- 04 Aug, 2020 2 commits
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van den Berg authored
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van den Berg authored
Add explanation on how to run the pipeline and the importance of using the --use-singularity flag. Add an example on manually running one of the test cases. Add an explanation on the different branches and how to use them.
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- 29 Jul, 2020 3 commits
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van den Berg authored
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van den Berg authored
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van den Berg authored
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- 27 Jul, 2020 1 commit
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van den Berg authored
Since external users cannot submit issues or pull requests without an account for the LUMC gitlab instance, we should refer them to the public github instance of HAMLET. The pipeline graph doesn't add a lot of information, and it doesn't render on github, so it was removed.
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- 01 Jul, 2020 1 commit
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van den Berg authored
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- 25 Jun, 2020 2 commits
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van den Berg authored
Use the tools library to determine file extension See merge request !8
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van den Berg authored
The previous code determined the extension by splitting the file path on a dot (.), which failed when the file path contains dots in folder names. This commit fixes issue #14
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- 24 Jun, 2020 2 commits
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van den Berg authored
Merge development into master See merge request !7
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van den Berg authored
Revert back to gmap 2014 12 23 See merge request !6
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- 23 Jun, 2020 2 commits
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van den Berg authored
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van den Berg authored
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- 17 Jun, 2020 1 commit
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van den Berg authored
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- 12 Jun, 2020 3 commits
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van den Berg authored
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van den Berg authored
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van den Berg authored
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- 03 Jun, 2020 3 commits
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van den Berg authored
This tests the fix for #issue-11, which was resolved by a new upstream release of the gmap aligner. The same upstream release also fixes #issue-12.
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van den Berg authored
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van den Berg authored
- Upgrade pytest-workflow to version 1.4.0, which adds support for contains_regex. - Update test cases to match the values produced by the new version of gsnap. Use contains_regex to reduce the sensitivity of the test cases to small changes in values. - Change the MV4-11 FLT3 hotspot mutation test to a different variant. The previous variant was in a hard to map region, so it is unclear if it is an error when it could not be found.
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- 18 May, 2020 1 commit
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van den Berg authored
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- 14 May, 2020 1 commit
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van den Berg authored
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- 13 May, 2020 2 commits
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van den Berg authored
To simplify the test, we compare the expression of the relevant MECOM exon with the MECOM gene itself, and reduce the threshold to call overexpression in the config file. This way, we do not have to add additional read data to the repository.
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van den Berg authored
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- 12 May, 2020 1 commit
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van den Berg authored
This was requested by Hematology, since they use the amino acid changes to determine the clinical relevance of a mutation.
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- 06 May, 2020 1 commit
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van den Berg authored
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- 29 Apr, 2020 5 commits
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van den Berg authored
Merge devel into master See merge request !5
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van den Berg authored
# Conflicts: # environment.yml # includes/fusion/Snakefile
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van den Berg authored
Merge Gitlab ci into devel Add gitlab-ci integration to HAMLET. The jobs run on the LUMC SLURM cluster. See merge request !4
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van den Berg authored
Also add the final pdf report as an artifact
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van den Berg authored
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- 28 Apr, 2020 1 commit
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van den Berg authored
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- 23 Apr, 2020 1 commit
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van den Berg authored
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- 17 Apr, 2020 1 commit
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van den Berg authored
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- 01 Apr, 2020 3 commits
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van den Berg authored
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van den Berg authored
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van den Berg authored
In some rare cases, the fastqc rules would randomly crash when the JVM could not allocate required space for the java temp folder. By explictly setting fastqc to use /tmp as java temp folder, this bug is resolved.
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- 30 Mar, 2020 2 commits
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van den Berg authored
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van den Berg authored
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- 26 Mar, 2020 1 commit
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van den Berg authored
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