Release v1.2.2

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

Release v1.2.1

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

Release v1.2.0

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

Release v1.1.0

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

Release v1.0.4

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

Release v1.0.3

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

Release v1.0.2

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

[1.0.2] - 2023-07-14

Fixed

• crash with combination of technical reps and biological reps when combining them.
• idr bug with numpy dependency > 1.20
• replacing all spaces with underscores in the samples.tsv
  • should only affect columns where this was not enforced already (custom columns)
  • required for rule multiqc_samplesconfig

Release v1.0.0

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

[1.0.0] - 2023-05-31

Added

• CRAM support for ATAC+ChIP+RNA-seq workflows (in addition to the existing alignment workflow cram support)

Changed

• sctk yaml simplified

Fixed

• DESeq2 should no longer crash without DE genes
• bug with single-ended reads and subread
• gimme maelstrom dependency missing
• gimme maelstrom bug when XDG_CACHE_DIR is not set

Release v0.9.9

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

[0.9.9] - 2023-04-21

Changed

• moved downloading fastqs to localrules
• bam indexes are kept (not automatically removed)
• Salmon updated to the latest version v1.10.1 (fixes a bug)
• upsetplot updated to the latest version (fixes a bug)
• genomepy updated to the latest version (no reason)
• tabulate updated to the latest version (longer python support)
• everything else updated to the latest version
• --snakemakeOption debug_dag=True can now be used with 1 core (required)
• creating conda environments now faster
  • updated conda & mamba
  • dropped indexing of Conda's defaults channel
• one less global variable! (sanitized_samples)
• dropped correlation scores from DESeq2 clusterplots
  • pheatmap is too finickey to get the fontsize right
• pheatmap uses the sample order (from the samples.tsv) as best as possible

Fixed

• edge case when a GSM sample is a reanalysis of another GSM sample.
• error message referring to --config while it should be --configfile
• cyclic dependency on rule samtools_sort (caused by tildes in config paths)
• bug in DESeq2 related rules when using custom assemblies
• clear error message when downloading single-end data annotated as paired-end.
• "Max retries exceeded with url" for CRX samples
• upsetplot & assembly_stats segfault due to interactive matplotlib backend
• DESeq2 error: "EOF within quoted string"
• conda environment channel priorities
• trackhub index generation now removes rogue spaces from the annotation (instead of crashing)

Release v0.9.8

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

Added

• (experimental) support for the Chinese Genome Sequence Archive (GSA). Samples can start with their CRX identifiers.
• a force_assembly_hub flag to make an ucsc assembly hub even though a trackhub already exists

Changed

• MultiQC version updated (1.14)

Fixed

• edge case with the downloading-fastq workflow when samples file has an assembly column
• workflow explanation not being properly added to qc report
• download-fastq finishing succesfully with an error message..