[1.2.0] - 2020-07-02 Added #138 - Add social preview image #153 - Add plotHeatmap #159 - expose bwa mem -T parameter nf-core/atacseq#63 - Added multicore support for Trim Galore! nf-core/atacseq#75 - Include gene annotation versions in multiqc report nf-core/atacseq#76 - featureCounts coupled to DESeq2 nf-core/atacseq#79 - Parallelize DESeq2 nf-core/atacseq#97 - PBC1, PBC2 from pipeline? nf-core/atacseq#107 - Add options to change MACS2 parameters 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 Removed --tss_bed parameter Fixed #118 - Running on with SGE #132 - BigWig Error: sort: cannot create temporary file in '': Read-only file system #154 - computeMatrix.val.mat.gz files not zipped nf-core/atacseq#71 - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated nf-core/atacseq#73 - macs_annotatePeaks.mLb.clN.summary.txt file is not created nf-core/atacseq#86 - bug in the plot_homer_annotatepeaks.r script nf-core/atacseq#102 - Incorrect Group ID assigned by featurecounts_deseq2.r nf-core/atacseq#109 - Specify custom gtf but gene bed is not generated from that gtf? 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 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 phantompeakqualtools 1.2 -> 1.2.2 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