts --------- Co-authored-by: Alastair Smith <[email protected]> Co-authored-by: alsmith <[email protected]>
* rule all in snp called twice * update default config to shared resources * make deseq2 optional * fix split fastq * test snps * fix snp tests and config * fix snp test and configs * remove resources from plot heatmap * add hub info to snp test * increase resources * fix call snps * make snp raw bams temp * resolve conflicts
* add chip ref norm with concat genome * add split_bam.py * split with samtools * amended norm to orlando method * add rx to chip as an option * fix fastqscreen to run * fix scaling factors for deeptools * change heatmap to scale regions and add metaplot * changed config to jinja2 * add deseq2 template * change config file ext to yml * fix indentation in too options * update chiprx in snakefile * fix typos for rna config * add preset genomes to config * fix for genome other * made jinja env work in other dir * updated chip test for jinja config * debug tests * remove --no-input from testpipeline * fix rna test * fix type in orlando spike in py * remove config test from test_pipeline.yml * tweek heatmap time limit
* fix: corrected conflicts in utils * feat: added --cores option to tests * feat: cores option passed to tests * fix: "spikein" * feat: show failed logs added by default
* feat(docs): added documentation * Update package installation in build_docs.yml * Update FAQ link in mkdocs.yml * Update design file format in pipeline.md
* Fix DESeq2 output file name * Update sample_name computation in FastqFile class * DESeq2 to deseq2 * Fix conditional statement for running DESeq2 * Refactor define_output_files function to use pathlib for creating hub_txt path * Fix index column in pd.read_csv() function * Modified hub path * Update project name in deseq2_rna.smk and snakefile_rna
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