From 0a1599ea4bf69779ab6c5963f81a97024f15fb41 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 10 Jul 2024 13:33:48 +0200 Subject: [PATCH 1/2] bump bclconvert --- modules/nf-core/bclconvert/Dockerfile | 6 ++---- modules/nf-core/bclconvert/README.md | 4 ++-- modules/nf-core/bclconvert/main.nf | 2 +- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/bclconvert/Dockerfile b/modules/nf-core/bclconvert/Dockerfile index 2124c7942dc..a165493c85b 100644 --- a/modules/nf-core/bclconvert/Dockerfile +++ b/modules/nf-core/bclconvert/Dockerfile @@ -3,7 +3,7 @@ # Push to nfcore/bclconvert: FROM debian:bullseye-slim -ARG BCLCONVERT_VERSION="4.2.7" +ARG BCLCONVERT_VERSION="4.3.6" LABEL org.opencontainers.image.authors="Matthias De Smet " LABEL org.opencontainers.image.description="Docker image containing bcl-convert" LABEL org.opencontainers.image.version="$BCLCONVERT_VERSION" @@ -25,9 +25,7 @@ RUN apt-get update \ # Link hostname cmd to fix hardcoded path RUN ln -s /bin/hostname /usr/bin/hostname # Install bcl-convert -ADD --checksum=sha256:ea508d763dc27d30d1a34f6a38d8da31ea67797d7b4971e8c10677bc48539565 \ - https://s3.amazonaws.com/webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-${BCLCONVERT_VERSION}-2.el7.x86_64.rpm \ - bcl-convert.rpm +ADD bcl-convert-4.3.6-2.el8.x86_64.rpm bcl-convert.rpm SHELL ["/bin/bash", "-o", "pipefail", "-c"] RUN rpm2cpio bcl-convert.rpm | cpio -idmv \ && rm bcl-convert.rpm diff --git a/modules/nf-core/bclconvert/README.md b/modules/nf-core/bclconvert/README.md index 54679d0f33a..63197d166eb 100644 --- a/modules/nf-core/bclconvert/README.md +++ b/modules/nf-core/bclconvert/README.md @@ -2,8 +2,8 @@ bcl-convert is a commercial tool from Illumina. The container provided for the bcl-convert nf-core module is not provided nor supported by Illumina. Updating the bcl-convert versions in the container and pushing the update to Dockerhub needs to be done manually. -1. Navigate to the appropriate download page. - [BCL Convert](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html): find the latest version of bcl-convert -2. Update the `BCL_VERSION` in the `Dockerfile` (You might have to update the link in the `ADD` statement) +1. Navigate to the appropriate download page. - [BCL Convert](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html): find and download the latest version of bcl-convert RPM package. +2. Update the `BCL_VERSION` in the `Dockerfile` 3. Create and test the container: ```bash diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf index 8e6886dfc6f..553bd318d32 100644 --- a/modules/nf-core/bclconvert/main.nf +++ b/modules/nf-core/bclconvert/main.nf @@ -2,7 +2,7 @@ process BCLCONVERT { tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" } label 'process_high' - container "nf-core/bclconvert:4.2.7" + container "nf-core/bclconvert:4.3.6" input: tuple val(meta), path(samplesheet), path(run_dir) From 1ad540d53551301894ada0f13bce1f5e4f2ef2cf Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Wed, 10 Jul 2024 11:38:10 +0000 Subject: [PATCH 2/2] fix snapshots --- modules/nf-core/bclconvert/tests/main.nf.test.snap | 8 ++++++-- .../nf-core/bcl_demultiplex/tests/main.nf.test.snap | 6 +++--- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/bclconvert/tests/main.nf.test.snap b/modules/nf-core/bclconvert/tests/main.nf.test.snap index 8b9d506c450..aa6eae8a61c 100644 --- a/modules/nf-core/bclconvert/tests/main.nf.test.snap +++ b/modules/nf-core/bclconvert/tests/main.nf.test.snap @@ -24,7 +24,7 @@ ] ], [ - "versions.yml:md5,375aa95eef22ad3b0cc39b325d7ac9e0" + "versions.yml:md5,3742a25082bc9f0ff8dca303c5c8cb8b" ], [ [ @@ -50,6 +50,10 @@ "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c" ] ], - "timestamp": "2024-01-31T13:06:35.609496414" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T11:36:50.00930061" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap index 50341f650cc..993f58fd9ff 100644 --- a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap @@ -24,7 +24,7 @@ ] ], [ - "versions.yml:md5,a52db0d612f5a3f30d54194d9f7393cf" + "versions.yml:md5,bcf8fd3ee65f301e48280750fe2524d5" ], [ [ @@ -60,9 +60,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-07T09:13:44.123805878" + "timestamp": "2024-07-10T11:37:10.291289677" }, "bcl2fastq": { "content": [