A small update on my previous message about the Error: https://nfcore.slack.com/archives/CGFUX04HZ/p1773782404493829 I don't see this error when I use STRELKA, but I do with MUTECT2. I'm using the 3.8.1 version. Should I downgrade the version?

OK, that's bad news, I'll try to see what could have gone wrong here

Hi Maxime...Thank you for the message. Small update. As mentioned in this GitHub post https://github.com/nf-core/sarek/issues/1455 I included that piece of block in the config file I'm using and there is no Error now. Completed successfully.

[77/b9cefa] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[29/74c16c] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[05/9fb27a] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[d6/af6d0e] NFC…(1228468_D1_vs_1223221_D1) | 21 of 21 ✔

[34/fc7298] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[18/9a4fa9] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[65/a3d07d] NFC…(1228468_D1_vs_1223221_D1) | 21 of 21 ✔

[ab/a06f39] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[88/316f68] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[9a/3a4a10] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[20/0971cb] NFC…MARIES_NORMAL (1223221_D1) | 21 of 21 ✔

[7b/5dbef0] NFC…MMARIES_TUMOR (1228468_D1) | 21 of 21 ✔

[32/a193b9] NFC…MARIES_NORMAL (1223221_D1) | 1 of 1 ✔

[2f/1c28d8] NFC…MMARIES_TUMOR (1228468_D1) | 1 of 1 ✔

[b2/ce07c1] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[29/e15817] NFC…(1228468_D1_vs_1223221_D1) | 1 of 1 ✔

[e8/450614] NFC…(1228468_D1_vs_1223221_D1) | 4 of 4 ✔

[1f/2f7822] NFC…(1228468_D1_vs_1223221_D1) | 4 of 4 ✔

[32/5bcd5f] NFC…(1228468_D1_vs_1223221_D1) | 4 of 4 ✔

[a0/ceba3a] NFC…(1228468_D1_vs_1223221_D1) | 4 of 4 ✔

[c8/da4d1f] NFCORE_SAREK:sarek:MULTIQC     | 1 of 1 ✔

Plus 9 more processes waiting for tasks…

-[nf-core/sarek] Pipeline completed successfully-

Completed at: 19-Mar-2026 20:36:17

Duration    : 7h 10m 50s

CPU hours   : 405.8 (1.4% failed)

Succeeded   : 172

Failed      : 1

The failed task is just the SLURM timeout.

Glad you solved the issue, good work! Some general comments: • The

sex

column in the samplesheet should either be left out or set to

ZZ

if you don't know the correct value (

XX

or

XY

),

NA

is not valid. Not sure if this would cause an error in some tools. • 32 GB and 8 cores is overkill for

nextflow

itself, 8 GB and 1-2 cores should be plenty. This would cause any errors, though, just wasted resources.

For now only control freec and ascat use the sex, and indeed I believe they only allow for XY or XX

Sure. Thank you. BTW, I have answered the issue I created https://github.com/nf-core/sarek/issues/2156