adding core-snp-filter version 0.2.0

Program_Licenses.md

@@ -39,6 +39,7 @@ The licenses of the open-source software that is contained in these Docker image
 | CirculoCov | GNU GPLv3 | https://github.com/erinyoung/CirculoCov/blob/main/LICENSE |
 | Clair3 | non-standard | https://github.com/HKU-BAL/Clair3/blob/main/LICENSE.md |
 | colorid | MIT | https://github.com/hcdenbakker/colorid/blob/master/LICENSE |
+| Core-SNP-filter | GNU General Public License v3.0 | https://github.com/rrwick/Core-SNP-filter/blob/main/LICENSE |
 | datasets-sars-cov-2 | Apache 2.0 | https://github.com/CDCgov/datasets-sars-cov-2/blob/master/LICENSE |
 | diamond | GNU GPLv3 | https://github.com/bbuchfink/diamond/blob/master/LICENSE |
 | dnaapler | MIT | https://github.com/gbouras13/dnaapler/blob/main/LICENSE |

README.md

@@ -148,6 +148,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Clair3](https://hub.docker.com/r/staphb/clair3) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/clair3)](https://hub.docker.com/r/staphb/clair3) | <ul><li>[1.0.9](./clair3/1.0.9/)</li><li>[1.0.10](./clair3/1.0.10/)</li></ul> | https://github.com/HKU-BAL/Clair3 |
 | [Clustalo](https://hub.docker.com/r/staphb/clustalo) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/clustalo)](https://hub.docker.com/r/staphb/clustalo) | <ul><li>1.2.4</li></ul> | http://www.clustal.org/omega/ |
 | [colorid](https://hub.docker.com/r/staphb/colorid) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/colorid)](https://hub.docker.com/r/staphb/colorid) | <ul><li>0.1.4.3</li></ul> | https://github.com/hcdenbakker/colorid |
+| [Core-SNP-filter](https://hub.docker.com/r/staphb/core-snp-filter) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/core-snp-filter)](https://hub.docker.com/r/staphb/core-snp-filter) | <ul><li>[0.2.0](./core-snp-filter/0.2.0/)</li></ul> | https://github.com/rrwick/Core-SNP-filter |
 | [cutshaw-report-env](https://hub.docker.com/r/staphb/cutshaw-report-env) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/cutshaw-report-env)](https://hub.docker.com/r/staphb/cutshaw-report-env) | <ul><li>1.0.0</li></ul> | https://github.com/VADGS/CutShaw |
 | [datasets-sars-cov-2](https://github.com/CDCgov/datasets-sars-cov-2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/datasets-sars-cov-2)](https://hub.docker.com/r/staphb/datasets-sars-cov-2) | <ul><li>0.6.2</li><li>0.6.3</li><li>0.7.2</li></ul> | https://github.com/CDCgov/datasets-sars-cov-2 |
 | [dnaapler](https://hub.docker.com/r/staphb/dnaapler) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dnaapler)](https://hub.docker.com/r/staphb/dnaapler) | <ul><li>[0.1.0](dnaapler/0.1.0/)</li></ul> <ul><li>[0.4.0](dnaapler/0.4.0/)</li><li>[0.5.0](dnaapler/0.5.0/)</li><li>[0.5.1](dnaapler/0.5.1/)</li><li>[0.7.0](dnaapler/0.7.0/)</li><li>[0.8.0](dnaapler/0.8.0/)</li><li>[1.0.1](dnaapler/1.0.1/)</li></ul> | https://github.com/gbouras13/dnaapler |

core-snp-filter/0.2.0/Dockerfile

@@ -0,0 +1,53 @@
+FROM ubuntu:jammy as app
+
+ARG CORESNPFILTER_VER="0.2.0"
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="Core-SNP-filter"
+LABEL software.version="${CORESNPFILTER_VER}"
+LABEL description="This is a tool to filter sites (i.e. columns) in a FASTA-format whole-genome pseudo-alignment"
+LABEL website="https://github.com/rrwick/Core-SNP-filter"
+LABEL license="https://github.com/rrwick/Core-SNP-filter/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /usr/local/bin
+
+RUN wget -q https://github.com/rrwick/Core-SNP-filter/releases/download/v${CORESNPFILTER_VER}/coresnpfilter-linux-x86_64-musl-v${CORESNPFILTER_VER}.tar.gz && \
+    tar -vxf coresnpfilter-linux-x86_64-musl-v${CORESNPFILTER_VER}.tar.gz && \
+    rm -rf coresnpfilter-linux-x86_64-musl-v${CORESNPFILTER_VER}.tar.gz
+
+ENV LC_ALL=C
+
+CMD [ "coresnpfilter", "--help" ]
+
+# 'WORKDIR' sets working directory
+WORKDIR /data
+
+##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- #####
+##### Step 2. Set up the testing stage.                                 #####
+##### The docker image is built to the 'test' stage before merging, but #####
+##### the test stage (or any stage after 'app') will be lost.           #####
+##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- #####
+
+# A second FROM insruction creates a new stage
+FROM app as test
+
+# set working directory so that all test inputs & outputs are kept in /test
+WORKDIR /test
+
+# print help and version info; check dependencies (not all software has these options available)
+# Mostly this ensures the tool of choice is in path and is executable
+RUN coresnpfilter --help && \
+    coresnpfilter --version
+
+RUN wget -q https://github.com/rrwick/Core-SNP-filter/raw/refs/heads/main/demo.fasta.gz && \
+    coresnpfilter -e -c 0.95 demo.fasta.gz > demo_core.fasta && \
+    head demo_core.fasta

core-snp-filter/0.2.0/README.md

@@ -0,0 +1,36 @@
+# Core-SNP-filter container
+
+Main tool: [Core-SNP-filter](https://github.com/rrwick/Core-SNP-filter)
+
+Code repository: https://github.com/rrwick/Core-SNP-filter
+
+Basic information on how to use this tool:
+- executable: coresnpfilter
+- help: -h
+- version: -V
+- description: |
+
+> This is a tool to filter sites (i.e. columns) in a FASTA-format whole-genome pseudo-alignment based on:
+> - Whether the site contains variation or not.
+> - How conserved the site is, i.e. contains an unambiguous base in a sufficient fraction of the sequences.
+
+Full documentation: https://github.com/rrwick/Core-SNP-filter
+
+## Example Usage
+
+```bash
+# Exclude invariant sites:
+coresnpfilter -e core.full.aln > filtered.aln
+
+# With a strict core threshold (same as Snippy's core.aln):
+coresnpfilter -e -c 1.0 core.full.aln > filtered.aln
+
+# With a slightly more relaxed core threshold:
+coresnpfilter -e -c 0.95 core.full.aln > filtered.aln
+
+# Use gzipped files to save disk space:
+coresnpfilter -e -c 0.95 core.full.aln.gz | gzip > filtered.aln.gz
+
+# Running without any options will work, but the output will be the same as the input:
+coresnpfilter core.full.aln > filtered.aln
+```