From a4751e91f4aa42873b78bc8912b53afcd0318259 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 1 Jul 2020 23:26:40 +0100 Subject: [PATCH] Update CHANGELOG --- CHANGELOG.md | 47 +++++++++++++++++++++++------------------------ 1 file changed, 23 insertions(+), 24 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bf2aad24..bf724afa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,14 +8,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Added` * [#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore! -* [#71](https://github.com/nf-core/atacseq/issues/71) - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated * [#75](https://github.com/nf-core/atacseq/issues/75) - Include gene annotation versions in multiqc report * [#76](https://github.com/nf-core/atacseq/issues/76) - featureCounts coupled to DESeq2 * [#79](https://github.com/nf-core/atacseq/issues/79) - Parallelize DESeq2 * [#80](https://github.com/nf-core/atacseq/pull/80) - Added social preview image * [#97](https://github.com/nf-core/atacseq/issues/97) - PBC1, PBC2 from pipeline? * [#107](https://github.com/nf-core/atacseq/issues/107) - Add options to change MACS2 parameters -* [#109](https://github.com/nf-core/atacseq/issues/109) - Specify custom gtf but gene bed is not generated from that gtf? * [nf-core/chipseq#153](https://github.com/nf-core/chipseq/issues/153) - Add plotHeatmap * [nf-core/chipseq#159](https://github.com/nf-core/chipseq/issues/159) - expose bwa mem -T parameter * Regenerated screenshots and added collapsible sections for output files in `docs/output.md` @@ -34,10 +32,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` +* [#71](https://github.com/nf-core/atacseq/issues/71) - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated * [#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created * [#86](https://github.com/nf-core/atacseq/issues/86) - bug in the plot_homer_annotatepeaks.r script * [#102](https://github.com/nf-core/atacseq/issues/102) - Incorrect Group ID assigned by featurecounts_deseq2.r * [#110](https://github.com/nf-core/atacseq/pull/110) - updated AWS test GitHub actions +* [#109](https://github.com/nf-core/atacseq/issues/109) - Specify custom gtf but gene bed is not generated from that gtf? * [nf-core/chipseq#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE * [nf-core/chipseq#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system * [nf-core/chipseq#154](https://github.com/nf-core/chipseq/issues/154) - computeMatrix.val.mat.gz files not zipped @@ -45,39 +45,38 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Dependencies` -* Add python `3.7.6` +* Add bioconductor-biocparallel `1.20.0` * Add markdown `3.2.2` -* Add pymdown-extensions `7.1` -* Add pygments `2.6.1` * Add pigz `2.3.4` -* Add r-tidyr `1.1.0` +* Add pygments `2.6.1` +* Add pymdown-extensions `7.1` +* Add python `3.7.6` * Add r-reshape2 `1.4.4` -* Add bioconductor-biocparallel `1.20.0` +* 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-optparse `1.6.0` -> `1.6.6` * Update r-ggplot2 `3.1.0` -> `3.3.2` -* Update r-pheatmap `1.0.10` -> `1.0.12` * 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-scales `1.0.0` -> `1.1.1` * Update r-xfun `0.3` -> `0.15` -* Update fastqc `0.11.8` -> `0.11.9` -* Update trim-galore `0.5.0` -> `0.6.5` * Update samtools `1.9` -> `1.10` -* Update picard `2.19.0` -> `2.23.1` -* Update pysam `0.15.2` -> `0.15.3` -* Update bedtools `2.27.1` -> `2.29.2` -* Update ucsc-bedgraphtobigwig `377` -> `357` -* Update deeptools `3.2.1` -> `3.4.3` -* Update macs2 `2.1.2` -> `2.2.7.1` -* Update homer `4.9.1` -> `4.11` -* Update ataqv `1.0.0` -> `1.1.1` * Update subread `1.6.4` -> `2.0.1` -* Update multiqc `1.7` -> `1.8` -* Update bioconductor-deseq2 `1.20.0` -> `1.26.0` -* Update bioconductor-vsn `3.46.0` -> `3.54.0` -* Remove r-reshape2 `1.4.3` +* Update trim-galore `0.5.0` -> `0.6.5` +* Update ucsc-bedgraphtobigwig `377` -> `357` ## [1.1.0] - 2019-11-05