Make Copy/Link replaceable

[apeltzer]

Is your feature request related to a problem? Please describe.
Sarek seems to link results to publishDir directories.

Describe the solution you'd like

I'd like to have this configurable, since we have some systems where this didn't work as of now. Making it possible to just copy results, would be nice here :-)

Describe alternatives you've considered
Manually copying data from work to publishDir, but this is incredibly cumbersome :-(

[apeltzer]

Yeah its a BeeGFS issue:

https://groups.google.com/forum/#!topic/fhgfs-user/8rJ2JzMVJRQ

So making it optional would be great !

[apeltzer]

[b8/68fdc8] Submitted process > MapReads (hroc113-S27)
WARN: Failed to publish file: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/work/3f/e6079a331483144a947e4729ccf99e/62476759_S38_R1_001_fastqc.html; to: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/Reports/FastQC/S27/62476759_S38_R1_001_fastqc.html [link] -- See log file for details
WARN: Failed to publish file: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/work/3f/e6079a331483144a947e4729ccf99e/62476759_S38_R1_001_fastqc.zip; to: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/Reports/FastQC/S27/62476759_S38_R1_001_fastqc.zip [link] -- See log file for details
WARN: Failed to publish file: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/work/3f/e6079a331483144a947e4729ccf99e/62476759_S38_R2_001_fastqc.html; to: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/Reports/FastQC/S27/62476759_S38_R2_001_fastqc.html [link] -- See log file for details
WARN: Failed to publish file: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/work/3f/e6079a331483144a947e4729ccf99e/62476759_S38_R2_001_fastqc.zip; to: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/Reports/FastQC/S27/62476759_S38_R2_001_fastqc.zip [link] -- See log file for details
WARN: Failed to publish file: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/work/59/ee9f25bba014f6b0f6a89fe1b9f18b/62495347_S27_R1_001_fastqc.html; to: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/Reports/FastQC/S27/62495347_S27_R1_001_fastqc.html [link] -- See log file for details
WARN: Failed to publish file: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/work/59/ee9f25bba014f6b0f6a89fe1b9f18b/62495347_S27_R1_001_fastqc.zip; to: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/Reports/FastQC/S27/62495347_S27_R1_001_fastqc.zip [link] -- See log file for details
WARN: Failed to publish file: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/work/59/ee9f25bba014f6b0f6a89fe1b9f18b/62495347_S27_R2_001_fastqc.html; to: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/Reports/FastQC/S27/62495347_S27_R2_001_fastqc.html [link] -- See log file for details
WARN: Failed to publish file: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/work/59/ee9f25bba014f6b0f6a89fe1b9f18b/62495347_S27_R2_001_fastqc.zip; to: /sfs/7/workspace/ws/iiipe01-sarektest-0/hroc113/Reports/FastQC/S27/62495347_S27_R2_001_fastqc.zip [link] -- See log file for details
[0d/346966] Submitted process > MarkDuplicates (hroc113-hroc113_tumor)

[maxulysse]

Basically, would you prefer:

• param like --publish, and then different options like copy, link...
• flags like --publishLink or --publishCopy

[apeltzer]

I think the first one is the better choice.

[maxulysse]

I agree.
I'll start working on this then ;-)