nf-core/chipseq

🐛 Enhancements & fixes

• Updated pipeline template to [nf-core/tools 2.7.2](https://github.com/nf-core/tools/releases/tag/2.7.2)
• [[#317](https://github.com/nf-core/chipseq/issues/317)] - Added metro map
• [[#288](https://github.com/nf-core/chipseq/issues/291)] - Bump `chromap` version 2 and enable all the steps below chromap again when paired-end data is processed.
• [[#311](https://github.com/nf-core/chipseq/issues/311)] - Add back `--skip_spp` parameter which was unintentionally removed from the code.
• Install available nf-core subworkflows and refactor code accordingly
• [[#318](https://github.com/nf-core/chipseq/issues/318)] - Update `bowtie2/align` module to fix issue when downloading its singularity image.
• [[#320](https://github.com/nf-core/chipseq/issues/320)] - Fix samplesheet control column in documentation examples.
• [[#328](https://github.com/nf-core/chipseq/issues/328)] - Modify documentation to clarify that is necessary to provide the `--read_length` when `--genome` is set and `--macs_gsize` has not provided.
• + 17 more

📦 Parameters

• | Old parameter | New parameter |
• | ---------------------- | ------------------------------------ |
• | `--show_hidden_params` | `--validationShowHiddenParams` |
• | | `--version` |
• | | `--hook_url` |
• | | `--multiqc_logo` |
• | | `--multiqc_methods_description` |
• | | `--pipelines_testdata_base_path` |
• + 3 more

📦 Software dependencies

• | Dependency | Old version | New version |
• | ----------------------- | ----------- | ----------- |
• | `bowtie2` | 2.4.4 | 2.5.2 |
• | `bwa` | 0.7.17 | 0.7.18 |
• | `chromap` | 0.2.1 | 0.2.6 |
• | `deeptools` | 3.5.1 | 3.5.5 |
• | `fastqc` | 0.11.9 | 0.12.1 |
• | `gffread` | 0.12.1 | 0.12.7 |
• + 10 more

📦 Credits

• Contributed by:
• @adamrtalbot
• @bjlang
• @krokicki
• @mashehu
• @maxulysse
• @samuelruizperez
• @g-sarah
• + 2 more

🐛 Enhancements & fixes

• Pipeline has been re-implemented in [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html)
• All software containers are now exclusively obtained from [Biocontainers](https://biocontainers.pro/#/registry)
• Updated pipeline template to [nf-core/tools 2.5.1](https://github.com/nf-core/tools/releases/tag/2.5.1)
• [[#128](https://github.com/nf-core/chipseq/issues/128)] - Filter files with no peaks to avoid errors in downstream processes
• [[#220](https://github.com/nf-core/chipseq/issues/220)] - Fix `phantompeakqualtools` protection stack overflow error
• [[#233](https://github.com/nf-core/chipseq/issues/233)] - Add `chromap` to the available aligners
• Bump minimum Nextflow version from `21.04.0` -> `21.10.3`
• Added `python3` shebang to appropriate scripts in `bin/` directory
• + 11 more

📦 Parameters

• | Old parameter | New parameter |
• | ---------------------- | ----------------------- |
• | `--conda` | `--enable_conda` |
• | `--skip_diff_analysis` | `--skip_deseq2_qc` |
• | | `--skip_qc` |
• | | `--aligner` |
• | | `--save_unaligned` |
• | | `--read_length` |
• + 15 more

📦 Software dependencies

• | Dependency | Old version | New version |
• | ----------------------- | ----------- | ----------- |
• | `samtools` | 1.10 | 1.15.1 |
• | `picard` | 2.23.1 | 2.27.4 |
• | `bamtools` | 2.5.1 | 2.5.2 |
• | `pysam` | 0.15.3 | 0.19.0 |
• | `bedtools` | 2.29.2 | 2.30.0 |
• | `ucsc-bedgraphtobigwig` | 357 | 377 |
• + 19 more

📦 [1.2.2] - 2021-04-22

• [#206](https://github.com/nf-core/chipseq/issues/206) - Minor patch release to fix Conda environment

