Update docs, CHANGELOG, bump version

Author: merszym

Diff for: CHANGELOG.md

@@ -7,9 +7,25 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## Unpublished
 
-### Bugfixes
+- Nothing to see here
 
-- change in parse-report script to account for taxa without order hierarchy
+## [v2.1] - 2024-03-21
+
+This version adds 4 columns to the end of the `final_report.tsv` file and adds an additional file `filtered_report_{n}p_{m}b.tsv` to the output-directory. This file should serve as a quick look on the final_report and shoult **not** be treated as the final output file
+
+### Changes
+
+This version alters the `final_report.tsv` file and adds an additional file `filtered_report_{n}p_{m}b.tsv` which is a filtered version of the final_report based on two freshly introduced filter-flags
+
+- `--reportfilter_percentage` sets the filter threshold for the FamPercentage column
+- `--reportfilter_breadth` sets the filter threshold for the ProportionExpectedBreadth column
+
+Within the workflow quicksand now takes additional information from the `samtools coverage` command that analyzes the deduplicated reads. This additional information is (or is used to calculate)
+
+- Depth of Coverage
+- Breadth of Coverage
+- Expected Breadth of Coverage, based on the [inStrain documentation](https://instrain.readthedocs.io/en/latest/important_concepts.html)
+- Proportion of Expected Breadth, based on the [inStrain documentation](https://instrain.readthedocs.io/en/latest/important_concepts.html)
 
 ## [v2.0] - 2023-11-20
 

Diff for: README.md

@@ -62,7 +62,7 @@ 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 v2.0 \
+nextflow run mpieva/quicksand -r v2.1 \
   --db        refseq/kraken/Mito_db_kmer22/ \
   --genomes   refseq/genomes/ \
   --bedfiles  refseq/masked/ \

Diff for: docs/source/conf.py

@@ -18,12 +18,12 @@
 # -- Project information -----------------------------------------------------
 
 project = 'quicksand'
-copyright = '2023, Merlin Szymanski'
+copyright = '2024, Merlin Szymanski'
 author = 'Merlin Szymanski'
 
 # The full version, including alpha/beta/rc tags
-release = 'v2.0'
-version = 'v2.0'
+release = 'v2.1'
+version = 'v2.1'
 
 # -- General configuration ---------------------------------------------------
 

Diff for: 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 v2.0 \
+    nextflow run mpieva/quicksand -r v2.1 \
         -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_v2.0
+    quicksand_v2.1
     ├── out
     │    └── {family}
     │         ├── 1-extracted
@@ -65,7 +65,7 @@ file-names and should be unique!::
 
 and start the execution with::
 
-    nextflow run mpieva/quicksand -r v2.0 \
+    nextflow run mpieva/quicksand -r v2.1 \
         -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_v2.0
+    quicksand_v2.1
     ├── 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 v2.0 \
+    nextflow run mpieva/quicksand -r v2.1 \
         -profile   singularity \
         --rerun    \
         --fixed    fixed-references.tsv
 
 The (additional) output files are the ones created by the :code:`--fixed` flag::
 
-    quicksand_v2.0
+    quicksand_v2.1
     ├── out
     │    └── {family}
     │         ├── 1-extracted

Diff for: docs/source/in_and_out.rst

@@ -24,10 +24,10 @@ as readgroups::
 Output
 ------
 
-quicksand writes all output files to the **quicksand_v2.0** directory. Within this directory the files are
+quicksand writes all output files to the **quicksand_v2.1** directory. Within this directory the files are
 layed out as follows::
 
-    quicksand_v2.0
+    quicksand_v2.1
     ├── out
     │    └── {taxon}
     │         ├── 1-extracted

Diff for: docs/source/quickstart.rst

@@ -44,16 +44,16 @@ Run quicksand
 
 nextflow pipelines can be executed directly from github. To run quicksand using the downloaded data-set type::
 
-    nextflow run mpieva/quicksand -r v2.0 \
+    nextflow run mpieva/quicksand -r v2.1 \
       -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_v2.0/**
-| See the :code:`final_report.tsv` for a summary of the results.
+| The output of quicksand can be found in the directory **quicksand_v2.1/**
+| 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.
 
 .. [1] http://ftp.eva.mpg.de/neandertal/Hohlenstein-Stadel/README

Diff for: nextflow.config

@@ -12,7 +12,7 @@ manifest {
     homePage         = 'https://mpieva.github.io/quicksand/'
     description      = 'quick analysis of sedimentary ancient DNA'
     nextflowVersion  = '>=22.10'
-    version          = 'v2.0'
+    version          = 'v2.1'
 }
 
 cleanup = true