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.

Release v0.5.0

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

Version 0.5.0 brings many quality of life improvements, such as seq2science automatically inferring what needs to be re-run when changing the samples.tsv and/or the config.yaml, differential peak analysis for chip/atac workflows and tab-completion!

To (hopefully) clear things up we changed the way technical and biological replicates are called, now technical and biological replicate, before technical replicate and condition.

It is important to note that the RNA-seq workflow DOES NOT remove duplicate reads anymore as a default, and that the sc/bulk ATAC-seq workflows now filters reads on the nucleosome-free region as a default.

Changed

• Keep all duplicate reads in RNA-seq by default
• Slimmed down the config printed at the start of a run
• Changed some rules into localrules when executed on a cluster
• moved onehot peaks to counts_dir
• DESeq2 contrasts now accept any column names
  • groups still cannot contain underscores
  • no longer accepts one group name
  • more examples added to the docs!

Added

• dupRadar module to analyse read duplication types in RNA-seq
• Differential peak analysis for ATAC- and ChIP-seq!
• Options to filter bams by minimum and maximum insert sizes (added to config of bulk/sc atac)
• Support experiment ids for EBI ENA and DDBJ for downloading public samples
• More robust expression handling for BUS format detection from kb-python arguments
• Short-hand BUS syntax for indrop v1/v2
• Seq2science now supports tab-completion
• Seq2science now outputs a logfile in the directory it is run

Fixed

• renamed more old "replicate" variables to the new "technical_replicate"
• minor logging tweak
• Chipseeker now works without defining descriptive name column
• fix bug in resources parsing of profiles
• small bug when naming a column condition in non peak-calling workflows

Release v0.4.3

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

Changed

• updated tximeta to 1.6.3 and related packages to fit (now uses R 4)
• RNA-seq: sample distance matrix font scales with number of samples (should improve readability)

Fixed

• RNA-seq: added sample distance matrix back to MulitQC
• RNA-seq: sample distance matrix legend fixed
• combine peaks with biological_replicates: keep now uses the correct peaks

Release v0.4.2

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

Changed

• Updated kb-python to 0.25.1
• RNA-seq with Salmon will still use bam-related QC files if bams are generated (create_trackhub = True)

Fixed

• gimmemotifs not working with newest pandas, now a fixed pandas version

Release v0.4.1

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

Added

• more explanations for rules

Fixed

• custom genome annotations for single-cell RNA-seq workflow
• trackhubs no longer looking for reversed strands if none are present

Release v0.4.0

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

Added

• new workflow: (BETA) single cell RNA!

Changed

• bwa-mem2 default aligner for genomic workflows, instead of bwa-mem
• interactive deeptools correlation heatmaps with static dendrograms in multiqc report
• trackhub file permissions are set to 755 so to host the files online you don't have to change those anymore

Fixed

• bug in chip/atac trackhub generation where peaks and bigwigs used the same name, resulting in collisions and a trackhub that does not want to load
• (literal) genome edge-case where taking the slop of peaks results in identical peaks. One of the duplicates is removed.
• IDR should work again

Release v0.3.2

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

Added

• a check to see if the downloaded fastq from ENA is not empty. Related to a recent internal error (guess) at the side of ENA sending empty fastq files
• a custom message when a rule fails, that redirect to docs

Changed

• sample layout lookup is split up in 100's, to avoid a jsondecodeerror which results from very long lists of samples
• the multiqc samples & config tables are generated in a script with its own environment to make base env smaller
• keep_mates for macs2 turned into a script with ts own environment ot make the base env smaller
• seq2science cache now respects the xdg cache
• moved genome downloading rules into scripts instead of run directives, should result in user-friendlier errors

Fixed

• make a trackhub index when the gene_name is not present in gtf file
• make a trackhub index when the gene_name is not present in gene all entries
• update Salmon & salmon rules