ramdaq version 1.2.2

v1.2.2 (-r 1.2.2) [2021-06-22]

v1.2.2 Fixed

• Fixed the problem where hyphens in sample names were converted in MultiQC

ramdaq version 1.2.1

v1.2.1 (-r 1.2.1) [2021-06-14]

v1.2.1 Added

• Added --entire_max_cpus and --entire_max_memory options to set upper limit of CPU and memory usage of the entire workflow.

v1.2.1 Fixed

• Fixed the problem of high load average for some alignment steps
• Fixed a typo in the name of the log file that is copied to the output directory

ramdaq version 1.2

v1.2 (-r 1.2) [2021-05-26]

Major enhancement

• Extended features for QC of 'full-lengtheness'
  • Support for outputting gene-level quantification results of RSEM
  • Added RSEM results of the number of detected genes and transcripts in MultiQC report
• Extended features for QC of 'strandness'
  • New bigWig file output from R1, R2, forward, and reverse BAM files

Added

• Support for outputting gene-level quantification results of RSEM
• Added RSEM results of the number of detected genes and transcripts in MultiQC report
• Changed the unit of the number of reads from M Seqs to K Seqs in MultiQC report
• New bigWig file output from R1, R2, forward, and reverse BAM files
• Save a copy of .nextflow.log in the output directory

Fixed

• Fixed the caluclation of read assgined rate of all genes, mitochondrial, rRNA, and histone by featureCounts
• Fixed rRNA annotation for GRCm39
• Fixed TPM calculation for ERCC
• Corrected URL of remote annotation files in conf/remote_annotation.config
• Improved human rRNA annotation GTF

ramdaq version 1.1

v1.1 [2021-03-30]

Major enhancement

• Extended features for QC of 'full-lengtheness'
  • Transcript-level expression quantification by RSEM-Bowtie2
  • Reports of RSeQC junction_annotation.py and inner_distance.py
  • Support for Spike-In RNA Variant (SIRV) Control Set-4 (Read coverage, transcript-level expression quantification)

Added

• The new CI-test pattern for github actions
• A new option to allow the number of ERCC copies to be specified arbitrarily
• The process of transcripts quantification using RSEM-Bowtie2
• A new annotation files (gencode mouse vM26, human v37)
• The ability to run a quantitative process for each transcript if samples contain Spike-In RNA Variant (SIRV) Control
• A new bamQC plot "Junction Annotation" from RSeQC
• The process of adjusting BED in the workflow to account for noncoding region assignments to correct
• A new config "remote_annotation.config" obtaining annotations from public data

Fixed

• Markdown linting error in github actions
• The problem of "_1" and "_2" in the file name being erased in MultiQC report
• The problem of MultiQC causing memory error
• An error that occurred frequently at the end of a long pipeline
• An error that occurred when drawing a histone assigned plot at only one sample.
• Hide the aggregate results of rRNA in "General Stats" of MultiQC report
• Corrected the notation "assigned to gene" to "assigned to genome"
• Output the plot even if the data are all 0

Dependencies

Deprecated

• igenomes.config

ramdaq version 1.0

Initial release of ramdaq! 😆