Skip to content

Latest commit

 

History

History
76 lines (59 loc) · 3.95 KB

changelog.md

File metadata and controls

76 lines (59 loc) · 3.95 KB

Changelog

Current Pipeline improvements

Improvements:

  • Removes network and subnetwork parameters because CloudOS now sets this automatically (#315).
  • Allows for better control of Lifebit memory resourses (#317).

Fixes:

  • Fixed a bug in the post processing that changed the order of the Bamlist (#322)
  • Forces usage of NXF_VER=20.04.1 on Sumner in main.pbs to circumvent that the pipeline is written in DSL = 1 (NF changed default language) (#326).

Updates:

  • rMATs 4.1.1 -> 4.1.2 (#316)

Maintenance:

v2.1 - Pipeline improvements

Improvements:

  • removed fasta file requirement from Gen3-DRS option (#297)
  • The google-lifesciences has been defined as the executor when google profile is used. (#305)
  • GTEXdownlod option has been removed due to being obsolete (#299)
  • Gen3-DRS was renamed to GTEX as it's now the only way to download GTEX file (#299)
  • Added a new --manifest parameter with the input being the .json manifest file downloaded from GTEX (#304)
  • Added --reads parameter which receives a CSV file with samples for which the analysis will be limited to when using GTEX (#304)

Fixes:

  • Fix pipeline crach when using Gen3-DRS input due to env(...)format being used in process output (#294)
  • Changed gtexinput to support new manifest file format (#296)

Updates:

  • None performed

Maintenance:

  • None added

v2.0 - Pipeline improvements

Improvements:

  • Adds saving of all the process .command* log files to results/process-logs folder (#251)
  • Adds pipeline workdir --cleanup option to clear all intermediate files on pipeline successful completion (true by default, false for CloudOS) (#238, #284, 089d6e3)
  • Adds pipeline --error_strategy parameter to be able to specify pipeline error strategy directly from command line (doesn't work if specified in config linked by -c or -config nextflow params) (#267)
  • Parametrizes google executor parameters so that pipeline can now be run on different CloudOS environments (#281)
  • Adds a new --download_from option FTP mode to download SRA samples from EBI FTP (#283)
  • Adds new parameter --save_unmapped that makes saving of STAR unmapped files optional (false by default) (#284)

Fixes:

  • Adds missing trimmomatic logs to the multiqc report (#244)
  • Implemented correct support for input strandness in star process when --stranded is second-strand (was hardcoded to strType=2 and only supported first-strand or false before) (#264)
  • Issue that stringti_merged results folder as well as some other folders are missing all or some files (#263)
  • Fix pipeline crash when params.stranded was set to false (#276)
  • Fixes old parameters in google.config that were undesirably overwriting nextflow.config parameters on CloudOS (#281, 217e202)

Updates:

  • Updates the following tools: (#248)
    • STAR 2.7.3 -> 2.7.9a NOTE: Requires a new index! (updated in test profile)
    • Samtools 1.10 -> 1.13
    • StringTie 2.1.3b -> 2.1.7
    • Gffread 0.11.7 -> 0.12.7
    • multiqc 1.8 -> 1.11
    • deeptools 3.4.0 -> 3.5.1
    • bioconductor-rtracklayer 1.46.0 -> 1.52.0
    • gffcompare 0.11.2 -> 0.12.6
    • bedtools 2.29.2 -> 2.30.0
    • sra-tools 2.10.8 -> 2.11.0
    • pigz 2.3.4 -> 2.6.0
    • gdc-client 1.5.0 -> 1.6.1
  • Moves all containers to https://hub.docker.com/u/anczukowlab

Maintenance:

  • Considerably reduces number of basic redundant CI tests by removing completely the max_retries matrix and push from on: [push, pull_request]
  • Adds CI test for sra-downloading pipeline pathway (only supported with docker profile for now) (#253)

v 1.0 - Initial pipeline release