Merge branch 'StaPH-B:master' into tkp-bindashtree

.github/workflows/update_freyja.yml

@@ -28,7 +28,7 @@ jobs:
           version=1.5.2
           echo "version=$version" >> $GITHUB_OUTPUT 
           
-          file=build-files/freyja/$version/Dockerfile
+          file=build-files/freyja/1.5.2-bf/Dockerfile
           ls $file
           echo "file=$file" >> $GITHUB_OUTPUT
 

Program_Licenses.md

@@ -56,6 +56,7 @@ The licenses of the open-source software that is contained in these Docker image
 | FastANI | Apache v2.0 | https://github.com/ParBLiSS/FastANI/blob/master/LICENSE |
 | fasten | MIT | https://github.com/lskatz/fasten/blob/master/LICENSE |
 | Fastp | MIT | https://github.com/OpenGene/fastp/blob/master/LICENSE |
+| Fastplong | MIT | https://github.com/OpenGene/fastplong/blob/main/LICENSE |
 | FastTree | GNU GPLv2 | http://www.microbesonline.org/fasttree/ |
 | FastQC | GNU GPLv3 | https://github.com/s-andrews/FastQC/blob/master/LICENSE.txt |
 | fastq-scan | MIT | https://github.com/rpetit3/fastq-scan/blob/master/LICENSE |

README.md

@@ -167,6 +167,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [FastANI](https://hub.docker.com/r/staphb/fastani) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastani)](https://hub.docker.com/r/staphb/fastani) | <ul><li>1.1</li><li>1.32</li><li>1.33</li><li>1.33 + RGDv2</li><li>[1.34](fastani/1.34)</li><li>[1.34 + RGDv2](fastani/1.34-RGDV2/)</li></ul> | https://github.com/ParBLiSS/FastANI |
 | [fasten](https://hub.docker.com/r/staphb/fasten) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fasten)](https://hub.docker.com/r/staphb/fasten) | <ul><li>[0.7.2](./fasten/0.7.2)</li><li>[0.8.1](./fasten/0.8.1/)</li></ul> | https://github.com/lskatz/fasten |
 | [Fastp](https://hub.docker.com/r/staphb/fastp) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastp)](https://hub.docker.com/r/staphb/fastp) | <ul><li>0.23.2</li><li>[0.23.4](fastp/0.23.4/)</li><li>[0.24.0](./fastp/0.24.0/)</li></ul> | http://opengene.org/fastp/ <br/> https://github.com/OpenGene/fastp |
+| [fastplong](https://hub.docker.com/r/staphb/fastplong) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastplong)](https://hub.docker.com/r/staphb/fastplong) | <ul><li>[0.2.2](./build-files/fastplong/0.2.2/)</li></ul> | https://github.com/OpenGene/fastplong |
 | [FastTree](https://hub.docker.com/r/staphb/fasttree) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fasttree)](https://hub.docker.com/r/staphb/fasttree) | <ul><li>2.1.11</li></ul> | http://www.microbesonline.org/fasttree/ |
 | [FastQC](https://hub.docker.com/r/staphb/fastqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastqc)](https://hub.docker.com/r/staphb/fastqc) | <ul><li>0.11.8</li><li>0.11.9</li><li>0.12.1</li></ul> | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ <br/> https://github.com/s-andrews/FastQC |
 | [fastq-scan](https://hub.docker.com/r/staphb/fastq-scan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastq-scan)](https://hub.docker.com/r/staphb/fastq-scan) | <ul><li>0.4.3</li><li>0.4.4</li><li>1.0.0</li><li>1.0.1</li></ul> | https://github.com/rpetit3/fastq-scan |

build-files/fastplong/0.2.2/Dockerfile

@@ -0,0 +1,57 @@
+ARG FASTPLONG_VER="0.2.2"
+
+FROM ubuntu:jammy AS app
+
+# List all software versions are ARGs near the top of the dockerfile
+# 'ARG' sets environment variables during the build stage
+# ARG variables are ONLY available during image build, they do not persist in the final image
+ARG FASTPLONG_VER
+
+# '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="fastplong"
+LABEL software.version="${FASTPLONG_VER}"
+LABEL description="Ultrafast preprocessing and quality control for long reads"
+LABEL website="https://github.com/OpenGene/fastplong"
+LABEL license="https://github.com/OpenGene/fastplong/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+# 'RUN' executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libdeflate-dev \
+    libisal-dev \
+    libhwy-dev \
+    wget && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget --no-check-certificate -q http://opengene.org/fastplong/fastplong.${FASTPLONG_VER} && \
+    mv fastplong.${FASTPLONG_VER} /usr/local/bin/fastplong && \
+    chmod a+x /usr/local/bin/fastplong
+
+# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.'
+CMD [ "fastplong", "--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
+
+RUN fastplong --help
+
+RUN wget --no-check-certificate -q https://zenodo.org/records/10733190/files/df_test_files.tar.gz && \
+    tar -xvf df_test_files.tar.gz && \
+    fastplong -i test_files/test.fastq.gz -o filtered.test.fastq.gz && \
+    ls filtered.test.fastq.gz

build-files/fastplong/0.2.2/README.md

@@ -0,0 +1,20 @@
+# fastplong container
+
+Main tool: [fastplong](https://github.com/OpenGene/fastplong)
+
+Code repository: https://github.com/OpenGene/fastplong
+
+Basic information on how to use this tool:
+- executable: fastplong
+- help: --help
+- version: --version
+- description: |
+> Ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.).
+
+Full documentation: https://github.com/OpenGene/fastplong
+
+## Example Usage
+
+```bash
+fastplong -i input.fastq.gz -o output.fastq.gz
+```