update for v1.0 release

bio15anu · bio15anu · commit b559933d4ef8 · 2020-09-03T11:59:26.000+02:00
diff --git a/README.md b/README.md
@@ -6,8 +6,8 @@ EpiDiverse-DMR Pipeline
 
 [![Nextflow](https://img.shields.io/badge/nextflow-20.07.1-45818e.svg)](https://www.nextflow.io/)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-45818e.svg)](http://bioconda.github.io/)
-[![Docker](https://img.shields.io/docker/cloud/automated/epidiverse/dmr.svg)](https://hub.docker.com/r/epidiverse/wgbs)
-[![Release](https://img.shields.io/github/v/release/epidiverse/dmr.svg?colorB=45818e)](https://github.com/EpiDiverse/wgbs/releases/latest)
+[![Docker](https://img.shields.io/docker/cloud/automated/epidiverse/dmr.svg)](https://hub.docker.com/r/epidiverse/dmr)
+[![Release](https://img.shields.io/github/v/release/epidiverse/dmr.svg?colorB=45818e)](https://github.com/EpiDiverse/dmr/releases/latest)
 [![Publication](https://img.shields.io/badge/Published-Bioinformatics-45818e.svg?colorB=45818e&style=popout)](https://academic.oup.com/bioinformatics/article-abstract/36/11/3314/5809142)
 [![Twitter](https://img.shields.io/twitter/follow/epidiverse?style=social)](https://twitter.com/intent/follow?screen_name=epidiverse)
 
@@ -35,7 +35,7 @@ NXF_VER=20.07.1 nextflow run epidiverse/dmr -profile test,<docker|singularity|co
 
 ```bash
 NXF_VER=20.07.1 nextflow run epidiverse/dmr -profile <docker|singularity|conda> \
---input /path/to/wgbs/directory --samples /path/to/samples.tsv
+--input /path/to/wgbs/bam --samples /path/to/samples.tsv
 ```
 
 > See the [usage documentation](docs/usage.md) for all of the available options when running the pipeline.
diff --git a/docs/images/directory.png b/docs/images/directory.png
diff --git a/env/environment.yml b/env/environment.yml
@@ -4,119 +4,149 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1=main
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_gnu
   - _r-mutex=1.0.1=anacondar_1
-  - bedtools=2.29.0=h6ed99ea_1
-  - binutils_impl_linux-64=2.31.1=h7fc9f1b_2
-  - binutils_linux-64=2.31.1=h6176602_12
-  - bwidget=1.9.13=0
-  - bzip2=1.0.8=h516909a_1
-  - ca-certificates=2019.9.11=hecc5488_0
-  - cairo=1.16.0=hfb77d84_1002
-  - curl=7.65.3=hf8cf82a_0
-  - fontconfig=2.13.1=h86ecdb6_1001
-  - freetype=2.10.0=he983fc9_1
-  - fribidi=1.0.5=h516909a_1002
-  - gcc_impl_linux-64=7.3.0=habb00fd_2
-  - gcc_linux-64=7.3.0=h553295d_12
+  - bedtools=2.29.2=hc088bd4_0
+  - binutils_impl_linux-64=2.34=h53a641e_7
+  - binutils_linux-64=2.34=hc952b39_20
+  - bwidget=1.9.14=0
