Update GATK version

[nkwang24]

No description provided.

[nwiltsie]

@nkwang24 I'm running the NFTest cases for sanity, hence the need for 2d52a74 (that image was automatically deleted after #8 was merged).

[nwiltsie]

Beep boop, a script is posting on @nwiltsie's behalf.

The following NFTest cases completed successfully:

• SNV
• SV

Summary log file: /hot/software/pipeline/pipeline-StableLift/Nextflow/development/unreleased/nkwang-update-gatk-version/log-nftest-20240820T161711Z.log

[nwiltsie]

So my script is lying - there was some weirdness associated with the NFTest run:

• The SNV test hung for an hour before fixing itself when I logged into the node... suspicious
• The SV test actually failed, but NFTest didn't register that... super weird.

------------------------------------
Starting workflow...
------------------------------------
2024-08-20 17:54:41,413 - nextflow - INFO - [77/e5edae] Submitted process > run_validate_PipeVal_with_metadata (1)
2024-08-20 17:54:47,398 - nextflow - INFO - [10/2ef032] Submitted process > run_validate_PipeVal_with_metadata (2)
2024-08-20 17:54:48,411 - nextflow - INFO - [91/238de2] Submitted process > workflow_extract_sv_annotations:liftover_SV_StableLift (1)
2024-08-20 17:54:49,454 - console - INFO - ERROR ~ Error executing process > 'workflow_extract_sv_annotations:liftover_SV_StableLift (1)'
2024-08-20 17:54:49,454 - nextflow - ERROR - Error executing process > 'workflow_extract_sv_annotations:liftover_SV_StableLift (1)'

Caused by:
  Process `workflow_extract_sv_annotations:liftover_SV_StableLift (1)` terminated with an error exit status (2)

Command executed:

  Rscript "/scratch/206501/nftest-_70r35p1/./module/scripts/liftover-Delly2-vcf.R"             --input-vcf "inputs/TCGA-SARC_WGS_Delly2_regenotype-gSV_bcftools-merge_filter-germline.vcf.gz"             --header-contigs "GRCh38-vcf-header-contigs.txt"             --chain-file "hg19ToHg38.over.chain"             --output "liftover.vcf.gz"

Command exit status:
  2

Command output:
  Fatal error: cannot open file '/scratch/206501/nftest-_70r35p1/./module/scripts/liftover-Delly2-vcf.R': No such file or directory

Command error:
  Fatal error: cannot open file '/scratch/206501/nftest-_70r35p1/./module/scripts/liftover-Delly2-vcf.R': No such file or directory

Work dir:
  /scratch/206501/nftest-_70r35p1/test/work/91/238de2e6695094bce8fec97926fb39

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
2024-08-20 17:54:49,459 - nextflow - INFO - Execution cancelled -- Finishing pending tasks before exit
2024-08-20 17:54:50,304 - console - INFO -
2024-08-20 17:54:51,252 - NFTest - INFO -  [ succeed ]
https://github.com/uclahs-cds/pipeline-StableLift/pull/12#issuecomment-2299425749
Got the one possible log file {PosixPath('/hot/software/pipeline/pipeline-StableLift/Nextflow/development/unreleased/nkwang-update-gatk-version/log-nftest-20240820T161711Z.log')}
Success! Posting to GitHub...
_Beep boop, a script is posting on @nwiltsie's behalf._

The following NFTest cases completed successfully:
* `SNV`
* `SV`

Summary log file: `/hot/software/pipeline/pipeline-StableLift/Nextflow/development/unreleased/nkwang-update-gatk-version/log-nftest-20240820T161711Z.log`

[nwiltsie]

I ran NFTest manually and the SV test case passed as expected: /hot/software/pipeline/pipeline-StableLift/Nextflow/development/unreleased/nkwang-update-gatk-version/log-nftest-20240820T180951Z.log

I don't know what's up with my automatic script, I'll have to dig in.