Release v0.7.1

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows.

Fixed

• issue with broad peaks and upsetplots

Release v0.7.0

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows.

Biggest change is that we revert back to snakemake 5.18 since higher versioned snakemake's cause instability.

Added

• upset plot as QC for peak calling. Should give a first feeling about the distribution of peaks between samples/conditions.

Changed

• downgraded the snakemake backend as snakemake 6+ is unstable for us.

Fixed

• corrupt environment creation with libreadline for edgeR normalization.
• subsampling causing a crash caused by bad syntax.

Release v0.6.1

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows.

Fixed

• corrupt environment creation with libcrypto in combination with strandedness rule

Release v0.6.0

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows.

Release 0.6.0 is a mix of bug fixes, small changes, and bigger stuff. Most importantly:

• added a deseq2science command to do differential expression analysis on user-supplied tables with seq2science settings
• for single-cell RNA-seq ADT-quantification is possible
• snakemake library updated, giving seq2science a new-ish look :)

The full changes are listed below:

Added

• added generic stats to the MultiQC report about the assembly, which might help pin point problems with the assembly used.
• added the slop parameter to the config.yaml of atac-seq and chip-seq workflows, just so they are more visible.
• added support for seurat object export and merging for kb workflow.
• added support for CITE-seq-count for ADT quantification
• added the option to downsample to a specific number of reads.
• new deseq2science command

Changed

• Seq2science now makes a separate blacklist file per blacklist option (encode & mitochondria), so that e.g. RNA-seq and ATAC-seq workflows can be run in parallel and don't conflict on the blacklist.
• error messages don't show the full traceback anymore, making it (hopefully) more clear what is going wrong.
• The effective genome size is now not calculated per sample, but per read length. When dealing with multiple samples (of similar) length this improves computational burden quite some.
• samtools environment updated to version 1.14

Fixed

• config option slop is now passed along to each rule using it
• edge-case where local samples are in the cache, but not present in the fastq_dir
• bug with differential peak/gene expression across multiple assemblies
• bug with kb ref not creating index for non-velocity analysis
• bug with count import in read_kb_counts.R for technical replicates and meta-data handling
• deseq2 ordering in multiqc report
• issue with slop not being used for the final count table
• bug with onehot peaks not reporting the sample names as columns

Release v0.5.6

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows.

Added

• MA plot, volcano plot, and PCA plots added to QC report for deseq2 related workflows

Changed

• updated salmon & tximeta versions
• colors for DESeq2 distance plots "fixed"
• updated bwa-mem2 version and reduced the expected memory usage of bwa-mem2 to 40GB
• seq2science now uses snakemake-minimal

Fixed

• stranded bigwigs are no longer inverted (forward containing reverse reads and vice-versa).
• fix in rename_sample preventing the inversion of R1 and R2 FASTQs.
• bug with parsing cli for explanations
• show/hide buttons for treps are actually made for multiqc report
• fixes in deseq2/utils.R
  • the samples.tsv will now work with only 2 columns
  • the samples.tsv column names will be stripped of excess whitespace, similar to the config.
• ATAC-seq pipeline removing the final bams, keeping the unsorted one

Release v0.5.5

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows.

Changed

• duplicate read marking happens before sieving and no reads get removed. Removal of duplicate reads now controlled with flag remove_dups in the config.
• changed option heatmap_deeptools_options to deeptools_heatmap_options
• Updated sra tools and parallel fastq-dump versions
• Updated genomepy version
• Gene annotations are no longer gzipped and ungzipped. This should reduce rerunning.

Fixed

• rerunning being triggered too easily by input order
• issue with qc plots and broad peaks
• magic with prefetch not having the same output location on all machines
• issue with explain having duplicate lines

Release v0.5.4

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows.

Added

• added support for kb-python kite workflow

Changed

• kb count output validation
• optional barcodefile argument for scRNA-seq workflow
• MultiQC updated to newest version
• updated kb-python version

Release v0.5.3

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows.

Added

• DESeq2 blind sample distance & correlation cluster heatmaps for RNA-, ATAC- ChIP-seq counts
  • find them annotated in the MultiQC when running >1 sample

Changed

• "biological_replicate" and "technical_replicate" renamed to *"_replicates" (matches between samples.tsv & config.yaml)
• fixed bug with seq2science making a {output.allsizes} file
• Changed explain to use 'passive style'
• Genrich peak calling defaults
  • Doesn't remove PCR duplicates anymore (best to do with markduplicates)
  • Changed extsize to 200 to be similar to macs settings
  • Turned off tn5 shift, since that is done by seq2science

Fixed

• depend less on local genomes (only when data is unavailable online)
• trackhub explanation was missing, added
• bug with broad peaks and qc that could not be made

Release v0.5.2

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows.

Added

• added rule for scRNA post-processing R Markdown for plate/droplet based scRNA protocols (experimental)
• added explanation for kb_seurat_pp rule
• heatmap of N random peaks to the multiqc report in the end

Fixed

• removed a warning of genome.fa.sizes already existing due to being already being downloaded beforehand (it's removed in between)
• genomepy's provider statuc checking not being used.

Release v0.5.1

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows.

Added

• added CLI functionality to the deseq2.R script (try it with Rscript /path/to/deseq2.R --help!)
• --force flag to seq2science init to automatically overwrite existing samples.tsv and config.yaml
• local fastqs with Illumina's '_100' are now recognized
• added the workflow explanation to the multiqc report

Changed

• config checks: all keys converted to lower case & duplicate keys throw an exception
• MultiQC updated to v1.10
• Link to seq2science log instead of snakemake log in final message

Fixed

• Issue when filtering a combination of single-end and paired-end reads on template length
• explain functionality testing
• scATAC can properly use SE fastqs
• scRNA can use fqexts other than R1/R2
• fastq renaming works again
• added missing schemas to extended docs

Fixed

• Bug with edgeR.upperquartile normalization. Now makes everything NaN, so pipeline finishes succesfully.