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nf-core/atacseq v2.0 - Iron Iguana
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@drpatelh drpatelh released this 30 Nov 20:17
· 183 commits to master since this release
2.0
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[2.0] - 2022-11-30

⚠️ Major enhancements

  • Samplesheet format has changed from group,replicate,fastq_1,fastq_2 to sample,fastq_1,fastq_2,replicate.
    • This is primarily because we have removed the differential accessibility from the pipeline in favour of using more formal statistical methods downstream with the pipeline results. We kept replicate information as mandatory to merge samples at the replicate level to improve coverage for footprinting analysis.
  • Pipeline has been re-implemented in Nextflow DSL2
  • Bump minimum Nextflow version from 19.10.0 -> 21.10.3
  • Updated pipeline template to nf-core/tools 2.6
  • [#135] - ERROR: Please check design file header
  • [#158] - Problem using hyphens in group names
  • [#182] - Update macs_gsize in igenomes.config, create a new --read_length parameter and implement the logic to calculate --macs_gsize when the parameter is missing
  • [#193] - TSS heatmap inconsistency between ChIPseeker and nf-core ATAC-seq pipeline
  • [#201] - Update blacklist bed files.
  • [#220] - Move FastQ files for minimal tests to S3
  • [nf-core/chipseq#160] - Add bowtie2 and star as available aligners, via the --aligner parameter
  • [nf-core/chipseq#233] - Add chromap to the available aligners
  • Add --save_unaligned parameter (only available for bowtie2 and star)
  • Preseq will be skipped by default (see nf-core/rnaseq#897)
  • --deseq2_vst will be turned on by default

Parameters

Old parameter New parameter
--clusterOptions
--conda --enable_conda
--skip_qc
--aligner
--save_unaligned
--bowtie2_index
--chromap_index
--star_index
--skip_diff_analysis --skip_deseq2_qc
--single_end
--read_length

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 1.1.1 1.3.0
bamtools 2.5.1 2.5.2
bedtools 2.29.2 2.30.0
bioconductor-deseq2 1.26.0 1.28.0
deeptools 3.4.3 3.5.1
multiqc 1.9 1.13
ucsc-bedgraphtobigwig 357 377
samtools 1.10 1.16.1
picard 2.23.1 2.27.4
preseq 2.0.3 3.1.2
pysam 0.15.3 0.19.0
r-base 3.6.1 4.0.3
r-ggplot2 3.3.2 3.3.3
trim-galore 0.6.5 0.6.7
khmer - 3.0.0a3
r-optparse - 1.7.1
r-tidyr - -
r-lattice - -
r-xfun - -
bioconductor-vsn - -

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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