nf-core

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Published May 16, 2022 | Version 2.4.1
Software Open

The nf-core framework for community-curated bioinformatics pipelines.

Authors/Creators

Description

v2.1.0 - 2022-10-25 Maroon Tin Dalmatian Enhancements & fixes
  • [#12] - Enabled the use of MirGeneDB as an alternative database insted of miRBase
  • [#113] - Added a optional contamination filtering step, including MultiQC plot
  • [#137] - Fixed issue with mirTop and MultiQC by upgrading to MultiQC V1.13dev
  • [#159] - Index files were not collected when bowtie_index was used and thus mapping was failing
  • [#161] - Trimmed output was not as documented and not correctly published
  • [#168] - Removed mirtrace_protocol as the parameter was redundant and params.protocol is entirely sufficient
  • Updated pipeline template to nf-core/tools 2.6.0
  • [#188] - Dropped TrimGalore in favor of fastp QC and adapter trimming, improved handling of adapters and trimming parameters
  • [#194] - Added default adapters file for FastP improved miRNA adapter trimming
Parameters
Old parameter New parameter
--mirgenedb
--mirgenedb_species
--mirgenedb_gff
--mirgenedb_mature
--mirgenedb_hairpin
--contamination_filter
--rrna
--trna
--cdna
--ncrna
--pirna
--other_contamination

Notes

If you use `nf-core tools` in your work, please cite the `nf-core` publication

Files

nf-core/smrnaseq-2.1.0.zip

Files (4.5 MB)

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md5:5e9067f02d031ce10ac388bdff9c03df
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Additional details

Related works

Is supplement to
https://github.com/nf-core/smrnaseq/tree/2.1.0 (URL)