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minute Changelog

v0.10.1

Bug fixes

  • Fix edge-case exception when trying to convert NA value to int after parsing an empty insert size metrics file.

Other

  • Prioritize reporting rules over bigWig generation rules.

v0.10.0

Features

  • New target rule no_scaling to skip the scaling process completely and produce only the unscaled bigWig files and a final MultiQC report with non-scaling related QC metrics.

v0.9.2

Minor

  • More thorough check of user input, including: validating minute.yaml has required fields, reference files exist, FASTQ files match libraries.tsv, bowtie2 index is not required if aligner strobealign is used.
  • More verbose command line messages when an error occurs.
  • More verbose docstring for minute run command.

v0.9.1

Features

  • Handle barcode dropouts. Zero values appear in the final report, and this does not prevent final stats report to be produced.
  • Carry barcode sequence to stats_summary.txt

Other

  • Minor: Styling changes made to the final Minute barcode barplots

v0.9.0

Features

  • Bowtie2 run mode can be configured in minute.yaml to any of the bowtie2 accepted modes. Default is still --fast.
  • Optionally align reads with strobealign instead of bowtie2.
  • Add read group RG to output BAM headers and read group ID to individual alignments.

v0.8.0

Features

  • New target rule pooled_only to skip individual replicates and generate bigwig tracks only for replicate pools.

v0.7.0

Features

  • minute init now can accept a --config parameter to copy an already existing minute.yaml into the run directory.

Bug fixes

  • Improved parameter check of minute init. Now a directory will not be created if an error occurs.

v0.6.0

Features

  • Barcode representation barplots, final number of mapped reads and percentage of total.
  • Stats summary table is now separated in replicates and pool for easier reading.

Other

  • Minor: expanded library name column so it is now wider.
  • Automatic formatting of QC pass for insert size and duplication rates are removed.

v0.5.0

Features

  • Added mapping_quality optional parameter to filter out reads under a certain mapping quality threshold. By default, this value is set to zero (keep all).
  • Added mapping_quality_bigwig specific to mapq_bigwigs new rule that generates both final unfiltered bigWigs and mapq.bw filtered bigWigs according to this parameter. By default, those filtered bigWigs are not generated.

v0.4.1

Bug fixes

  • Handle missing/incorrect --input parameter values on minute init.

v0.4.0

Features

  • Added --barcodes and --input parameters to minute init functionality to streamline configuration of standard minute runs.

v0.3.1

Bug fixes

  • Issue #159: Temporary removed dynamically renaming of dynamically generated rules to avoid issues with recent versions of snakemake.

v0.3.0

Bug fixes

  • Recover missing rows from Statistics Summary table on the MultiQC report when a sample is mapped to more than one reference.
  • Issue #159: Pin snakemake version to 7.16.

Features

  • Improved MultiQC reporting by adding:
    • Picard CollectInsertSizeMetrics figure.
    • Custom library complexity estimate based on Picard, adapted to use the single-end numbers from Je.
    • Number of demultiplexed reads per sample.
    • Reorder tables on MultiQC report (Statistics Summary first).

Other

  • Minor numerical formatting changes on final stats summary tables.