+  - bzip2=1.0.8=h516909a_3
+  - c-ares=1.16.1=h516909a_3
+  - ca-certificates=2020.6.20=hecda079_0
+  - cairo=1.16.0=h3fc0475_1005
+  - certifi=2020.6.20=py38h32f6830_0
+  - curl=7.71.1=he644dc0_5
+  - expat=2.2.9=he1b5a44_2
+  - fontconfig=2.13.1=h1056068_1002
+  - freetype=2.10.2=he06d7ca_0
+  - fribidi=1.0.10=h516909a_0
+  - gcc_impl_linux-64=7.5.0=hd420e75_6
+  - gcc_linux-64=7.5.0=h09487f9_20
   - gettext=0.19.8.1=hc5be6a0_1002
-  - gfortran_impl_linux-64=7.3.0=hdf63c60_2
-  - gfortran_linux-64=7.3.0=h553295d_12
-  - glib=2.58.3=h6f030ca_1002
-  - graphite2=1.3.13=hf484d3e_1000
-  - gsl=2.5=h294904e_1
-  - gxx_impl_linux-64=7.3.0=hdf63c60_2
-  - gxx_linux-64=7.3.0=h553295d_12
-  - harfbuzz=2.4.0=h9f30f68_3
-  - icu=64.2=he1b5a44_1
-  - jpeg=9c=h14c3975_1001
-  - krb5=1.16.3=h05b26f9_1001
-  - libblas=3.8.0=13_openblas
-  - libcblas=3.8.0=13_openblas
-  - libcurl=7.65.3=hda55be3_0
-  - libedit=3.1.20170329=hf8c457e_1001
-  - libffi=3.2.1=he1b5a44_1006
-  - libgcc-ng=9.1.0=hdf63c60_0
-  - libgfortran-ng=7.3.0=hdf63c60_2
-  - libiconv=1.15=h516909a_1005
-  - liblapack=3.8.0=13_openblas
-  - libopenblas=0.3.7=h6e990d7_1
-  - libpng=1.6.37=hed695b0_0
-  - libssh2=1.8.2=h22169c7_2
-  - libstdcxx-ng=9.1.0=hdf63c60_0
-  - libtiff=4.0.10=h57b8799_1003
+  - gfortran_impl_linux-64=7.5.0=hdf63c60_6
+  - gfortran_linux-64=7.5.0=h09487f9_20
+  - glib=2.58.3=py38h73cb85d_1004
+  - graphite2=1.3.13=he1b5a44_1001
+  - graphviz=2.42.3=h0511662_0
+  - gsl=2.6=h294904e_0
+  - gxx_impl_linux-64=7.5.0=hdf63c60_6
+  - gxx_linux-64=7.5.0=h09487f9_20
+  - harfbuzz=2.7.2=hee91db6_0
+  - icu=67.1=he1b5a44_0
+  - jpeg=9d=h516909a_0
+  - krb5=1.17.1=hfafb76e_3
+  - ld_impl_linux-64=2.34=h53a641e_7
+  - libblas=3.8.0=17_openblas
+  - libcblas=3.8.0=17_openblas
+  - libcurl=7.71.1=hcdd3856_5
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libffi=3.2.1=he1b5a44_1007
+  - libgcc-ng=9.3.0=h24d8f2e_16
+  - libgfortran-ng=7.5.0=hdf63c60_16
+  - libgomp=9.3.0=h24d8f2e_16
+  - libiconv=1.16=h516909a_0
+  - liblapack=3.8.0=17_openblas
+  - libnghttp2=1.41.0=h8cfc5f6_2
+  - libopenblas=0.3.10=pthreads_hb3c22a3_4
+  - libpng=1.6.37=hed695b0_2
+  - libssh2=1.9.0=hab1572f_5
+  - libstdcxx-ng=9.3.0=hdf63c60_16
+  - libtiff=4.1.0=hc7e4089_6
+  - libtool=2.4.6=h516909a_1004
   - libuuid=2.32.1=h14c3975_1000
+  - libwebp-base=1.1.0=h516909a_3
   - libxcb=1.13=h14c3975_1002
-  - libxml2=2.9.9=hee79883_5
-  - lz4-c=1.8.3=he1b5a44_1001
-  - make=4.2.1=h14c3975_2004
+  - libxml2=2.9.10=h68273f3_2
