Skip to content

Latest commit

 

History

History
169 lines (105 loc) · 5.21 KB

CHANGELOG.md

File metadata and controls

169 lines (105 loc) · 5.21 KB

CHANGELOG

ramdaq: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.9.2 (-r 1.9.2) [2022-02-17]

v1.9.2 Added

  • Update the MultiQC version to 1.13

v1.9.2 Fixed

  • Fixed an incorrect calculating paired-end reads counts in the FastQC process
  • Fixed a bug in the report when using 1 sample
  • Fixed an error in the R script when using integer samplename
  • Changed default threshold for the minimum number of mapped reads filter

v1.9.1 (-r 1.9.1) [2022-10-25]

v1.9.1 Added

  • Support for genocode v41/vM30 annotations
  • Add barplot expression of nucluear RNA genes

v1.9.1 Fixed

  • Changed URL for downloading all external files
  • Fixed an error in the FastQC for uncompressed fastq

v1.9 (-r 1.9) [2022-07-20]

v1.9 Added

  • Add barplot alligned genome rates of initial fastq reads

v1.9 Fixed

  • Change setting testcase resource limits
  • Fixed the unintended samples omit problem in low mapped reads bam QC processes
  • Remove duplicate column from General statistics
  • Changed bamtools filter option for create strand-specific bams

v1.8 (-r 1.8) [2022-06-21]

v1.8 Fixed

  • Fixed a problem with Fastq-mcf incorrect arguments that prevented fastq trimming from working properly

v1.7 (-r 1.7) [2022-05-19]

v1.7 Added

  • Support for genocode v39/vM28, v40/vM29 annotations

v1.7 Fixed

  • Fixed an error in the RSEM-SIRV process when execute PE unstranded mode
  • Extended "max time" of process-specific resource requirements
  • Added hidden option to changed SIRV coverage process to off by default
  • Added hidden option to avoid error when only short introns are detected in RSeQC

v1.6 (-r 1.6) [2022-02-22]

v1.6 Added

  • Add troubleshooting.md

v1.6 Fixed

  • Fixed an error when running only one sample

v1.5 (-r 1.5) [2021-12-20]

v1.5 Added

  • Add surge.sh publish action to all CI test cases
  • Support for genocode v38/vM27 annotations
  • Update the docker image (some technical changes)

v1.4.1 (-r 1.4.1) [2021-09-09]

v1.4.1 Fixed

  • Fixed the problem that dimensional reduction plots are not displayed in the MulitiQC report

v1.4 (-r 1.4) [2021-08-23]

v1.4 Added

  • Added new rRNA quantification process and multiQC plot. More accurate % rRNA is achieved by mapping reads on rRNA sequences using HISAT2.
  • Gzip-compressed output of merge_readcoverage_sirv

v1.3 (-r 1.3) [2021-07-29]

v1.3 Added

  • Added SIRV entropy bar plot as new SIRV QC plot
  • Added columns to the General Statistics table for all bar plots
  • Added the summary plot of featurecounts in MultiQC

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

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

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

v1.2 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

v1.2 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

v1.1 (-r 1.1) [2021-03-30]

v1.1 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