From ac66c0ec78757713688db1f7aadd0652e6b5d6d8 Mon Sep 17 00:00:00 2001 From: Christie-Rose Woodside <144174658+cwoodside1278@users.noreply.github.com> Date: Sun, 8 Mar 2026 15:02:32 -0400 Subject: [PATCH 1/8] Create README.md for 2.8.3 --- build-files/toulligqc/2.7.1/2.8.3/README.md | 61 +++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 build-files/toulligqc/2.7.1/2.8.3/README.md diff --git a/build-files/toulligqc/2.7.1/2.8.3/README.md b/build-files/toulligqc/2.7.1/2.8.3/README.md new file mode 100644 index 000000000..c35f0e5c7 --- /dev/null +++ b/build-files/toulligqc/2.7.1/2.8.3/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 +``` From 1ebd81d992b57c63ff7e34cc72f08b0d31843d62 Mon Sep 17 00:00:00 2001 From: Christie-Rose Woodside <144174658+cwoodside1278@users.noreply.github.com> Date: Sun, 8 Mar 2026 15:07:36 -0400 Subject: [PATCH 2/8] Create README.md --- build-files/toulligqc/2.8.3/README.md | 61 +++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 build-files/toulligqc/2.8.3/README.md diff --git a/build-files/toulligqc/2.8.3/README.md b/build-files/toulligqc/2.8.3/README.md new file mode 100644 index 000000000..c35f0e5c7 --- /dev/null +++ b/build-files/toulligqc/2.8.3/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 +``` From f879495fd0befe9fa9ef77a082b78b7eb175265f Mon Sep 17 00:00:00 2001 From: Christie Woodside Date: Sun, 8 Mar 2026 19:10:12 +0000 Subject: [PATCH 3/8] Move 2.8.3 folder to correct location under toulligqc --- build-files/toulligqc/{2.7.1 => }/2.8.3/README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename build-files/toulligqc/{2.7.1 => }/2.8.3/README.md (100%) diff --git a/build-files/toulligqc/2.7.1/2.8.3/README.md b/build-files/toulligqc/2.8.3/README.md similarity index 100% rename from build-files/toulligqc/2.7.1/2.8.3/README.md rename to build-files/toulligqc/2.8.3/README.md From 3db9906c6409374fe8dfd94ea295e8ecf859c325 Mon Sep 17 00:00:00 2001 From: Christie-Rose Woodside <144174658+cwoodside1278@users.noreply.github.com> Date: Sun, 8 Mar 2026 15:13:18 -0400 Subject: [PATCH 4/8] Create Dockerfile to 2.8.3 --- build-files/toulligqc/2.8.3/Dockerfile | 65 ++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 build-files/toulligqc/2.8.3/Dockerfile diff --git a/build-files/toulligqc/2.8.3/Dockerfile b/build-files/toulligqc/2.8.3/Dockerfile new file mode 100644 index 000000000..eb6f04431 --- /dev/null +++ b/build-files/toulligqc/2.8.3/Dockerfile @@ -0,0 +1,65 @@ +FROM python:3.11.11-slim AS app + +ARG TOULIGQC_VER="2.8.3" + +# '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 From 79d607659c16725a5dae1cae27eefa829ef8c57a Mon Sep 17 00:00:00 2001 From: Christie-Rose Woodside <144174658+cwoodside1278@users.noreply.github.com> Date: Sun, 8 Mar 2026 15:14:13 -0400 Subject: [PATCH 5/8] Update README.md to include 2.8.3 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9952638d1..e9d4a8398 100644 --- a/README.md +++ b/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/)
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| https://github.com/jodyphelan/TBProfiler
https://github.com/jodyphelan/tbdb | | [TipToft](https://hub.docker.com/r/staphb/tiptoft/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/tiptoft)](https://hub.docker.com/r/staphb/tiptoft) |
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| https://github.com/andrewjpage/tiptoft | | [Tostadas](https://hub.docker.com/r/staphb/tostadas/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/tostadas)](https://hub.docker.com/r/staphb/tostadas) |
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| https://github.com/CDCgov/tostadas | -| [toulligQC](https://hub.docker.com/r/staphb/toulligqc/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/toulligqc)](https://hub.docker.com/r/staphb/toulligqc) |
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| https://github.com/GenomiqueENS/toulligQC | +| [toulligQC](https://hub.docker.com/r/staphb/toulligqc/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/toulligqc)](https://hub.docker.com/r/staphb/toulligqc) |
