Add VEP annotation via subworkflow #21
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Problem so far: The index file is older than the vcf.gz file... executor > local (6)
[53/d41436] process > QBICPIPELINES_VCFTOMAF:VCFTOMAF:UNTAR (vep.tar.gz) [100%] 1 of 1 ✔
[d1/ad6aac] process > QBICPIPELINES_VCFTOMAF:VCFTOMAF:ENSEMBLVEP_VEP (test2) [100%] 2 of 2 ✔
[0c/80a19f] process > QBICPIPELINES_VCFTOMAF:VCFTOMAF:TABIX_TABIX (test2) [100%] 2 of 2 ✔
[7a/b3cb1c] process > QBICPIPELINES_VCFTOMAF:VCFTOMAF:BCFTOOLS_VIEW (test) [ 50%] 1 of 2, failed: 1
[- ] process > QBICPIPELINES_VCFTOMAF:VCFTOMAF:GUNZIP -
[- ] process > QBICPIPELINES_VCFTOMAF:VCFTOMAF:VCF2MAF -
[- ] process > QBICPIPELINES_VCFTOMAF:VCFTOMAF:MULTIQC -
[DUMP: vcf-before] [['id':'test', 'index':true, 'normal_id':'testN', 'vcf_normal_id':'testN'], /home/paifb01/vcftomaf/work/80/5d0858f352f14c963373766c511701/test.vcf.gz]
[DUMP: vcf-sfter] [['id':'test', 'index':true, 'normal_id':'testN', 'vcf_normal_id':'testN'], /home/paifb01/vcftomaf/work/80/5d0858f352f14c963373766c511701/test.vcf.gz, /home/paifb01/vcftomaf/work/81/bbdcd6d89e3166b3629350da6aea6e/test.vcf.gz.tbi]
[DUMP: vcf-before] [['id':'test2', 'index':false, 'tumor_id':'testT', 'vcf_tumor_id':'testT'], /home/paifb01/vcftomaf/work/d1/ad6aacd5607f07379d37d7619767f5/test2.vcf.gz]
[DUMP: vcf-sfter] [['id':'test2', 'index':false, 'tumor_id':'testT', 'vcf_tumor_id':'testT'], /home/paifb01/vcftomaf/work/d1/ad6aacd5607f07379d37d7619767f5/test2.vcf.gz, /home/paifb01/vcftomaf/work/0c/80a19f8f4a5a74ae77648d7ff60263/test2.vcf.gz.tbi]
Execution cancelled -- Finishing pending tasks before exit
-[qbic-pipelines/vcftomaf] Pipeline completed with errors-
ERROR ~ Error executing process > 'QBICPIPELINES_VCFTOMAF:VCFTOMAF:BCFTOOLS_VIEW (test)'
Caused by:
Process `QBICPIPELINES_VCFTOMAF:VCFTOMAF:BCFTOOLS_VIEW (test)` terminated with an error exit status (9)
Command executed:
bcftools view \
--output test.vcf.gz \
--regions-file genome.bed \
\
\
--output-type z \
--threads 4 \
test.vcf.gz
cat <<-END_VERSIONS > versions.yml
"QBICPIPELINES_VCFTOMAF:VCFTOMAF:BCFTOOLS_VIEW":
bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS
Command exit status:
9
Command output:
(empty)
Command error:
Error: BCF read error
Work dir:
/home/paifb01/vcftomaf/work/7a/b3cb1cf4b5c49a62635b8e8284521c
Container:
quay.io/biocontainers/bcftools:1.20--h8b25389_0
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details |
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).