log file name - choice and/or character escaping

[dkj]

I see some seq_alignment jobs failing (wr executor) with

StdErr:
bash: 26398:2:4: command not found
bash: 26398:3:4: command not found
bash: 26398:4:4.out: command not found

where the submitted command ended with

tee /export/esa-sv-20180712-04/tmp/180726_A00512_0011_AH3W35DSXX_npg_pipeline/log/seq_alignment/seq_alignment-20180729-010819-26398:1:4;26398:2:4;26398:3:4;26398:4:4.out

I think the wr executor framework needs to escape shell characters in the filename generation in its logging.

[mgcam]

On 29/07/2018 17:22, dkj wrote: where the submitted command ended with |tee /export/esa-sv-20180712-04/tmp/180726_A00512_0011_AH3W35DSXX_npg_pipeline/log/seq_alignment/seq_alignment-20180729-010819-26398:1:4;26398:2:4;26398:3:4;26398:4:4.out | I think the wr executor framework needs to escape shell characters in the filename generation in its logging.

What about using file name root here? In this example 26398#4|. Escape still needed |

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