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matthdsmmatthdsm
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bump bcl-convert (#11749)
* bump bcl-convert * fix linting * update snapshot
1 parent 251885f commit 8b798ea

4 files changed

Lines changed: 32 additions & 32 deletions

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‎modules/nf-core/bclconvert/Dockerfile‎

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@@ -4,7 +4,7 @@
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# Build stage: unpack the RPM file
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FROM debian:bullseye-slim AS build
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ARG BCLCONVERT_VERSION="4.4.6"
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ARG BCLCONVERT_VERSION="4.5.4"
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# Install tools needed to extract RPM
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RUN apt-get update \
@@ -15,13 +15,13 @@ RUN apt-get update \
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&& rm -rf /var/lib/apt/lists/*
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# Extract bcl-convert from RPM
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COPY bcl-convert-4.4.6-2.el8.x86_64.rpm bcl-convert.rpm
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COPY bcl-convert-${BCLCONVERT_VERSION}-2.el8.x86_64.rpm bcl-convert.rpm
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RUN rpm2cpio bcl-convert.rpm | cpio -idmv \
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&& rm bcl-convert.rpm
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# Final stage: minimal image with only necessary components
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FROM debian:bullseye-slim
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ARG BCLCONVERT_VERSION="4.4.6"
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ARG BCLCONVERT_VERSION="4.5.4"
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LABEL org.opencontainers.image.description="Docker image containing bcl-convert"
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LABEL org.opencontainers.image.version="$BCLCONVERT_VERSION"
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LABEL org.opencontainers.image.documentation="https://github.com/nf-core/modules/blob/master/modules/nf-core/bclconvert/README.md"

‎modules/nf-core/bclconvert/main.nf‎

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@@ -2,7 +2,7 @@ process BCLCONVERT {
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tag "${ meta.lane ? meta.id + "." + meta.lane : meta.id }"
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label 'process_high'
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container "quay.io/nf-core/bclconvert:4.4.6"
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container "quay.io/nf-core/bclconvert:4.5.4"
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input:
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tuple val(meta), path(samplesheet), path(run_dir)
@@ -70,8 +70,8 @@ process BCLCONVERT {
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stub:
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"""
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mkdir -p output
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echo "fake fastq file" | gzip > output/Sample1_S1_L001_R1_001.fastq.gz
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echo "fake fastq file" | gzip > output/Undetermined_S0_L001_R1_001.fastq.gz
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echo "" | gzip > output/Sample1_S1_L001_R1_001.fastq.gz
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echo "" | gzip > output/Undetermined_S0_L001_R1_001.fastq.gz
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mkdir -p output/Reports
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echo "fake report file" > output/Reports/Adapter_Cycle_Metrics.csv

‎modules/nf-core/bclconvert/tests/main.nf.test.snap‎

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@@ -49,16 +49,16 @@
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[
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"BCLCONVERT",
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"bclconvert",
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"4.4.6"
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"4.5.4"
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]
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]
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}
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],
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"timestamp": "2026-05-22T13:52:39.325893",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.4"
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},
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"timestamp": "2026-03-04T20:03:26.54479"
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"nf-test": "0.9.5",
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"nextflow": "26.04.1"
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}
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},
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"homo_sapiens illumina [bcl] - stub": {
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"content": [
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"id": "test",
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"lane": 1
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},
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"Sample1_S1_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc"
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"Sample1_S1_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
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]
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],
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"1": [
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"id": "test",
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"lane": 1
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},
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"Undetermined_S0_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc"
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"Undetermined_S0_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
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]
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],
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"3": [
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[
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"BCLCONVERT",
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"bclconvert",
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"4.4.6"
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"4.5.4"
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]
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],
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"fastq": [
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"id": "test",
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"lane": 1
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},
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"Sample1_S1_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc"
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"Sample1_S1_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
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]
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],
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"fastq_idx": [
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"id": "test",
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"lane": 1
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},
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"Undetermined_S0_L001_R1_001.fastq.gz:md5,1495c2d7a9b129c0968b84b149991bfc"
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"Undetermined_S0_L001_R1_001.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
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]
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],
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"undetermined_idx": [
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[
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"BCLCONVERT",
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"bclconvert",
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"4.4.6"
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"4.5.4"
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]
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]
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}
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],
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"timestamp": "2026-05-27T10:04:20.149645",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.4"
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},
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"timestamp": "2026-02-17T14:13:11.717962"
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"nf-test": "0.9.5",
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"nextflow": "26.04.2"
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}
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},
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"homo_sapiens illumina [bcl]": {
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"content": [
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[
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"BCLCONVERT",
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"bclconvert",
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"4.4.6"
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"4.5.4"
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]
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]
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}
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],
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"timestamp": "2026-05-22T13:52:14.995144",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.4"
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},
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"timestamp": "2026-03-04T20:02:51.80369"
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"nf-test": "0.9.5",
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"nextflow": "26.04.1"
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}
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}
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}

‎subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap‎

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@@ -182,10 +182,10 @@
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]
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}
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],
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"timestamp": "2026-03-16T13:47:40.083238326",
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"timestamp": "2026-05-22T13:53:21.033652",
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"meta": {
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"nf-test": "0.9.4",
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"nextflow": "25.10.4"
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"nf-test": "0.9.5",
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"nextflow": "26.04.1"
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}
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},
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"bcl2fastq": {
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]
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}
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],
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"timestamp": "2026-03-16T13:48:09.325036018",
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"timestamp": "2026-05-22T12:11:17.997148",
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"meta": {
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"nf-test": "0.9.4",
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"nextflow": "25.10.4"
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"nf-test": "0.9.5",
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"nextflow": "26.04.1"
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}
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}
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}

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