From 4e3a9bfb89154a91855884c9bd71307f9c556942 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Fri, 22 May 2026 14:13:26 +0200 Subject: [PATCH 1/3] bump bcl-convert --- modules/nf-core/bclconvert/Dockerfile | 6 ++-- modules/nf-core/bclconvert/main.nf | 2 +- .../bclconvert/tests/main.nf.test.snap | 32 +++++++++---------- .../bcl_demultiplex/tests/main.nf.test.snap | 12 +++---- 4 files changed, 26 insertions(+), 26 deletions(-) diff --git a/modules/nf-core/bclconvert/Dockerfile b/modules/nf-core/bclconvert/Dockerfile index c5594cf2f09b..11ceb3232ff4 100644 --- a/modules/nf-core/bclconvert/Dockerfile +++ b/modules/nf-core/bclconvert/Dockerfile @@ -4,7 +4,7 @@ # Build stage: unpack the RPM file FROM debian:bullseye-slim AS build -ARG BCLCONVERT_VERSION="4.4.6" +ARG BCLCONVERT_VERSION="4.5.4" # Install tools needed to extract RPM RUN apt-get update \ @@ -15,13 +15,13 @@ RUN apt-get update \ && rm -rf /var/lib/apt/lists/* # Extract bcl-convert from RPM -COPY bcl-convert-4.4.6-2.el8.x86_64.rpm bcl-convert.rpm +COPY bcl-convert-${BCLCONVERT_VERSION}-2.el8.x86_64.rpm bcl-convert.rpm RUN rpm2cpio bcl-convert.rpm | cpio -idmv \ && rm bcl-convert.rpm # Final stage: minimal image with only necessary components FROM debian:bullseye-slim -ARG BCLCONVERT_VERSION="4.4.6" +ARG BCLCONVERT_VERSION="4.5.4" LABEL org.opencontainers.image.description="Docker image containing bcl-convert" LABEL org.opencontainers.image.version="$BCLCONVERT_VERSION" LABEL org.opencontainers.image.documentation="https://github.com/nf-core/modules/blob/master/modules/nf-core/bclconvert/README.md" diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf index 6b32e54e03f6..c8664325f95a 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 "quay.io/nf-core/bclconvert:4.4.6" + container "quay.io/nf-core/bclconvert:4.5.4" input: tuple val(meta), path(samplesheet), path(run_dir) diff --git a/modules/nf-core/bclconvert/tests/main.nf.test.snap b/modules/nf-core/bclconvert/tests/main.nf.test.snap index b228a5b221a4..3cc0f401c1dd 100644 --- a/modules/nf-core/bclconvert/tests/main.nf.test.snap +++ b/modules/nf-core/bclconvert/tests/main.nf.test.snap @@ -49,16 +49,16 @@ [ "BCLCONVERT", "bclconvert", - "4.4.6" + "4.5.4" ] ] } ], + "timestamp": "2026-05-22T13:52:39.325893", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-04T20:03:26.54479" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } }, "homo_sapiens illumina [bcl] - stub": { "content": [ @@ -144,7 +144,7 @@ [ "BCLCONVERT", "bclconvert", - "4.4.6" + "4.5.4" ] ], "fastq": [ @@ -228,16 +228,16 @@ [ "BCLCONVERT", "bclconvert", - "4.4.6" + "4.5.4" ] ] } ], + "timestamp": "2026-05-22T13:52:50.412893", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-02-17T14:13:11.717962" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } }, "homo_sapiens illumina [bcl]": { "content": [ @@ -281,15 +281,15 @@ [ "BCLCONVERT", "bclconvert", - "4.4.6" + "4.5.4" ] ] } ], + "timestamp": "2026-05-22T13:52:14.995144", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-04T20:02:51.80369" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } } } \ 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 3620536c8e42..6b3e38cf3133 100644 --- a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap @@ -182,10 +182,10 @@ ] } ], - "timestamp": "2026-03-16T13:47:40.083238326", + "timestamp": "2026-05-22T13:53:21.033652", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.1" } }, "bcl2fastq": { @@ -324,10 +324,10 @@ ] } ], - "timestamp": "2026-03-16T13:48:09.325036018", + "timestamp": "2026-05-22T12:11:17.997148", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.1" } } } \ No newline at end of file From 016b365da33e5a6307f1ece188b2030c4a0a987b Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Fri, 22 May 2026 20:41:54 +0200 Subject: [PATCH 2/3] fix linting --- modules/nf-core/bclconvert/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf index c8664325f95a..413c3014c0e7 100644 --- a/modules/nf-core/bclconvert/main.nf +++ b/modules/nf-core/bclconvert/main.nf @@ -70,8 +70,8 @@ process BCLCONVERT { stub: """ mkdir -p output - echo "fake fastq file" | gzip > output/Sample1_S1_L001_R1_001.fastq.gz - echo "fake fastq file" | gzip > output/Undetermined_S0_L001_R1_001.fastq.gz + echo "" | gzip > output/Sample1_S1_L001_R1_001.fastq.gz + echo "" | gzip > output/Undetermined_S0_L001_R1_001.fastq.gz mkdir -p output/Reports echo "fake report file" > output/Reports/Adapter_Cycle_Metrics.csv From 670fbb1182b85ae026833944af1e1f01b15d35d3 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 27 May 2026 10:04:51 +0200 Subject: [PATCH 3/3] update snapshot --- modules/nf-core/bclconvert/tests/main.nf.test.snap | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/bclconvert/tests/main.nf.test.snap b/modules/nf-core/bclconvert/tests/main.nf.test.snap index 3cc0f401c1dd..2d03f38bd98a 100644 --- a/modules/nf-core/bclconvert/tests/main.nf.test.snap +++ b/modules/nf-core/bclconvert/tests/main.nf.test.snap @@ -69,7 +69,7 @@ "id": "test", "lane": 1 }, - "Sample1_S1_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc" + "Sample1_S1_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -81,7 +81,7 @@ "id": "test", "lane": 1 }, - "Undetermined_S0_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc" + "Undetermined_S0_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "3": [ @@ -153,7 +153,7 @@ "id": "test", "lane": 1 }, - "Sample1_S1_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc" + "Sample1_S1_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "fastq_idx": [ @@ -218,7 +218,7 @@ "id": "test", "lane": 1 }, - "Undetermined_S0_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc" + "Undetermined_S0_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "undetermined_idx": [ @@ -233,10 +233,10 @@ ] } ], - "timestamp": "2026-05-22T13:52:50.412893", + "timestamp": "2026-05-27T10:04:20.149645", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.1" + "nextflow": "26.04.2" } }, "homo_sapiens illumina [bcl]": {