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nf-core/atacseq v2.1.0 - Iron Cow
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@JoseEspinosa JoseEspinosa released this 21 Jul 14:13
· 18 commits to master since this release
2.1.0
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Learn about vigilant mode.

[2.1.0] - 2023-07-21

Credits

Special thanks to the following for their contributions to the release:

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Enhancements & fixes

  • [#226] - Add ataqv_mito_reference parameter.
  • Optional support of control data analog to nf-core/chipseq.
  • [#277] - Fix error when using a gunziped fasta file.
  • [#286] - Fix error when no --mito_name parameter is provided.
  • [#268] - Fix error when a bed file is provided using the --blacklist option.
  • [#278] - Make genome fasta file available when IGV process is run.
  • [#276] - Bump version 1.3.1 of ataqv to fix enrichment plots rendering.
  • [#290] - Fix case-sensitivity issue while sorting bedGraph.
  • [#295] - Enable downstream steps for bam files produced from paired-end reads by chromap after its upgrade.
  • Updated pipeline template to nf-core/tools 2.9
  • Make fasta index available for IGV session.
  • [nf-core/chipseq#347] - Add read group tag to bam files processed by bowtie2

Parameters

Old parameter New parameter
--with_control
--ataqv_mito_reference

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

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
ataqv 1.3.0 1.3.1
chromap 0.2.1 0.2.4
multiqc 1.13 1.14
picard 2.27.4 3.0.0
samtools 1.15.1 1.17
ucsc-bedgraphtobigwig 377 445

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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