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nf-core/rnaseq v3.7 - Iron Iguana
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@drpatelh drpatelh released this 03 May 11:13
· 1928 commits to master since this release
3.7
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[3.7] - 2022-05-03

⚠️ Major enhancements

  • Updated default STAR version to latest available (2.7.10a; see #808)
  • Vanilla Linux Docker container changed from biocontainers/biocontainers:v1.2.0_cv1 to ubuntu:20.04 to fix issues observed on GCP (see #764)

Enhancements & fixes

  • [#762] - Explicitly set --skip_bbsplit false with --bbsplit_fasta_list to use BBSplit
  • [#764] - Test fails when using GCP due to missing tools in the basic biocontainer
  • [#765] - Add docs for the usage of nf-core/rnaseq with prokaryotic data
  • [#775] - Incorrect columns in Salmon transcript files
  • [#791] - Add outputs for umitools dedup summary stats
  • [#797] - Add --skip_umi_extract to account for pre-existing UMIs header embeddings.
  • [#798] - Decompress transcript fasta error
  • [#799] - Issue with using --retain_unpaired with the FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE module
  • [#802] - --bam_csi_index error generated if --skip_alignment specified
  • [#808] - Auto-detect usage of Illumina iGenomes reference
  • [#809] - Add metro map for pipeline
  • [#814] - Use decimal values for --min_mapped_reads
  • Updated pipeline template to nf-core/tools 2.3.2

Parameters

Old parameter New parameter
--skip_umi_extract

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency Old version New version
samtools 1.14 1.15.1
star 2.6.1d 2.7.10a
stringtie 2.1.7 2.2.1

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

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