From 3bda2a82ad48d23025de6ce748f3b188f5aa1a46 Mon Sep 17 00:00:00 2001 From: Merlin Szymanski Date: Thu, 26 Sep 2024 18:27:30 +0200 Subject: [PATCH] bump version --- CHANGELOG.md | 2 +- README.md | 2 +- assets/pipeline/help.txt | 2 +- docs/source/conf.py | 4 ++-- docs/source/examples.rst | 12 ++++++------ docs/source/in_and_out.rst | 4 ++-- docs/source/quickstart.rst | 4 ++-- nextflow.config | 2 +- 8 files changed, 16 insertions(+), 16 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2ac5913..343dbc4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ 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/). -## Unpublished +## [v2.2] - 2024-09-26 ### Changes diff --git a/README.md b/README.md index 4784c0a..32a7923 100644 --- a/README.md +++ b/README.md @@ -61,7 +61,7 @@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 v2.1 \ +nextflow run mpieva/quicksand -r v2.2 \ --db refseq/kraken/Mito_db_kmer22/ \ --genomes refseq/genomes/ \ --bedfiles refseq/masked/ \ diff --git a/assets/pipeline/help.txt b/assets/pipeline/help.txt index 0c37db1..eec159c 100644 --- a/assets/pipeline/help.txt +++ b/assets/pipeline/help.txt @@ -1,4 +1,4 @@ -Usage: nextflow run mpieva/quicksand -r v2.1 {--bam PATH --rg PATH | --split DIR} --db PATH --genome PATH --bedfiles PATH [options] -profile singularity +Usage: nextflow run mpieva/quicksand -r v2.2 {--bam PATH --rg PATH | --split DIR} --db PATH --genome PATH --bedfiles PATH [options] -profile singularity required arguments: Either: diff --git a/docs/source/conf.py b/docs/source/conf.py index 3ad62ad..de1d082 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -22,8 +22,8 @@ author = 'Merlin Szymanski' # The full version, including alpha/beta/rc tags -release = 'v2.1' -version = 'v2.1' +release = 'v2.2' +version = 'v2.2' # -- General configuration --------------------------------------------------- diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 6f36a56..a888d45 100644 --- a/docs/source/examples.rst +++ b/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 v2.1 \ + nextflow run mpieva/quicksand -r v2.2 \ -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_v2.1 + quicksand_v2.2 ├── out │ └── {family} │ ├── 1-extracted @@ -65,7 +65,7 @@ file-names and should be unique!:: and start the execution with:: - nextflow run mpieva/quicksand -r v2.1 \ + nextflow run mpieva/quicksand -r v2.2 \ -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_v2.1 + quicksand_v2.2 ├── 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 v2.1 \ + nextflow run mpieva/quicksand -r v2.2 \ -profile singularity \ --rerun \ --fixed fixed-references.tsv The (additional) output files are the ones created by the :code:`--fixed` flag:: - quicksand_v2.1 + quicksand_v2.2 ├── out │ └── {family} │ ├── 1-extracted diff --git a/docs/source/in_and_out.rst b/docs/source/in_and_out.rst index 9a48142..f25f4c6 100644 --- a/docs/source/in_and_out.rst +++ b/docs/source/in_and_out.rst @@ -24,10 +24,10 @@ as readgroups:: Output ------ -quicksand writes all output files to the **quicksand_v2.1** directory. Within this directory the files are +quicksand writes all output files to the **quicksand_v2.2** directory. Within this directory the files are layed out as follows:: - quicksand_v2.1 + quicksand_v2.2 ├── out │ └── {taxon} │ ├── 1-extracted diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst index 363c2c0..0f26b82 100644 --- a/docs/source/quickstart.rst +++ b/docs/source/quickstart.rst @@ -44,7 +44,7 @@ Run quicksand nextflow pipelines can be executed directly from github. To run quicksand using the downloaded data-set type:: - nextflow run mpieva/quicksand -r v2.1 \ + nextflow run mpieva/quicksand -r v2.2 \ -profile singularity \ --db refseq/kraken/Mito_db_kmer22 \ --genomes refseq/genomes/ \ @@ -52,7 +52,7 @@ nextflow pipelines can be executed directly from github. To run quicksand using --split split/ -| The output of quicksand can be found in the directory **quicksand_v2.1/** +| The output of quicksand can be found in the directory **quicksand_v2.2/** | 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. diff --git a/nextflow.config b/nextflow.config index 6950324..4ab8d6a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,7 +12,7 @@ manifest { homePage = 'https://mpieva.github.io/quicksand/' description = 'quick analysis of sedimentary ancient DNA' nextflowVersion = '>=22.10' - version = 'v2.1' + version = 'v2.2' } cleanup = true