Merge pull request #21 from umccr/feature/bcl-convert-4.2.4

repositories/bcl-convert/4.2.4/Dockerfile

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+FROM oraclelinux:8
+
+LABEL author="Alexis Lucattini" \
+      description="Run bcl-convert 4.2.4 from a container" \
+      maintainer="[email protected]"
+
+ARG GROUP="centos_group"
+ARG GID="1000"
+ARG USER="centos_user"
+ARG UID="1000"
+
+# This docker file was created with inspiration from
+# https://gist.github.com/pansapiens/f66bdb59230004eba0d7fdec9e7eb5d8
+# 
+# You'll need to download bcl-convert.4.2.4.rpm from
+# https://sapac.support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html
+# Yay clickwrap licenses !
+#
+# Building:
+#
+# docker build -t umccr/bcl-convert:latest -t umccr/bcl-convert:4.2.4
+#
+# Running:
+#
+# bcl-convert wants to be able to write to /var/logs/bcl-convert, so we bind a user writable directory for it
+# mkdir logs
+# singularity exec --bind logs:/var/log/bcl-convert bcl-convert.sif bcl-convert --help
+# _or_
+# singularity exec -wf bcl-convert.sif bcl-convert --help
+#
+
+# Add in RPM file
+ADD bcl-convert.4.2.4.rpm /tmp/bcl-convert.rpm
+
+# Create group/user
+RUN groupadd \
+        --system \
+        --gid "$GID" \
+        "$GROUP" && \
+    useradd \
+        --system \
+        --gid "$GID" \
+        --no-create-home \
+        --uid "$UID" \
+        "$USER"
+
+# Install with groupinstall compiler tools
+# -y -q for peace and quietness
+RUN dnf update -y -q && \
+    dnf groupinstall -y -q "Development Tools" && \
+    dnf update -y -q && \
+    rpm -i /tmp/bcl-convert.rpm && \
+    rm /tmp/bcl-convert.rpm && \
+    dnf clean all && \
+    rm -rf /var/cache/dnf
+
+# Create and chown bcl-convert log dir so user can write to it
+RUN mkdir -p /var/log/bcl-convert && \
+    chown -R "$UID:$GID" /var/log/bcl-convert
+
+# This is so that bcl-convert can write a small little file to this folder
+# When running with singularity use 
+# --bind $(mktemp -d):/var/log/bcl-convert
+# Docker should be able to handle with just this if --read-only=true is set
+# as is done when running through cwltool locally
+VOLUME /var/log/bcl-convert
+
+# Set the entrypoint to null so that the Dockerfile
+# is compatible with the cwl spec
+ENTRYPOINT []
+
+USER centos_user
+
+RUN bcl-convert --help
+
+CMD [ "bcl-convert" ]

repositories/bcl-convert/4.2.4/Readme.md

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+# bcl-convert
+
+## Version 4.2.4
+
+## Package link
+[docker-who/bcl-convert](https://github.com/umccr/docker-who/pkgs/container/bcl-convert)
+
+## Platforms
+* linux/amd64
+* linux/arm64
+
+### Usage
+
+```bash
+docker pull ghcr.io/umccr/bcl-convert:4.2.4
+```
+
+
+### Description
+
+bcl-convert is used to convert Illumina basecall files (raw output) to fastq files (sequencing reads) split
+by samples as per the samplesheet.  
+More information on the bcl-convert algorithm and parameters can be found [here](https://sapac.support.illumina.com/sequencing/sequencing_software/bcl-convert.html)
+
+### Notes
+
+The bcl-convert rpm file in this directory is tracked via git lfs

repositories/bcl-convert/4.2.4/config.yaml

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+# Specify particular platforms to build
+platforms:
+  - linux/amd64
+