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nf-core/atacseq: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[2.1.2] - 2022-08-07

Enhancements & fixes

  • [#322]Remove fasta from required schema parameters so that when launching from tools it is not required.
  • Updates homer_annotatepeaks module.

[2.1.1] - 2022-07-21

  • Minor patch release to fix AWS full test.

[2.1.0] - 2022-07-21

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.

[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.

[1.2.2] - 2022-05-12

  • Minor patch release to fix Conda environment and enable DSL1 by default in the nextflow.config.

Dependencies

  • Update r-base 3.6.2 -> 3.6.3
  • Update r-xfun 0.15 -> 0.22

[1.2.1] - 2020-07-29

  • #118 - Minor patch release to update pipeline schema

[1.2.0] - 2020-07-02

Added

  • #63 - Added multicore support for Trim Galore!
  • #75 - Include gene annotation versions in multiqc report
  • #76 - featureCounts coupled to DESeq2
  • #79 - Parallelize DESeq2
  • #80 - Added social preview image
  • #97 - PBC1, PBC2 from pipeline?
  • #107 - Add options to change MACS2 parameters
  • nf-core/chipseq#153 - Add plotHeatmap
  • nf-core/chipseq#159 - expose bwa mem -T parameter
  • Regenerated screenshots and added collapsible sections for output files in docs/output.md
  • Update template to tools 1.9
  • Replace set with tuple and file() with path() in all processes
  • Capitalise process names
  • Parameters:
    • --bwa_min_score to set minimum alignment score for BWA MEM
    • --macs_fdr to provide FDR threshold for MACS2 peak calling
    • --macs_pvalue to provide p-value threshold for MACS2 peak calling
    • --skip_peak_qc to skip MACS2 peak QC plot generation
    • --skip_peak_annotation to skip annotation of MACS2 and consensus peaks with HOMER
    • --skip_consensus_peaks to skip consensus peak generation
    • --deseq2_vst to use variance stabilizing transformation (VST) instead of regularized log transformation (rlog) with DESeq2
    • --publish_dir_mode to customise method of publishing results to output directory nf-core/tools#585

Fixed

  • #71 - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated
  • #73 - macs_annotatePeaks.mLb.clN.summary.txt file is not created
  • #86 - bug in the plot_homer_annotatepeaks.r script
  • #102 - Incorrect Group ID assigned by featurecounts_deseq2.r
  • #110 - updated AWS test GitHub actions
  • #109 - Specify custom gtf but gene bed is not generated from that gtf?
  • nf-core/chipseq#118 - Running on with SGE
  • nf-core/chipseq#132 - BigWig Error: sort: cannot create temporary file in '': Read-only file system
  • nf-core/chipseq#154 - computeMatrix.val.mat.gz files not zipped
  • Make executables in bin/ compatible with Python 3

Dependencies

  • Add bioconductor-biocparallel 1.20.0
  • Add markdown 3.2.2
  • Add pigz 2.3.4
  • Add pygments 2.6.1
  • Add pymdown-extensions 7.1
  • Add python 3.7.6
  • Add r-reshape2 1.4.4
  • Add r-tidyr 1.1.0
  • Update ataqv 1.0.0 -> 1.1.1
  • Update bedtools 2.27.1 -> 2.29.2
  • Update bioconductor-deseq2 1.20.0 -> 1.26.0
  • Update bioconductor-vsn 3.46.0 -> 3.54.0
  • Update deeptools 3.2.1 -> 3.4.3
  • Update fastqc 0.11.8 -> 0.11.9
  • Update gawk 4.2.1 -> 5.1.0
  • Update homer 4.9.1 -> 4.11
  • Update macs2 2.1.2 -> 2.2.7.1
  • Update multiqc 1.7 -> 1.8
  • Update picard 2.19.0 -> 2.23.1
  • Update pysam 0.15.2 -> 0.15.3
  • Update r-base 3.4.1 -> 3.6.2
  • Update r-ggplot2 3.1.0 -> 3.3.2
  • Update r-lattice 0.20_35 -> 0.20_41
  • Update r-optparse 1.6.0 -> 1.6.6
  • Update r-pheatmap 1.0.10 -> 1.0.12
  • Update r-scales 1.0.0 -> 1.1.1
  • Update r-upsetr 1.3.3 -> 1.4.0
  • Update r-xfun 0.3 -> 0.15
  • Update samtools 1.9 -> 1.10
  • Update subread 1.6.4 -> 2.0.1
  • Update trim-galore 0.5.0 -> 0.6.5
  • Update ucsc-bedgraphtobigwig 377 -> 357

[1.1.0] - 2019-11-05

Added

  • #35 - Add deepTools plotFingerprint
  • #46 - Missing gene_bed path in igenomes config
  • Merged in TEMPLATE branch for automated syncing
  • Update template to tools 1.7
  • Add CITATIONS.md file
  • Capitalised process names
  • Add parameters:
    • --seq_center
    • --trim_nextseq
    • --fingerprint_bins
    • --broad_cutoff
    • --min_reps_consensus
    • --save_macs_pileup
    • --skip_diff_analysis
    • --skip_* for skipping QC steps

Fixed

  • Change all parameters from camelCase to snake_case (see Deprecated)
  • #41 - Docs: Add example plot images
  • #44 - Output directory missing: macs2/consensus/deseq2
  • #45 - Wrong x-axis scale for the HOMER: Peak annotation Counts tab plot?
  • #46 - Stage blacklist file in channel properly
  • #50 - HOMER number of peaks does not correspond to found MACS2 peaks
  • Fixed bug in UpSetR peak intersection plot
  • IGV now uses relative instead of absolute paths
  • Smaller logo for completion email
  • Renamed all channels to start with ch_ prefix
  • Increase default resource requirements in base.config
  • Increase process-specific requirements based on user-reported failures

Dependencies

  • Update Nextflow 0.32.0 -> 19.10.0
  • Add preseq 2.0.3
  • Add deeptools 3.2.1
  • Add r-xfun 0.3
  • Add gawk 4.2.1

Deprecated

Deprecated Replacement
--design --input
--singleEnd --single_end
--saveGenomeIndex --save_reference
--skipTrimming --skip_trimming
--saveTrimmed --save_trimmed
--keepMito --keep_mito
--keepDups --keep_dups
--keepMultiMap --keep_multi_map
--skipMergeReplicates --skip_merge_replicates
--saveAlignedIntermediates --save_align_intermeds
--narrowPeak --narrow_peak

[1.0.0] - 2019-04-09

Added

Initial release of nf-core/atacseq Created with version 1.1 of the nf-core template.