Feature/chip spikein #116
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Feature/chip spikein #116
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* 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
Conflicts: .github/workflows/publish_pypi_test.yml seqnado/utils.py seqnado/workflow/rules/align.smk seqnado/workflow/snakefile_snp tests/test_atac.py tests/test_chip.py tests/test_rna.py tests/test_snp.py
* 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
* feat: added new slurm profile * fix: updated all memory values for cluster usage
* fix: deduplicated normalisation * feat: added check for presence of spikein index
* fix blacklist populating from cookiecutter (#81) * fix profile for jade
* small fixes for deseq2 * fix deseq2 report minimal design sample and deseq2 * add docs for minimal deseq2
* 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
Performs merging of bam files and re-calls peaks using lancotron. Provides increased accuracy for quantitative differences in peaks
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