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nf-core / raredisease

Call and score variants from WGS/WES of rare disease patients.
https://nf-co.re/raredisease
MIT License
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Number of ENSEMBLVEP_SNV instances when using CADD #405

Closed fa2k closed 1 year ago

fa2k commented 1 year ago

Description of the bug

When using CADD, the number of VEP processes seems to be the square of the number of scatters of the genome. I expect it should instead be equal to the number of scatters, which is the number of CADD jobs.

(Not related to the problem: In the example below I had to manually lower the scatter count to 2 to get it to run on a small test dataset)

Command used and terminal output

[6a/7d8489] process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:ANNOTATE_CADD:BCFTOOLS_ANNOTATE (NA12878)                                [100%] 2 of 2 ✔
[a7/c53176] process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:ANNOTATE_CADD:TABIX_ANNOTATE (NA12878)                                   [100%] 2 of 2 ✔
[ce/8c77e1] process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:ENSEMBLVEP_SNV (NA12878)                                                 [100%] 4 of 4 ✔
[30/b53874] process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:TABIX_VEP (NA12878)                                                      [100%] 4 of 4 ✔
[-        ] process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:BCFTOOLS_CONCAT                                                          -

[---]

Execution cancelled -- Finishing pending tasks before exit
-[nf-core/raredisease] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:BCFTOOLS_CONCAT (1)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:BCFTOOLS_CONCAT` input file name collision -- There are multiple input files for each of the following file names: NA12878_0001-scattered_ann_rohann_vcfanno_filter_vep.vcf.gz.tbi, NA12878_0000-scattered_ann_rohann_vcfanno_filter_vep.vcf.gz, NA12878_0001-scattered_ann_rohann_vcfanno_filter_vep.vcf.gz, NA12878_0000-scattered_ann_rohann_vcfanno_filter_vep.vcf.gz.tbi

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

nextflow 23.04.2 pipeline 1.1.1

ramprasadn commented 1 year ago

Fix here https://github.com/nf-core/raredisease/pull/421

ramprasadn commented 1 year ago

Closing this issue since the fix has been merged into dev.