+  - lz4-c=1.9.2=he1b5a44_3
+  - make=4.3=h516909a_0
   - metilene=0.2.8=h516909a_0
-  - ncurses=6.1=hf484d3e_1002
-  - openssl=1.1.1c=h516909a_0
-  - pango=1.42.4=ha030887_1
-  - pcre=8.41=he1b5a44_1004
-  - perl=5.26.2=h516909a_1006
+  - ncurses=6.2=he1b5a44_1
+  - openssl=1.1.1g=h516909a_1
+  - pango=1.42.4=h7062337_4
+  - pcre=8.44=he1b5a44_0
+  - pcre2=10.35=h2f06484_0
+  - perl=5.30.3=h516909a_1
+  - pip=20.2.2=py_0
   - pixman=0.38.0=h516909a_1003
   - pthread-stubs=0.4=h14c3975_1001
-  - r-assertthat=0.2.1=r36h6115d3f_1
-  - r-backports=1.1.5=r36hcdcec82_0
-  - r-base=3.6.1=hba50c9b_4
-  - r-bitops=1.0_6=r36hcdcec82_1003
-  - r-catools=1.17.1.2=r36h0357c0b_1
-  - r-cli=1.1.0=r36h6115d3f_2
-  - r-colorspace=1.4_1=r36hcdcec82_1
-  - r-crayon=1.3.4=r36h6115d3f_1002
-  - r-digest=0.6.21=r36h0357c0b_0
-  - r-ellipsis=0.3.0=r36hcdcec82_0
-  - r-fansi=0.4.0=r36hcdcec82_1001
-  - r-gdata=2.18.0=r36h6115d3f_1002
-  - r-ggplot2=3.2.1=r36h6115d3f_0
-  - r-glue=1.3.1=r36hcdcec82_1
-  - r-gplots=3.0.1.1=r36h6115d3f_1
-  - r-gtable=0.3.0=r36h6115d3f_2
-  - r-gtools=3.8.1=r36hcdcec82_1003
-  - r-kernsmooth=2.23_15=r36h9bbef5b_1004
-  - r-labeling=0.3=r36h6115d3f_1002
-  - r-lattice=0.20_38=r36hcdcec82_1002
-  - r-lazyeval=0.2.2=r36hcdcec82_1
-  - r-magrittr=1.5=r36h6115d3f_1002
-  - r-mass=7.3_51.4=r36hcdcec82_1
-  - r-matrix=1.2_17=r36hcdcec82_1
-  - r-mgcv=1.8_29=r36hcdcec82_0
-  - r-munsell=0.5.0=r36h6115d3f_1002
-  - r-nlme=3.1_141=r36h9bbef5b_1
-  - r-pillar=1.4.2=r36h6115d3f_2
-  - r-pkgconfig=2.0.3=r36h6115d3f_0
-  - r-plyr=1.8.4=r36h0357c0b_1003
-  - r-r6=2.4.0=r36h6115d3f_2
-  - r-rcolorbrewer=1.1_2=r36h6115d3f_1002
-  - r-rcpp=1.0.2=r36h0357c0b_0
-  - r-reshape2=1.4.3=r36h0357c0b_1004
-  - r-rlang=0.4.0=r36hcdcec82_1
-  - r-scales=1.0.0=r36h0357c0b_1002
-  - r-stringi=1.4.3=r36h0e574ca_3
-  - r-stringr=1.4.0=r36h6115d3f_1
-  - r-tibble=2.1.3=r36hcdcec82_1
-  - r-utf8=1.1.4=r36hcdcec82_1001
-  - r-vctrs=0.2.0=r36hcdcec82_1
-  - r-viridislite=0.3.0=r36h6115d3f_1002
-  - r-withr=2.1.2=r36h6115d3f_1001
-  - r-zeallot=0.1.0=r36h6115d3f_1001
-  - readline=8.0=hf8c457e_0
-  - sed=4.7=h1bed415_1000
-  - tk=8.6.9=hed695b0_1003
+  - python=3.8.5=h1103e12_7_cpython
+  - python_abi=3.8=1_cp38
+  - r-assertthat=0.2.1=r40h6115d3f_2
+  - r-backports=1.1.9=r40hcdcec82_0
+  - r-base=4.0.2=he766273_1
+  - r-bitops=1.0_6=r40hcdcec82_1004
+  - r-callr=3.4.3=r40h6115d3f_1
+  - r-catools=1.18.0=r40h0357c0b_1
+  - r-cli=2.0.2=r40h6115d3f_1
+  - r-colorspace=1.4_1=r40hcdcec82_2
