Toulligqc 2.8.4

README.md

@@ -333,7 +333,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [TBProfiler](https://hub.docker.com/r/staphb/tbprofiler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tbprofiler)](https://hub.docker.com/r/staphb/tbprofiler) | <details><summary>Click to see all versions</summary> <ul><li>[4.3.0](./build-files/tbprofiler/4.3.0/)</li><li>[4.4.0](./build-files/tbprofiler/4.4.0/)</li><li>[4.4.2](./build-files/tbprofiler/4.4.2/)</li><li>[5.0.1](./build-files/tbprofiler/5.0.1/)</li><li>[6.2.0](./build-files/tbprofiler/6.2.0/)</li><li>[6.2.1](./build-files/tbprofiler/6.2.1/)</li><li>[6.3.0](./build-files/tbprofiler/6.3.0/)</li><li>[6.4.0](./build-files/tbprofiler/6.4.0/)</li><li>[6.4.1](./build-files/tbprofiler/6.4.1/)</li><li>[6.6.2](./build-files/tbprofiler/6.6.2/)</li><li>[6.6.3](./build-files/tbprofiler/6.6.3/)</li><li>[6.6.5](./build-files/tbprofiler/6.6.5/)</li><li>[6.6.6](./build-files/tbprofiler/6.6.6/)</li></ul> </details> | https://github.com/jodyphelan/TBProfiler <br/> https://github.com/jodyphelan/tbdb |
 | [TipToft](https://hub.docker.com/r/staphb/tiptoft/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tiptoft)](https://hub.docker.com/r/staphb/tiptoft) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.0](./build-files/tiptoft/1.0.0/)</li><li>[1.0.2](./build-files/tiptoft/1.0.2/)</li></ul> </details> | https://github.com/andrewjpage/tiptoft |
 | [Tostadas](https://hub.docker.com/r/staphb/tostadas/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tostadas)](https://hub.docker.com/r/staphb/tostadas) | <details><summary>Click to see all versions</summary> <ul><li>[0.2.0-beta](./build-files/tostadas/0.2.0-beta/)</li><li>[3.1.0](./build-files/tostadas/3.1.0/)</li><li>[4.0.0](./build-files/tostadas/4.0.0/)</li></ul> </details> | https://github.com/CDCgov/tostadas |
-| [toulligQC](https://hub.docker.com/r/staphb/toulligqc/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/toulligqc)](https://hub.docker.com/r/staphb/toulligqc) | <details><summary>Click to see all versions</summary> <ul><li>[2.7.1](./build-files/toulligqc/2.7.1/)</li></ul> </details> | https://github.com/GenomiqueENS/toulligQC |
+| [toulligQC](https://hub.docker.com/r/staphb/toulligqc/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/toulligqc)](https://hub.docker.com/r/staphb/toulligqc) | <details><summary>Click to see all versions</summary> <ul><li>[2.7.1](./build-files/toulligqc/2.7.1/)</li><li>[2.8.4](./build-files/toulligqc/2.8.4/)</li></ul> </details> | https://github.com/GenomiqueENS/toulligQC |
 | [transcluster](https://hub.docker.com/r/staphb/transcluster/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/transcluster)](https://hub.docker.com/r/staphb/transcluster) | <details><summary>Click to see all versions</summary> <ul><li>[77f4909](./build-files/transcluster/77f4909/)</li></ul> </details> | https://github.com/JamesStimson/transcluster |
 | [Treemmer](https://hub.docker.com/r/staphb/treemmer/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/treemmer)](https://hub.docker.com/r/staphb/treemmer) | <details><summary>Click to see all versions</summary> <ul><li>[0.3](./build-files/treemmer/0.3/)</li></ul> </details> | https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub) </br> https://github.com/fmenardo/Treemmer |
 | [trimal](https://hub.docker.com/r/staphb/trimal) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/trimal)](https://hub.docker.com/r/staphb/trimal) | <details><summary>Click to see all versions</summary> <ul><li>[1.2](./build-files/trimal/1.2/)</li><li>[1.5.0](./build-files/trimal/1.5.0/)</li><li>[1.5.1](./build-files/trimal/1.5.1/)</li></ul> </details> | https://github.com/inab/trimal |

