Merge pull request #77 from vpbrendel/main

various updates (references)

Author: vpbrendel

HOWTO.md

@@ -9,7 +9,7 @@ Please go to [data/README](./data/README.md) for production-level workflow scrip
 
 At this stage, you should have completed the BWASP installation steps
 documented in the [INSTALL](./INSTALL.md) document; we'll assume that you have
-downloaded the `bwasp.sif` singularity container.
+downloaded the `bwasp.sif` Singularity container.
 
 The BWASP script [xgetSRAacc](./bin/xgetSRAacc) uses NCBI SRA Toolkit to download data from NCBI SRA.
 If you have been using SRA Toolkit already and allow local file-caching, you need to make sure that your file-caching location is accessible to singularity.
@@ -20,13 +20,13 @@ To do this, run:
   singularity exec -e bwasp.sif  vdb-config -i
 ```
 
-navigate to CACHE by entering C and disable local file-caching by toggeling i, followed by x for exit, and possibley o for ok.
+navigate to CACHE by entering C and disable local file-caching by toggeling i, followed by x for exit, and possibly o for ok.
 
 __Note: If this is the first time you are using SRA Toolkit on the current machine, you will have to invoke _vdb-config_ at least once to set your preferences (as per NCBI instructions).__
 
 
 We explain BWASP use with an example from our
-[publication](http://brendelgroup.org/).
+[2021 publication](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13566).
 
 
 ## Samples
@@ -150,7 +150,7 @@ $BWASP_EXEC make &> bwasp.log
 ```
 
 The preceding `$BWASP_EXEC` makes sure that `make` runs from inside the
-singularity container, where we made sure all the moving parts are in working
+Singularity container, where we made sure all the moving parts are in working
 condition (i.e. all required binaries are of correct version and in the path).
 
 The first *make* command with the -n flag simply shows what _make_ will do and
@@ -172,7 +172,7 @@ After completion of the BWASP workflow, the working directory should contain a
 fair number of output files.
 Please refer to the documentation of the various constituent programs for
 details as well as our
-[manuscript](http://brendelgroup.org/research/publications.php).
+[2021 publication](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13566).
 To remove unneeded intermediate files and archive files that may be of
 interest later but are not needed in subsequent __BWASP__ analysis steps
 we recommend running the following commands at this stage:

INSTALL.md

@@ -2,7 +2,7 @@
 
 ## Requirements
 
-  * BWASP should run on any platform that supports [Singularity](https://www.sylabs.io/docs/) (Linux, MacOS, Windows), although we have only tested on Linux.
+  * BWASP should run on any platform that supports [Singularity](https://apptainer.org/) (Linux, MacOS), although we have only tested on Linux.
 
   * BWASP can execute on a single processor machine, but realistically you would want to have 10-20 cores available.
 
@@ -36,7 +36,7 @@ BWASP use via the singularity container is highly recommended, with no known
 drawbacks.
 However, if desired, you can of course install all the required software and
 packages individually on your computer system.
-The singularity [recipe file](./Singularity) in this repository should serve as
+The Singularity [definition file](./bwasp.def) in this repository should serve as
 a guide to perform such an installation.
 The `bwasp.sif` container was built on the 
 [current long-term supported Ubuntu 20.04 distribution](https://www.ubuntu.com/download/desktop)

README.md

@@ -12,7 +12,7 @@ results; it is __open__ (source) and designed to be __scalable__ and
 __easy__ to use.
 
 
-## Quick Start [![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/1203)
+## Quick Start
 
 Input to the BWASP workflow consists of accession numbers or fastq files of
 bisulfite-sequencing reads as well as the appropriate genome assembly (and, if
@@ -25,7 +25,7 @@ workflow, but configuration and execution is via
 [GNU make](https://www.gnu.org/software/make/) using edited copies of the
 makefiles provided in the _makefiles_ directory.
 All the BWASP dependencies are encapsulated in a
-[Singularity](https://www.sylabs.io/docs/) container available from our
+[Singularity](https://apptainer.org/) container available from our
 [Singularity Hub](http://BrendelGroup.org/SingularityHub/).
 Thus, once you know what you are doing, execution could be as simple as
 
@@ -47,10 +47,11 @@ document for a complete example of how to implement and run a workflow.
 
 ## Reference
 
-Claire Morandine and Volker P. Brendel
-(2021) _Tools and applications for integrative analysis of DNA methylation
-in social insects._ Molecular Ecology Resources, in print.
-Pre-print: [at BioRxiv](https://www.biorxiv.org/content/10.1101/2021.08.19.457008v3)
+__Claire Morandin and Volker P. Brendel (2021)__
+ _Tools and applications for integrative analysis of DNA methylation in social insects._
+Molecular Ecology Resources, 00, 1-19. [https://doi.org/10.1111/1755-0998.13566](https://doi.org/10.1111/1755-0998.13566).
+
+Original pre-print: [at BioRxiv](https://www.biorxiv.org/content/10.1101/2021.08.19.457008v3).
 
 
 ## Contact