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nf-core_modules/modules/bclconvert
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Matthias De Smet f4c69bc427
Module/bclconvert (#1485) 
* bclconvert: initial commit

* add most of tool

* attempt at adding testing stub

* add dockerfile + instructions

* add container to module

* update readme

* more attempts at making stubs work

* finish stub run

* fix ci issues

* more fixes to stub

* add read version check to stub

* fix some tests

* update readme

* fix version number

* syntax fix

* revert edit to output directory

* Update modules/bclconvert/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/bclconvert/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* update meta.yaml

* update thread usage

* Update modules/bclconvert/main.nf

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>

* Escape env variable

* Update modules/bclconvert/Dockerfile

Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>

* fix comments by @Emiller88

* fix task.cpus

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 15:39:22 +02:00
..
.gitignore Module/bclconvert (#1485) 2022-04-21 15:39:22 +02:00
Dockerfile Module/bclconvert (#1485) 2022-04-21 15:39:22 +02:00
LICENSE Module/bclconvert (#1485) 2022-04-21 15:39:22 +02:00
main.nf Module/bclconvert (#1485) 2022-04-21 15:39:22 +02:00
meta.yml Module/bclconvert (#1485) 2022-04-21 15:39:22 +02:00
README.md Module/bclconvert (#1485) 2022-04-21 15:39:22 +02:00

README.md

Updating the docker container and making a new module release

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: download the rpm of the desired bcl-convert version with curl or wget.

  2. Unpack the RPM package using rpm2cpio bcl-convert-*.rpm | cpio -i --make-directories. Place the executable located in <unpack_dir>/usr/bin/bcl-convert in the same folder where the Dockerfile lies.

  3. Create and test the container:

    docker build . -t nfcore/bclconvert:<VERSION>

  4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.

    docker push nfcore/bclconvert:<VERSION>