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icgc-argo / workflow-roadmap

Roadmap and management for genomic data processing
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Test: E2E alignment #71

Closed rosibaj closed 3 years ago

rosibaj commented 3 years ago
lepsalex commented 3 years ago

@junjun-zhang @rosibaj workflows are correctly using using the tempDir parameter as can be seen by looking at a running process:

I have no name!@nf-49563bc443d4b7aab2bff4c09649dec6:/nfs-dev-1-vol-dev-2/alex-work/49/563bc443d4b7aab2bff4c09649dec6$ cd /icgc-argo-scratch/
I have no name!@nf-49563bc443d4b7aab2bff4c09649dec6:/icgc-argo-scratch$ ls
tmp1.0000.bam  tmp1.0002.bam  tmp1.0004.bam  tmp1.0006.bam  tmp1.0008.bam  tmp1.0010.bam  tmp1.0012.bam  tmp1.0014.bam
                                      tmp1.0016.bam  tmp1.0018.bam  tmp1.0020.bam  tmp1.0022.bam
tmp1.0001.bam  tmp1.0003.bam  tmp1.0005.bam  tmp1.0007.bam  tmp1.0009.bam  tmp1.0011.bam  tmp1.0013.bam  tmp1.0015.bam
                                      tmp1.0017.bam  tmp1.0019.bam  tmp1.0021.bam  tmp1.0023.bam

@rtisma @yalturmes @henro001 good work on this everyone!