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| https://github.com/GenomiqueENS/toulligQC | | [transcluster](https://hub.docker.com/r/staphb/transcluster/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/transcluster)](https://hub.docker.com/r/staphb/transcluster) |
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| https://github.com/JamesStimson/transcluster | | [Treemmer](https://hub.docker.com/r/staphb/treemmer/)
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| https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub)
https://github.com/fmenardo/Treemmer | | [trimal](https://hub.docker.com/r/staphb/trimal)
[![docker pulls](https://badgen.net/docker/pulls/staphb/trimal)](https://hub.docker.com/r/staphb/trimal) |
Click to see all versions
| https://github.com/inab/trimal | From 49b986b741f20b802fa257e8b8d6888422f718d8 Mon Sep 17 00:00:00 2001 From: Christie-Rose Woodside <144174658+cwoodside1278@users.noreply.github.com> Date: Wed, 11 Mar 2026 17:58:31 -0400 Subject: [PATCH 6/8] Update Dockerfile from 2.8.3 to 2.8.4 --- build-files/toulligqc/2.8.3/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build-files/toulligqc/2.8.3/Dockerfile b/build-files/toulligqc/2.8.3/Dockerfile index eb6f04431..0c331631a 100644 --- a/build-files/toulligqc/2.8.3/Dockerfile +++ b/build-files/toulligqc/2.8.3/Dockerfile @@ -1,6 +1,6 @@ FROM python:3.11.11-slim AS app -ARG TOULIGQC_VER="2.8.3" +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" From 9b8f472e5b3686b8db0a7165a8246b1bcf03a9e8 Mon Sep 17 00:00:00 2001 From: Christie-Rose Woodside <144174658+cwoodside1278@users.noreply.github.com> Date: Wed, 11 Mar 2026 17:59:02 -0400 Subject: [PATCH 7/8] Update README.md from 2.8.3 to 2.8.4 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e9d4a8398..7a9b47b2e 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/tbprofiler)](https://hub.docker.com/r/staphb/tbprofiler) |
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| https://github.com/jodyphelan/TBProfiler
https://github.com/jodyphelan/tbdb | | [TipToft](https://hub.docker.com/r/staphb/tiptoft/)
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| https://github.com/andrewjpage/tiptoft | | [Tostadas](https://hub.docker.com/r/staphb/tostadas/)
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| https://github.com/CDCgov/tostadas | -| [toulligQC](https://hub.docker.com/r/staphb/toulligqc/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/toulligqc)](https://hub.docker.com/r/staphb/toulligqc) |
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| https://github.com/GenomiqueENS/toulligQC | +| [toulligQC](https://hub.docker.com/r/staphb/toulligqc/)
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| https://github.com/GenomiqueENS/toulligQC | | [transcluster](https://hub.docker.com/r/staphb/transcluster/)
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| https://github.com/JamesStimson/transcluster | | [Treemmer](https://hub.docker.com/r/staphb/treemmer/)
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| https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub)
https://github.com/fmenardo/Treemmer | | [trimal](https://hub.docker.com/r/staphb/trimal)
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| https://github.com/inab/trimal | From 191cfbad34f1d1b19879cdb26c86bc87ecee1415 Mon Sep 17 00:00:00 2001 From: Christie Woodside Date: Wed, 11 Mar 2026 22:04:57 +0000 Subject: [PATCH 8/8] Rename folder to 2.8.4 --- build-files/toulligqc/{2.8.3 => 2.8.4}/Dockerfile | 0 build-files/toulligqc/{2.8.3 => 2.8.4}/README.md | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename build-files/toulligqc/{2.8.3 => 2.8.4}/Dockerfile (100%) rename build-files/toulligqc/{2.8.3 => 2.8.4}/README.md (100%) diff --git a/build-files/toulligqc/2.8.3/Dockerfile b/build-files/toulligqc/2.8.4/Dockerfile similarity index 100% rename from build-files/toulligqc/2.8.3/Dockerfile rename to build-files/toulligqc/2.8.4/Dockerfile diff --git a/build-files/toulligqc/2.8.3/README.md b/build-files/toulligqc/2.8.4/README.md similarity index 100% rename from build-files/toulligqc/2.8.3/README.md rename to build-files/toulligqc/2.8.4/README.md