Bump version to v0.9.6

README.md

@@ -13,19 +13,19 @@ To run `wg-blimp` you need a UNIX environment that contains a [Bioconda](http://
 It is advised to install `wg-blimp` through Bioconda. It is also recommended to install `wg-blimp` in a fresh environment, as it has many dependencies that may conflict with other packages, for this you can use:
 
 ```
-conda create -n wg-blimp wg-blimp python=3.6.7 r-base=3.6.2 snakemake-minimal=5.8.1 methyldackel==0.4.0
+conda create -n wg-blimp wg-blimp python=3.6.7 r-base=4.0.2 methyldackel==0.4.0
 ```
 
 ### Docker
 
 We bundled a full `wg-blimp` installation into a Docker container. You may pull our image using
 ```
-docker pull imimarw/wg-blimp:v0.9.5
+docker pull imimarw/wg-blimp:v0.9.6
 ```
 
 Once the image was downloaded and extracted, you can start the docker container with
 ```
-docker run -it -v <directory-to-be-mounted>:<mounted-directory-in-container> imimarw/wg-blimp:v0.9.5
+docker run -it -v <directory-to-be-mounted>:<mounted-directory-in-container> imimarw/wg-blimp:v0.9.6
 ```
 
 ### From source
@@ -101,18 +101,18 @@ The following entries are used for running the Snakemake pipeline and may be spe
 
 | Key | Value |
 | --- | ----- |
-| *annotation_allowed_biotypes* | Only genes with this biotype will be annotated in the DMR table |
+| *annotation_allowed_biotypes* | Only genes with this biotype will be annotated in the DMR table (see https://www.gencodegenes.org/pages/biotypes.html ). |
 | *annotation_min_mapq* | When annotating coverage, only use reads with a minimum mapping quality |
 | *bsseq_local_correct* | Use local correction for bsseq DMR calling. Usually, setting this to FALSE will increase the number of calls. |
-| *cgi_annotation_file* | Gzipped csv file used for cg island annotation. |
+| *cgi_annotation_file* | Gzipped csv file used for cg island annotation. Mandatory for MethylSeekR segmentation. Usually downloaded from UCSC Table Browser. |
 | *computing_threads* | Number of processors a single job is allowed to use. Remember to use `--cores` parameter for Snakemake. |
 | *dmr_tools* | Tools to use for DMR calling. Available: `bsseq`, `camel`, `metilene`
-| *gene_annotation_file* | File used for genetic annotation. |
 | *group1* | Samples in first group for DMR analysis |
 | *group2* | Samples in second group for DMR analysis |
+| *gtf_annotation_file* | GTF file used for annotation of genes and promoters. |
 | *io_threads* | IO intensive tools virtually reserve this many cores (while actually using only one) to reduce file system IO load. |
-| *methylation_rate_on_chromosomes* | Compute methylation rates for these chromosome during qc |
-| *methylseekr_cgi_genome* | Reference genome to use for MethylSeekR CGI queries. |
+| *java_memory_gb* | Gigabytes of RAM to allocate for Java-based tools. If samples are too large, this must be increased to prevent crashes. |
+| *methylation_rate_on_chromosomes* | Compute methylation rates for these chromosome during QC |
 | *methylseekr_fdr_cutoff* | FDR cutoff for MethylSeekR segmentation. |
 | *methylseekr_methylation_cutoff* | Methylation cutoff for MethylSeekR segmentation. |
 | *methylseekr_pmd_chromosome* | Chromosome to compute MethylSeekR alpha values for. |
@@ -121,16 +121,14 @@ The following entries are used for running the Snakemake pipeline and may be spe
 | *min_diff* | Minimum average difference between the two groups for DMR calling |
 | *output_dir* | Directory containing all files created by the pipeline |
 | *promoter_tss_distances* | Distance interval around TSS's to be recognized as promoters in DMR annotation. |
-| *qualimap_memory_gb* | Gigabytes of RAM to allocate for Qualimap. If samples are too large, this must be increased to prevent crashes. |
 | *rawdir* | Directory containing .fastq files |
 | *rawsuffixregex* | The regular expressions to match for paired reads. By default, Illumina naming conventions are accepted. |
-| *ref* | .fasta reference file |
-| *repeat_masker_annotation_file* | File containing repeat masker annotation |
-| *repeat_masker_links* | Repeat masker files are relatively big and are only downloaded on demand from the links specified here. |
+| *ref* | .fasta reference file. "Bisulfited" references and BWA indices will be created automatically by bwa-meth) |
+| *repeat_masker_annotation_file* | File containing repetitive regions. Usually generated by RepeatMasker and downloaded from UCSC Table Browser. |
 | *sample_fastq_csv* | Optional CSV file containing association between samples and read files. The CSV must contain a header with column names `sample`, `forward` and `reverse`. When this option is set, parameters *rawdir* and *rawsuffixregex* are ignored. |
 | *samples* | All samples (usually concatenation of group1 and group2) |
 | *target_files* | Files to be generated by the Snakemake workflow |
-| *transcript_start_site_file* | File to read transcription start sites from (for DMR annotation) |
+| *temp_dir* | Directory for temporary files. This option may be used for instances where computation node disk space is limited. |
 
 ## Reporting errors / Requesting features
 If anything goes wrong using `wg-blimp` or any features are missing, feel free to open an issue or to contact Marius Wöste ( [email protected] )

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name='wg-blimp',
-    version='0.9.5',
+    version='0.9.6',
     author='Marius Woeste',
     author_email='[email protected]',
     description='WGBS methylation analysis pipeline',