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update bcf_tools version from v1.9 to v1.20. #43

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ZaahidShaik
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Change Report :

  • Updating the bcf_tools version used in the dockerfile from v1.9 to v1.20.
  • Adding @jylee-bcm and @hyunhwan-bcm for review.

Testing step:

  • Build the new docker image using the Dockerfile.
  • Change the image version in the nextflow.config under

process {
      .....
     ......
    container = "<YOUR IMAGE NAME>"
    ......
    .....
}

  • Run the nextflow command using your VCF and HPO.

My Test Output :

  • Tested with Both regular vcf and WGS vcf.
  • Run completed without issue.
Launching `./main.nf` [desperate_escher] DSL2 - revision: b6ff1ac22e
executor >  local (14)
[8b/fb28eb] process > INDEX_VCF                  [100%] 1 of 1 ✔
[ab/816b8a] process > VCF_PRE_PROCESS            [100%] 1 of 1 ✔
[2d/a180c9] process > ANNOT_PHRANK               [100%] 1 of 1 ✔
[df/8d07ec] process > ANNOT_ENSMBLE              [100%] 1 of 1 ✔
[9e/53737a] process > TO_GENE_SYM                [100%] 1 of 1 ✔
[79/17c7e7] process > PHRANK_SCORING             [100%] 1 of 1 ✔
[91/ddaf87] process > HPO_SIM                    [100%] 1 of 1 ✔
[e4/4ae337] process > REMOVE_MITO_AND_UNKOWN_CHR [100%] 1 of 1 ✔
[ad/700573] process > FILTER_EXONIC              [100%] 1 of 1 ✔
[b7/a7bdab] process > FILTER_PROBAND             [100%] 1 of 1 ✔
[17/8dafb3] process > VEP_ANNOTATE               [100%] 1 of 1 ✔
[56/57058d] process > FEATURE_ENGINEERING_PART1  [100%] 1 of 1 ✔
[70/fd765a] process > FEATURE_ENGINEERING_PART2  [100%] 1 of 1 ✔
[92/2e3365] process > PREDICTION                 [100%] 1 of 1 ✔
Completed at: 07-Aug-2024 16:30:58
Duration    : 16m 36s
CPU hours   : 4.3
Succeeded   : 14

@ZaahidShaik ZaahidShaik self-assigned this Aug 7, 2024
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@jylee-bcm jylee-bcm left a comment

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LGTM

@hyunhwan-bcm
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Good job 👍

@hyunhwan-bcm hyunhwan-bcm merged commit 85de284 into LiuzLab:nextflow_conversion Aug 7, 2024
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3 participants