expand README

.gitignore

@@ -11,9 +11,10 @@ results/*
 !.gitignore
 !.gitattributes
 !.editorconfig
-!.travis.yml
 !.test
 !.test/config/*
 !.test/ngs-test-data
 !LICENSE
 !README.md
+!Dockerfile
+!CHANGELOG.md

CHANGELOG.md

+
+## v0.1.0
+
+- added a changelog
+
+## v0.0.9
+
+
+### Main changes from the snakemake worlflow template
+
+- [Singularity](https://sylabs.io/singularity/) using a docker image published on [Docker hub](https://hub.docker.com/r/ginolhac/snake-chip-seq)
+- [AdapterRemoval](https://adapterremoval.readthedocs.io/en/latest/) for trimming (replacement of `cutadapt`)
+- add [FastqScreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
+- drop `DESeq2` for contrast in favor to the dedicated tool: [`DiffBind`](https://bioconductor.org/packages/release/bioc/html/DiffBind.html)
+- don't import the IGV session in report, the HTML becomes too large
\ No newline at end of file

Dockerfile

@@ -140,10 +140,9 @@ RUN python3 -m pip install snakemake multiqc pandas pyBigWig pysam macs2 deeptoo
 # R is 4.0.0
 # BiocManager 1.30.16, for BioC 3.12, #FIXME SPP is 1.16.0 if fine, avoid installing 1.15.2 line 148
 RUN install2.r --error littler BiocManager && \
-    /usr/local/lib/R/site-library/littler/examples/installBioc.r DESeq2 Rsubread apeglm pheatmap vsn Rsamtools && \
-    install2.r --error hexbin ggrepel cowplot tidyverse UpSetR # spp
+    /usr/local/lib/R/site-library/littler/examples/installBioc.r DESeq2 apeglm pheatmap vsn Rsamtools && \
+    install2.r --error hexbin ggrepel cowplot tidyverse UpSetR
 # DESeq2 is 1.30.1
-# Rsubread is 2.4.3
 # apeglm 1.12.0
 
 # Install phantompeakqualtools, SPP fixed version 1.15.2
@@ -163,9 +162,7 @@ RUN cd /opt && \
     unzip bowtie2-${BT2_VERSION}-linux-x86_64.zip && rm bowtie2-${BT2_VERSION}-linux-x86_64.zip && \
     mv bowtie2-${BT2_VERSION}-linux-x86_64/bowtie2* /usr/local/bin/ && rm -rf bowtie2-${BT2_VERSION}-linux-x86_64
 
-
-
-    # clean up
+# clean up
 RUN apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
     apt-get autoclean && \

README.md

@@ -2,24 +2,191 @@
 
 [![Snakemake](https://img.shields.io/badge/snakemake-≥6.4.0-brightgreen.svg)](https://snakemake.github.io)
 
-This workflow is a Snakemake port of the [nextflow chipseq pipeline](https://nf-co.re/chipseq) and performs ChIP-seq peak-calling, QC and differential analysis.
+This [workflow](https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-chip-seq) is derived from [Snakemake template](https://github.com/snakemake-workflows/chipseq) (itself port of the [nextflow chipseq pipeline](https://nf-co.re/chipseq)) and performs ChIP-seq peak-calling, QC and differential analysis.
+
+
+## Overview
+
+As displayed in the final [**report**](https://xsOdPxjHMEpp3hc:123456@owncloud.lcsb.uni.lu/public.php/webdav/report.html) the pipeline looks like:
+
+![](https://i.imgur.com/mNn5aYx.png)
+
+## Install
+
+On the [UL-HPC](https://hpc.uni.lu/), what is needed is:
+
+
+- `snakemake`, version at least `6.4`
+- `singularity`, provided the HPC as an **EasyBuild module**.
+- this workflow template
+
+For snakemake, you could install it via conda
+and installing snakemake as in the RFTM
+
+### Install conda
+
+- Follow the instructions from **Sarah Peter** in her [tutorial](https://r3.pages.uni.lu/school/snakemake-tutorial/#conda for installing `Miniconda3` (downloading 90 MB).
+
+```bash
+user@access $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+user@access $ bash ./Miniconda3-latest-Linux-x86_64.sh
+```
+
+Follow the instructions, press `ENTER`.
+
+You must enter the full path for the installation, like `/home/users/username/tools/miniconda3` where `username` is your login.
+
+And answer `yes` to initialize `conda`, note that your `.bashrc` will be modified, and for this session activated with
+
+```bash
+user@access source ~/.bashrc
+```
+
+the prompt then has the `(base)` prefix, indicating that the `base` environment is activated by default.
+Of note, it will be at each login, you can disable this is you dislike by removing the relevant part in your `.bashrc` 
+between the line `# >>> conda initialize >>>` and `# <<< conda initialize <<<`
+
+### Install snakemake with mamba
+
+`mamba` is the [recommended](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) tool for managing environments.
+
+Those 2 commands installed `mamba` in the default `base` environment then `snakemake` in a dedicated environment named `snakemake`
+
+```bash
+(base) user@access $ conda install -n base -c conda-forge mamba
+(base) user@access $ mamba create -c conda-forge -c bioconda -n snakemake snakemake
+```
+
+Once successfull, you need to activate the newly created environment, obsered the new name before you prompt:
+
+```bash
+(base) user@access $ conda activate snakemake
+(snakemake) user@access $ snakemake --version
+```
+
+### Install the ChIP-seq template
+
+In the destination folder of your choice, run the following commands:
+
+```bash
+VERSION="v0.0.9"
+wget -qO- https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-chip-seq/-/archive/${VERSION}/snakemake-chip-seq-.tar.gz | tar xfz - --strip-components=1
+```
+
+this command will download, extract (without the root folder) the following files:
+
+```
+CHANGELOG.md
+config/
+Dockerfile
+LICENSE
+README.md
+resources/
+workflow/
+```
+
+you may want to delete the `LICENSE`, `Dockerfile`, `CHANGELOG.md` and `README.md` if you wish, 
+they are not used by `snakemake` for runtime.
+
+
+#### (Optional) Useful aliases
+
+The following lines can be added to your `.bashrc`. 
+
+The 3 first ones are handy shortcuts:
+
+- `dag` is often run to see which steps are to be re-run or not
+- `smk` to load necessary on **ULHPC** in interactive sessions
+- the `complete` command loads the auto-completion for snakemake
+
+The `PYTHONNOUSERSITE` variable sets to `True` ensures that your installed python packages superseed the default system installed ones. 
+
+```bash
+alias dag='snakemake --dag | dot -Tpdf > dag.pdf'
+alias smk='conda activate snakemake && module load tools/Singularity'
+complete -o bashdefault -C snakemake-bash-completion snakemake
+# From Sarah Peter 
+export PYTHONNOUSERSITE=True
+```
+
+##### (Optional) Update `snakemake`
+
+Once `(base)` *conda* activated, you can update your `snakemake` version with:
+
+`mamba upgrade -n snakemake snakemake`
+
+
 
