Bump Version

Author: merszym

CHANGELOG.md

@@ -5,12 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
-## [WIP]
+## [v2.4]
 
 ### Changes
 
 - Publish the "KrakenUniq parsed report" in the 'stats' directory
-- Add an R-friendly version of the final summary report (column names w/o special characters)
+- Add an R-friendly version of the final summary report (column names w/o special characters, `R_final_report.tsv`)
 - In the final_report, replace `SpeciesKmers` name with `Kmers` and include the "best" and "(family)" level stats. E.g. "4 (129)"
 - for the `KmerCoverage` and `KmerDupRate` columns, also combine "best" and "(family)"
 - Add a `--fixed_bedfiltering` flag to run dustmasking and bedfiltering also for fixed references (off by default)    

README.md

@@ -71,7 +71,7 @@ quicksand is executed directly from github. With the databases created and the t
 # set this if you encounter a heap-space error to increase the memory that is used by nextflow
 export NXF_OPTS="-Xms10g -Xmx15g" # increase or decrease the numbers as required
 
-nextflow run mpieva/quicksand -r v2.3 \
+nextflow run mpieva/quicksand -r v2.4 \
   --db        refseq/kraken/Mito_db_kmer22/ \
   --genomes   refseq/genomes/ \
   --bedfiles  refseq/masked/ \

assets/pipeline/help.txt

@@ -1,4 +1,4 @@
-Usage: nextflow run mpieva/quicksand -r v2.3 {--bam PATH --rg PATH | --split DIR} --db PATH --genome PATH --bedfiles PATH [options] -profile singularity
+Usage: nextflow run mpieva/quicksand -r v2.4 {--bam PATH --rg PATH | --split DIR} --db PATH --genome PATH --bedfiles PATH [options] -profile singularity
 
 required arguments:
   Either:

docs/source/conf.py

@@ -22,8 +22,8 @@
 author = 'Merlin Szymanski'
 
 # The full version, including alpha/beta/rc tags
-release = 'v2.3'
-version = 'v2.3'
+release = 'v2.4'
+version = 'v2.4'
 
 # -- General configuration ---------------------------------------------------
 

docs/source/examples.rst

@@ -18,7 +18,7 @@ families and the number of ancient sequences found.
 
 Execute quicksand like this::
 
-    nextflow run mpieva/quicksand -r v2.3 \
+    nextflow run mpieva/quicksand -r v2.4 \
         -profile   singularity \
         --split    split/ \
         --db       refseq/kraken/Mito_db_kmer22/ \
@@ -29,7 +29,7 @@ The output files are grouped by family-level in the :code:`out/` directory. Sequ
 (after KrakenUniq) are stored in :code:`out/{family}/1-extracted/` while mapped, deduped and bedfiltered sequences are saved in the
 :code:`out/{family}/best/{step}/` directories after the respective processing step::
 
-    quicksand_v2.3
+    quicksand_v2.4
     ├── out
     │    └── {family}
     │         ├── 1-extracted
@@ -72,7 +72,7 @@ The 'Tags' used are used in the same way as the 'Species' (e.g. in the file-name
 
 Run quicksand with::
 
-    nextflow run mpieva/quicksand -r v2.3 \
+    nextflow run mpieva/quicksand -r v2.4 \
         -profile   singularity \
         --split    split/ \
         --db       refseq/kraken/Mito_db_kmer22/ \
@@ -84,7 +84,7 @@ The output file structure remains mostly the same. For families specified in the
 appear in the :code:`out/{family}/fixed/{step}/` directory, together with additional output-files
 that might be useful for additional downstream-analyses, such as the extracted deaminated reads::
 
-    quicksand_v2.3
+    quicksand_v2.4
     ├── out
     │    └── {family}
     │         ├── 1-extracted
@@ -130,14 +130,14 @@ So after collecting more reference genome(s) for the Suidae family, prepare a fr
 
 and rerun the pipeline with::
 
-    nextflow run mpieva/quicksand -r v2.3 \
+    nextflow run mpieva/quicksand -r v2.4 \
         -profile   singularity \
         --rerun    \
         --fixed    fixed-references.tsv
 
 The (additional) output files are then the ones created by the :code:`--fixed` flag::
 
-    quicksand_v2.3
+    quicksand_v2.4
     ├── out
     │    └── Suidae
     │         ├── 1-extracted

docs/source/in_and_out.rst

@@ -24,10 +24,10 @@ as readgroups::
 Output
 ------
 
-quicksand writes all output files to the **quicksand_v2.3** directory. Within this directory the files are
+quicksand writes all output files to the **quicksand_v2.4** directory. Within this directory the files are
 layed out as follows::
 
-    quicksand_v2.3
+    quicksand_v2.4
     ├── out
     │    └── {taxon}
     │         ├── 1-extracted

docs/source/quickstart.rst

@@ -58,15 +58,15 @@ Run quicksand
 
 quicksand is executed directly from github. With the databases created and the testdata downloaded, run the pipeline as follows::
 
-    nextflow run mpieva/quicksand -r v2.3 \
+    nextflow run mpieva/quicksand -r v2.4 \
       -profile   singularity \
       --db       refseq/kraken/Mito_db_kmer22 \
       --genomes  refseq/genomes/ \
       --bedfiles refseq/masked/ \
       --split    split/
 
 
-The output of quicksand can be found in the directory **quicksand_v2.3/**
+The output of quicksand can be found in the directory **quicksand_v2.4/**
 
 See the :code:`final_report.tsv` and :code:`filtered_report_0.5p_0.5b.tsv` for a summary of the results.
 

nextflow.config

@@ -12,7 +12,7 @@ manifest {
     homePage         = 'https://mpieva.github.io/quicksand/'
     description      = 'quick analysis of sedimentary ancient DNA'
     nextflowVersion  = '>=22.10'
-    version          = 'v2.3'
+    version          = 'v2.4'
 }
 
 cleanup = true