magpie issueshttps://git.lumc.nl/rig-framework/magpie/-/issues2018-05-02T02:01:07+02:00https://git.lumc.nl/rig-framework/magpie/-/issues/4Add a clean target2018-05-02T02:01:07+02:00MeiAdd a clean targetWe should have a clean target in makefile to remove all intermmediate files, e.g., bam. Once a run is successful, we can run "make clean" to release the space.
If this can be fixed, issue #3 can be rejected.We should have a clean target in makefile to remove all intermmediate files, e.g., bam. Once a run is successful, we can run "make clean" to release the space.
If this can be fixed, issue #3 can be rejected.https://git.lumc.nl/rig-framework/magpie/-/issues/3duplicate bams are stored between gatk01 and gatk022018-05-02T02:01:07+02:00Meiduplicate bams are stored between gatk01 and gatk02This might apply to all pipelines that are composing separate modules. magpie pipeline connects gatk01 to gatk02. ready bams generated at the end of gatk01 are copied to the input directory of gatk02. So we have duplicated files. This co...This might apply to all pipelines that are composing separate modules. magpie pipeline connects gatk01 to gatk02. ready bams generated at the end of gatk01 are copied to the input directory of gatk02. So we have duplicated files. This could be dealt more efficiently using symlinks.