build-files/toulligqc/2.8.4/Dockerfile

@@ -0,0 +1,65 @@
+FROM python:3.11.11-slim AS app
+
+ARG TOULIGQC_VER="2.8.4"
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="python:3.11.11-slim"
+LABEL dockerfile.version="1"
+LABEL software="ToulligQC"
+LABEL software.version="${TOULIGQC_VER}"
+LABEL description="QC analyses of Oxford Nanopore runs"
+LABEL website="https://github.com/GenomiqueENS/toulligQC"
+LABEL license="https://github.com/GenomiqueENS/toulligQC/blob/master/LICENSE.txt"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+# 'RUN' executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates\
+    procps \
+    bzip2 && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget -q https://github.com/GenomiqueENS/toulligQC/archive/refs/tags/v${TOULIGQC_VER}.tar.gz && \
+    pip install --no-cache-dir v${TOULIGQC_VER}.tar.gz && \
+    rm -rf v${TOULIGQC_VER}.tar.gz
+
+# 'ENV' instructions set environment variables that persist from the build into the resulting image
+# Use for e.g. $PATH and locale settings for compatibility with Singularity
+ENV PATH="$PATH" \
+    LC_ALL=C
+
+# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.'
+CMD [ "toulligqc", "--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
+
+ARG TOULIGQC_VER
+
+# 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 toulligqc --help && \
+    toulligqc --version
+
+RUN wget -q http://outils.genomique.biologie.ens.fr/leburon/downloads/toulligqc-example/toulligqc_demo_data.tar.bz2 && \
+    tar -xvjf toulligqc_demo_data.tar.bz2 && \
+    cd toulligqc_demo_data && \
+    ./run-toulligqc.sh && \
+    ls /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/report.html \
+    /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/report.data \
+    /test/toulligqc_demo_data/output/ToulligQC_Demo_Data/images/*html

build-files/toulligqc/2.8.4/README.md

@@ -0,0 +1,61 @@
+# toulligQC container
+
+Main tool: [toulligQC](https://github.com/GenomiqueENS/toulligQC)
+
+Code repository: https://github.com/GenomiqueENS/toulligQC
+
+
+Basic information on how to use this tool:
+- executable: toulligqc
+- help: --help
+- version: --version
+- description: |
+> ToulligQC is dedicated to the QC analyses of Oxford Nanopore runs.
+
+Full documentation: https://github.com/GenomiqueENS/toulligQC
+
+## Example Usage
+
+```bash
+# Sequencing summary alone
+toulligqc --report-name summary_only \
+            --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \
+            --html-report-path /path/to/output/report.html
+
+# Sequencing summary + telemetry file
+toulligqc --report-name summary_plus_telemetry \
+            --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \
+            --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \
+            --html-report-path /path/to/output/report.html
+
+# Telemetry file + fast5 files
+toulligqc --report-name telemetry_plus_fast5 \
+            --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \
+            --fast5-source /path/to/basecaller/output/fast5_files.fast5.gz \ 
+            --html-report-path /path/to/output/report.html
+# Fastq/ bam files only
+toulligqc --report-name FAF0256 \
+            --fastq /path/to/basecaller/output/fastq_files.fq.gz \ # (replace with --bam)
+            --html-report-path /path/to/output/report.html
+
+# Optional arguments for 1D² analysis
+toulligqc --report-name FAF0256 \
+            --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \
+            --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \
+            --sequencing-summary-1dsqr-source /path/to/basecaller/output/sequencing_1dsqr_summary.txt \ # (optional)
+            --html-report-path /path/to/output/report.html
+
+# Optional arguments to deal with barcoded samples
+toulligqc --report-name FAF0256 \
+            --barcoding \
+            --telemetry-source /path/to/basecaller/output/sequencing_telemetry.js \
+            --sequencing-summary-source /path/to/basecaller/output/sequencing_summary.txt \
+            --sequencing-summary-source /path/to/basecaller/output/barcoding_summary_pass.txt \         # (optional)
+            --sequencing-summary-source /path/to/basecaller/output/barcoding_summary_fail.txt \         # (optional)
+            --sequencing-summary-1dsqr-source /path/to/basecaller/output/sequencing_1dsqr_summary.txt \ # (optional)
+            --sequencing-summary-1dsqr-source /path/to/basecaller/output/barcoding_summary_pass.txt \   # (optional)
+            --sequencing-summary-1dsqr-source /path/to/basecaller/output/barcoding_summary_fail.txt \   # (optional)
+            --html-report-path /path/to/output/report.html \
+            --data-report-path /path/to/output/report.data \                                            # (optional)
+            --barcodes BC01,BC02,BC03
+```