📦 `Dependencies`

• Update r-base `3.6.2` -> `3.6.3`
• Update r-xfun `0.15` -> `0.20`

📦 [1.2.1] - 2020-07-29

• [#171](https://github.com/nf-core/chipseq/issues/171) - Minor patch release to update pipeline schema

✨ `Added`

• [#138](https://github.com/nf-core/chipseq/issues/138) - Add social preview image
• [#153](https://github.com/nf-core/chipseq/issues/153) - Add plotHeatmap
• [#159](https://github.com/nf-core/chipseq/issues/159) - expose bwa mem -T parameter
• [nf-core/atacseq#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore!
• [nf-core/atacseq#75](https://github.com/nf-core/atacseq/issues/75) - Include gene annotation versions in multiqc report
• [nf-core/atacseq#76](https://github.com/nf-core/atacseq/issues/76) - featureCounts coupled to DESeq2
• [nf-core/atacseq#79](https://github.com/nf-core/atacseq/issues/79) - Parallelize DESeq2
• [nf-core/atacseq#97](https://github.com/nf-core/atacseq/issues/97) - PBC1, PBC2 from pipeline?
• + 14 more

🗑️ `Removed`

• `--tss_bed` parameter

🐛 `Fixed`

• [#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
• [#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system
• [#154](https://github.com/nf-core/chipseq/issues/154) - computeMatrix.val.mat.gz files not zipped
• [nf-core/atacseq#71](https://github.com/nf-core/atacseq/issues/71) - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated
• [nf-core/atacseq#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created
• [nf-core/atacseq#86](https://github.com/nf-core/atacseq/issues/86) - bug in the plot_homer_annotatepeaks.r script
• [nf-core/atacseq#102](https://github.com/nf-core/atacseq/issues/102) - Incorrect Group ID assigned by featurecounts_deseq2.r
• [nf-core/atacseq#109](https://github.com/nf-core/atacseq/issues/109) - Specify custom gtf but gene bed is not generated from that gtf?
• + 1 more

📦 `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`
• + 24 more

✨ `Added`

• [#46](https://github.com/nf-core/atacseq/issues/46) - Missing gene_bed path in igenomes config
• Update template to tools `1.7`
• Add `--trim_nextseq` parameter
• Add `CITATIONS.md` file
• Capitalised process names

🐛 `Fixed`

• Change all parameters from `camelCase` to `snake_case` (see [Deprecated](#Deprecated))
• [#44](https://github.com/nf-core/atacseq/issues/44) - Output directory missing: macs2/consensus/deseq2
• [#45](https://github.com/nf-core/atacseq/issues/45) - Wrong x-axis scale for the HOMER: Peak annotation Counts tab plot?
• [#46](https://github.com/nf-core/atacseq/issues/46) - Stage blacklist file in channel properly
• [#50](https://github.com/nf-core/atacseq/issues/50) - HOMER number of peaks does not correspond to found MACS2 peaks
• Fixed bug in UpSetR peak intersection plot
• 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`

🗑️ `Deprecated`

• | Deprecated | Replacement |
• |------------------------------|---------------------------|
• | `--design` | `--input` |
• | `--singleEnd` | `--single_end` |
• | `--saveGenomeIndex` | `--save_reference` |
• | `--skipTrimming` | `--skip_trimming` |
• | `--saveTrimmed` | `--save_trimmed` |
• | `--keepDups` | `--keep_dups` |
• + 13 more

📦 [1.0.0] - 2019-06-06

• Initial release of nf-core/chipseq pipeline.

✨ `Added`

• Raw read QC (FastQC)
• Adapter trimming (Trim Galore!)
• Map and filter reads (BWA, picard, SAMtools, BEDTools, BAMTools, Pysam)
• Create library-size normalised bigWig tracks (BEDTools, bedGraphToBigWig)
• Alignment QC metrics (Preseq, picard)
• ChIP-seq QC metrics (deepTools, phantompeakqualtools)
• Call and annotate broad/narrow peaks (MACS2, HOMER)
• Create consensus set of peaks per antibody (BEDTools)
• + 3 more