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bump bcl-convert #11749

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4e3a9bf
bump bcl-convert
matthdsm May 22, 2026
016b365
fix linting
matthdsm May 22, 2026
0e7b9b7
Merge branch 'master' into bump/bclconvert
matthdsm May 22, 2026
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6 changes: 3 additions & 3 deletions modules/nf-core/bclconvert/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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 \
Expand All @@ -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="$BCLCONVERT_VERSION"
LABEL org.opencontainers.image.documentation="https://github.com/nf-core/modules/blob/master/modules/nf-core/bclconvert/README.md"
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bclconvert/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BCLCONVERT {
tag "${ 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)
Expand Down Expand Up @@ -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
Expand Down
32 changes: 16 additions & 16 deletions modules/nf-core/bclconvert/tests/main.nf.test.snap
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Expand Up @@ -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": [
Expand Down Expand Up @@ -144,7 +144,7 @@
[
"BCLCONVERT",
"bclconvert",
"4.4.6"
"4.5.4"
]
],
"fastq": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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"
}
}
}
12 changes: 6 additions & 6 deletions subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap
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Expand Up @@ -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": {
Expand Down Expand Up @@ -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"
}
}
}
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