--ignore-flags fails to affect messaging

[vreuter]

Samples are submitted as intended, but the messaging is misleading (for security filepaths are omitted):

## [1 of 4] GSM3080992 (WGBS)
> Skipping sample 'GSM3080992' for pipeline 'WGBS', flag found: WGBS_failed.flag
Submitted batch job 4476055
## [2 of 4] GSM3080993 (WGBS)
> Skipping sample 'GSM3080993' for pipeline 'WGBS', flag found: WGBS_failed.flag
Submitted batch job 4476056
## [3 of 4] GSM3080994 (WGBS)
> Skipping sample 'GSM3080994' for pipeline 'WGBS', flag found: WGBS_failed.flag
Submitted batch job 4476057
## [4 of 4] GSM3080995 (WGBS)
> Skipping sample 'GSM3080995' for pipeline 'WGBS', flag found: WGBS_failed.flag
Submitted batch job 4476058

Looper finished
Samples valid for job generation: 4 of 4
Successful samples: 4 of 4
Commands submitted: 4 of 4
Jobs submitted: 4

[vreuter]

This is in conductor.py