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nf-core/atacseq v1.2.0 - Iron Swan

6F05

drpatelh released this 02 Jul 10:27

· 559 commits to master since this release

766424e

[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

Assets 2

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