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bump bclconvert #5952

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Jul 10, 2024
Merged

bump bclconvert #5952

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0a1599e
bump bclconvert
matthdsm Jul 10, 2024
1ad540d
fix snapshots
matthdsm Jul 10, 2024
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6 changes: 2 additions & 4 deletions modules/nf-core/bclconvert/Dockerfile
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Expand Up @@ -3,7 +3,7 @@
# Push to nfcore/bclconvert:<VER>

FROM debian:bullseye-slim
ARG BCLCONVERT_VERSION="4.2.7"
ARG BCLCONVERT_VERSION="4.3.6"
LABEL org.opencontainers.image.authors="Matthias De Smet <[email protected]>"
LABEL org.opencontainers.image.description="Docker image containing bcl-convert"
LABEL org.opencontainers.image.version="$BCLCONVERT_VERSION"
Expand All @@ -25,9 +25,7 @@ RUN apt-get update \
# Link hostname cmd to fix hardcoded path
RUN ln -s /bin/hostname /usr/bin/hostname
# Install bcl-convert
ADD --checksum=sha256:ea508d763dc27d30d1a34f6a38d8da31ea67797d7b4971e8c10677bc48539565 \
https://s3.amazonaws.com/webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-${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
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4 changes: 2 additions & 2 deletions modules/nf-core/bclconvert/README.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion 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 "nf-core/bclconvert:4.2.7"
container "nf-core/bclconvert:4.3.6"

input:
tuple val(meta), path(samplesheet), path(run_dir)
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8 changes: 6 additions & 2 deletions modules/nf-core/bclconvert/tests/main.nf.test.snap
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Expand Up @@ -24,7 +24,7 @@
]
],
[
"versions.yml:md5,375aa95eef22ad3b0cc39b325d7ac9e0"
"versions.yml:md5,3742a25082bc9f0ff8dca303c5c8cb8b"
],
[
[
Expand All @@ -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"
}
}
6 changes: 3 additions & 3 deletions subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap
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Expand Up @@ -24,7 +24,7 @@
]
],
[
"versions.yml:md5,a52db0d612f5a3f30d54194d9f7393cf"
"versions.yml:md5,bcf8fd3ee65f301e48280750fe2524d5"
],
[
[
Expand Down Expand Up @@ -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": [
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