update CHANGELOG, bump version

Author: merszym

CHANGELOG.md

@@ -5,13 +5,24 @@ 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/).
 
+## [v2.3] - 2024-11-19
+
+### Bugfixes
+
+- Remove the default read filters in the `samtools coverage` function. (This caused results with ReadsDeduped > 0 but CoveredBP 0).
+- Remove bug in the `final_report.tsv` report generation, the bug kept duplicated families (from Kraken) with MappedReads 0 in the report.
+- Update default values in the report to match the format of the `final_report.tsv` (e.g. 0.0 instead of 0)  
+
 ## [v2.2] - 2024-09-26
 
 ### Changes
 
 - Add a `--doublestranded` flag to adjust damage pattern analysis to the ones observed in data created from double stranded libraries.
   - Changes the `bam_deam_stats.py` and the `mask_deamination.py` scripts to look at 3' G to A substitutions instead of the C to T changes as done before.
   - Nothing changes for default runs
+
+### Bugfixes 
+
 - Fix a bug in the processing of paired fastq-files.
   - removes the "1" flag from the resulting bam files (make sure to merge your reads before quicksand!)
 

README.md

@@ -61,7 +61,7 @@ http://ftp.eva.mpg.de/neandertal/Hohlenstein-Stadel/BAM/mtDNA/HST.raw_data.ALL.b
 quicksand is executed directly from github, no local build is required. With the databases and the testdata downloaded, run the pipeline.
 
 ```bash
-nextflow run mpieva/quicksand -r v2.2 \
+nextflow run mpieva/quicksand -r v2.3 \
   --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 v2.2 {--bam PATH --rg PATH | --split DIR} --db PATH --genome PATH --bedfiles PATH [options] -profile singularity
+Usage: nextflow run mpieva/quicksand -r v2.3 {--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 = 'v2.2'
-version = 'v2.2'
+release = 'v2.3'
+version = 'v2.3'
 
 # -- 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 v2.2 \
+    nextflow run mpieva/quicksand -r v2.3 \
         -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. Extr
 after the KrakenUniq run are stored in :code:`out/{family}/1-extracted/` while mapped, deduped and filtered sequences are saved to the
 :code:`out/{family}/best/{step}/` directory after the respective processing step::
 
-    quicksand_v2.2
+    quicksand_v2.3
     ├── out
     │    └── {family}
     │         ├── 1-extracted
@@ -65,7 +65,7 @@ file-names and should be unique!::
 
 and start the execution with::
 
-    nextflow run mpieva/quicksand -r v2.2 \
+    nextflow run mpieva/quicksand -r v2.3 \
         -profile   singularity \
         --split    split/ \
         --db       refseq/kraken/Mito_db_kmer22/ \
@@ -77,7 +77,7 @@ The output file structure remains the same as before. For families specified in
 appear in the :code:`out/{family}/fixed/{step}/` directory, together with additional output-files
 that are useful in additional downstream-analyses, such as the extracted deaminated reads::
 
-    quicksand_v2.2
+    quicksand_v2.3
     ├── out
     │    └── {family}
     │         ├── 1-extracted
@@ -122,14 +122,14 @@ After collecting the reference genome(s) for the Suidae family, prepare a fresh
 
 and rerun the pipeline with::
 
-    nextflow run mpieva/quicksand -r v2.2 \
+    nextflow run mpieva/quicksand -r v2.3 \
         -profile   singularity \
         --rerun    \
         --fixed    fixed-references.tsv
 
 The (additional) output files are the ones created by the :code:`--fixed` flag::
 
-    quicksand_v2.2
+    quicksand_v2.3
     ├── out
     │    └── {family}
     │         ├── 1-extracted

docs/source/in_and_out.rst

@@ -24,10 +24,10 @@ as readgroups::
 Output
 ------
 
-quicksand writes all output files to the **quicksand_v2.2** directory. Within this directory the files are
+quicksand writes all output files to the **quicksand_v2.3** directory. Within this directory the files are
 layed out as follows::
 
-    quicksand_v2.2
+    quicksand_v2.3
     ├── out
     │    └── {taxon}
     │         ├── 1-extracted

docs/source/quickstart.rst

@@ -44,15 +44,15 @@ Run quicksand
 
 nextflow pipelines can be executed directly from github. To run quicksand using the downloaded data-set type::
 
-    nextflow run mpieva/quicksand -r v2.2 \
+    nextflow run mpieva/quicksand -r v2.3 \
       -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_v2.2/**
+| The output of quicksand can be found in the directory **quicksand_v2.3/**
 | See the :code:`final_report.tsv` and :code:`filtered_report_0.5p_0.5b.tsv` for a summary of the results.
 | See the :ref:`output-page` section for a detailed explaination of all the output files.
 

nextflow.config

@@ -12,7 +12,7 @@ manifest {
     homePage         = 'https://mpieva.github.io/quicksand/'
     description      = 'quick analysis of sedimentary ancient DNA'
     nextflowVersion  = '>=22.10'
-    version          = 'v2.2'
+    version          = 'v2.3'
 }
 
 cleanup = true