seq2science

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

• trackhub: automatic color selection
• trackhub: specify colors with the "colors" column in the samples.tsv. Accepts RGB and matplotlib colors.
• trackhub: grouped samples in a composite track with sample filters and composite control

• updated genomepy to 0.9.1: genomes will have alternative regions removed (if designated with "alt" in the name)
• trackhub: better defaults for each track
• layouts are stored per version, as to not have collisions in the way these are stored between versions.
• scATAC no longer supports trackhub
• bigwigs are now (BPM) normalized by default

• markduplicates now uses $TMP_DIR, if it is defined
• RNA-seq cluster figures werent displaying text on some platforms
• not using the local annotation files
• not recognizing a mix of gzipped and unzipped annotation files
• bigwigs are now correctly labelled forward/reverse (when protocol was stranded)
• trackhub: RNA-seq trackhub now displays both strands of the bigwig (when protocol was stranded)
• trackhub: track order is now identical to the samples.tsv (was alphabetical for ChIP-/ATAC-seq)
• trackhub: assembly hub index now returns gene_name instead of transcript_id.
• bug with edgeR (upperquartile) normalization failed. Not sure why it fails, but when is does, it now returns a dataframe of nan instead of failing the rule, and thus the whole pipeline.
• use gimmemotifs 0.15.0, so gimme.combine_peaks works with numeric chromosome names
• s2s is slightly more lenient with an edge-case when running seq2science in parallel
• clearer error message when trying samples that can not be found
• edge case with trying to dump sra from empty directory
• now give a nice error message when a technical replicate consists of a mix of paired-end and single-end samples
• issue with large number of inputs for multiqc exceeding the os command max length
• bug with downloading only SRR/DRR samples (but no GSM)
• issue with async generation of genome support files
• checking for sequencing runs when sample is already downloaded