 ## Usage
 
 The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=snakemake-workflows/chipseq).
 
+
+After booking ressources on the access node, like for example here, 1 hour and 6 cores:
+
 ```
-snakemake --use-singularity --singularity-args "-B /scratch/users/aginolhac:/scratch/users/aginolhac"  -j 6
+si -c 6 -t 1:00:00
 ```
 
+### Singularity
+
+this is the easy part as the [HPC team](https://hpc.uni.lu/about/team.html) is providing us with available [modules](https://hpc.uni.lu/users/software/)
+
+the command once on a `node` is:
+
+```bash
+(base) user@access module load tools/Singularity
+```
+
+### Conda activate
+
+
+```bash
+(base) user@access $ conda activate snakemake
+```
+
+Of note, the 2 above steps can be replaced by the alias `smk` if you added the alias in your `.bashrc`
+
+### Dry-run
+
+
+```bash
+(snakemake) user@access $ snakemake --use-singularity --singularity-args "-B /scratch/users/aginolhac:/scratch/users/aginolhac"  -j 6 -n
+```
+
+
+Of note the following messages:
+```
+Workflow defines that rule get_genome is eligible for caching between workflows (use the --cache argument to enable this).
+Workflow defines that rule get_annotation is eligible for caching between workflows (use the --cache argument to enable this).
+Workflow defines that rule genome_faidx is eligible for caching between workflows (use the --cache argument to enable this).
+Workflow defines that rule bwa_index is eligible for caching between workflows (use the --cache argument to enable this).
+```
+
+are warning you that 
+
+
+### Activate the cache 
+
+To save download and computation times in between workflows
+
+1. Set-up
+
+```
+mkdir -p ${SCRATCH}/tmp
+export SNAKEMAKE_OUTPUT_CACHE=${SCRATCH}/tmp
+```
+
+2. Run command
+
+```
+snakemake --use-singularity --singularity-args "-B /scratch/users/aginolhac:/scratch/users/aginolhac"  --cache -j 6
+```
+
+
 
 # Credits
 
 This template is derived from the official [Snakemake-workflow](https://github.com/snakemake-workflows/chipseq) by [Antonie Vietor](https://github.com/AntonieV) and [David Laehnemann](https://github.com/dlaehnemann).
 Initially a port of the [Next-Flow ChIP-seq](https://nf-co.re/chipseq) (https://doi.org/10.5281/zenodo.3240506) by [Harshil Patel](https://github.com/drpatelh) [et al.](https://github.com/nf-core/chipseq/graphs/contributors)
 
-## Main changes
-
-- [Singularity](https://sylabs.io/singularity/) using a docker image publish on [Docker hub](https://hub.docker.com/r/ginolhac/snake-chip-seq)
-- [AdapterRemoval](https://adapterremoval.readthedocs.io/en/latest/) for trimming (replacement of `cutadapt`)
-- add [FastqScreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)