+  - r-crayon=1.3.4=r40h6115d3f_1003
+  - r-desc=1.2.0=r40h6115d3f_1003
+  - r-digest=0.6.25=r40h0357c0b_2
+  - r-ellipsis=0.3.1=r40hcdcec82_0
+  - r-evaluate=0.14=r40h6115d3f_2
+  - r-fansi=0.4.1=r40hcdcec82_1
+  - r-farver=2.0.3=r40h0357c0b_1
+  - r-gdata=2.18.0=r40h6115d3f_1003
+  - r-ggplot2=3.3.2=r40h6115d3f_0
+  - r-glue=1.4.2=r40hcdcec82_0
+  - r-gplots=3.0.4=r40h6115d3f_0
+  - r-gtable=0.3.0=r40h6115d3f_3
+  - r-gtools=3.8.2=r40hcdcec82_1
+  - r-isoband=0.2.2=r40h0357c0b_0
+  - r-kernsmooth=2.23_17=r40hfa343cc_1
+  - r-labeling=0.3=r40h6115d3f_1003
+  - r-lattice=0.20_41=r40hcdcec82_2
+  - r-lifecycle=0.2.0=r40h6115d3f_1
+  - r-magrittr=1.5=r40h6115d3f_1003
+  - r-mass=7.3_52=r40hcdcec82_0
+  - r-matrix=1.2_18=r40h7fa42b6_3
+  - r-mgcv=1.8_33=r40h7fa42b6_0
+  - r-munsell=0.5.0=r40h6115d3f_1003
+  - r-nlme=3.1_149=r40h9bbef5b_0
+  - r-pillar=1.4.6=r40h6115d3f_0
+  - r-pkgbuild=1.1.0=r40h6115d3f_0
+  - r-pkgconfig=2.0.3=r40h6115d3f_1
+  - r-pkgload=1.1.0=r40h0357c0b_0
+  - r-praise=1.0.0=r40h6115d3f_1004
+  - r-prettyunits=1.1.1=r40h6115d3f_1
+  - r-processx=3.4.3=r40hcdcec82_0
+  - r-ps=1.3.4=r40hcdcec82_0
+  - r-r6=2.4.1=r40h6115d3f_1
+  - r-rcolorbrewer=1.1_2=r40h6115d3f_1003
+  - r-rcpp=1.0.4.6=r40h0357c0b_1
+  - r-rlang=0.4.7=r40hcdcec82_0
+  - r-rprojroot=1.3_2=r40h6115d3f_1003
+  - r-rstudioapi=0.11=r40h6115d3f_1
+  - r-scales=1.1.1=r40h6115d3f_0
+  - r-testthat=2.3.2=r40h0357c0b_1
+  - r-tibble=3.0.3=r40hcdcec82_0
+  - r-utf8=1.1.4=r40hcdcec82_1003
+  - r-vctrs=0.3.4=r40hcdcec82_0
+  - r-viridislite=0.3.0=r40h6115d3f_1003
+  - r-withr=2.2.0=r40h6115d3f_1
+  - r-zeallot=0.1.0=r40h6115d3f_1002
+  - readline=8.0=he28a2e2_2
+  - sed=4.8=hbfbb72e_0
+  - setuptools=49.6.0=py38h32f6830_0
+  - sqlite=3.33.0=h4cf870e_0
+  - tk=8.6.10=hed695b0_0
   - tktable=2.10=h555a92e_3
+  - wheel=0.35.1=pyh9f0ad1d_0
   - xorg-kbproto=1.0.7=h14c3975_1002
   - xorg-libice=1.0.10=h516909a_0
   - xorg-libsm=1.2.3=h84519dc_1000
-  - xorg-libx11=1.6.9=h516909a_0
+  - xorg-libx11=1.6.12=h516909a_0
   - xorg-libxau=1.0.9=h14c3975_0
   - xorg-libxdmcp=1.1.3=h516909a_0
   - xorg-libxext=1.3.4=h516909a_0
+  - xorg-libxpm=3.5.13=h516909a_0
   - xorg-libxrender=0.9.10=h516909a_1002
+  - xorg-libxt=1.1.5=h516909a_1003
   - xorg-renderproto=0.11.1=h14c3975_1002
   - xorg-xextproto=7.3.0=h14c3975_1002
   - xorg-xproto=7.0.31=h14c3975_1007
-  - xz=5.2.4=h14c3975_1001
-  - zlib=1.2.11=h516909a_1006
-  - zstd=1.4.0=h3b9ef0a_0
+  - xz=5.2.5=h516909a_1
+  - zlib=1.2.11=h516909a_1009
+  - zstd=1.4.5=h6597ccf_2
