Extensive testing of subworkflows

[kubranarci]

No description provided.

[kubranarci]

Please create sub-issues for each subworkflow.

[zehrahazalsezer]

dup_to_ins parameter does not exist

[zehrahazalsezer]

sample parameter into truth-id

[zehrahazalsezer]

It is written nextflow run nf-core/benchmark -profile test_liftover,<docker/singularity> --outdir <OUTDIR> in test_liftover.config file.

It should be nextflow run nf-core/variantbenchmarking ....

[kubranarci]

add info about truth samples, link GIAB truth ftp directories.

[zehrahazalsezer]

I added normalization and deduplication preprocess into test_somatic.config. When I run nextflow run . -profile test_somatic,docker --outdir test_results, I got this error:

Command error:
  [W::vcf_parse_info] INFO 'STRANDS' is not defined in the header, assuming Type=String
  REF_MISMATCH  chr1    669501  N       A
  REF_MISMATCH  chr1    964661  N       G
  [E::vcf_format] Invalid BCF, the INFO tag id=13 is too large at chr1:669501
  [flush_buffer] Error: cannot write to 13059_2022_2816_MOESM4_ESM.rh.dedup.vcf.gz

Similar issue: samtools/bcftools#1720

[zehrahazalsezer]

I added filter_contig into the test_stub.config. And then run nextflow run . -profile test_stub,docker --outdir test_results -stub

Error message:

Execution cancelled -- Finishing pending tasks before exit
-[nf-core/variantbenchmarking] Pipeline completed with errors-
WARN: Killing running tasks (9)
ERROR ~ Error executing process > 'NFCORE_VARIANTBENCHMARKING:VARIANTBENCHMARKING:SMALL_GERMLINE_BENCHMARK:HAPPY_HAPPY (freebayes)'

Caused by:
  Process `NFCORE_VARIANTBENCHMARKING:VARIANTBENCHMARKING:SMALL_GERMLINE_BENCHMARK:HAPPY_HAPPY (freebayes)` terminated with an error exit status (1)


Command executed:

  echo "" | gzip > freebayes.HG002.small.freebayes.roc.all.csv.gz
  echo "" | gzip > freebayes.HG002.small.freebayes.roc.Locations.INDEL.csv.gz
  echo "" | gzip > freebayes.HG002.small.freebayes.roc.Locations.INDEL.PASS.csv.gz
  echo "" | gzip > freebayes.HG002.small.freebayes.roc.Locations.SNP.csv.gz
  echo "" | gzip > freebayes.HG002.small.freebayes.roc.Locations.SNP.PASS.csv.gz
  echo "" | gzip > freebayes.HG002.small.freebayes.metrics.json.gz
  echo "" | gzip > freebayes.HG002.small.freebayes.vcf.gz
  touch freebayes.HG002.small.freebayes.vcf.gz.tbi
  touch freebayes.HG002.small.freebayes.summary.csv
  touch freebayes.HG002.small.freebayes.extended.csv
  touch freebayes.HG002.small.freebayes.runinfo.json
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_VARIANTBENCHMARKING:VARIANTBENCHMARKING:SMALL_GERMLINE_BENCHMARK:HAPPY_HAPPY":
      hap.py: 0.3.14
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.sh: line 14: freebayes.HG002.small.freebayes.vcf.gz: cannot overwrite existing file

Work dir:
  /workspace/variantbenchmarking/work/41/4240508390b8f5c64ca437a44466ea

Container:
  quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- 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
Join mismatch for the following entries: key=[id:tiddit2, caller:tiddit, vartype:sv, subsample:HCC1395_HCC1395T, normshift:null, normdist:null, normsizediff:null, maxdist:null, pctsize:null, pctseq:null, pctovl:null, refdist:null, chunksize:null, dup_to_ins:null, typeignore:null, bpDistance:null, percentThreshold:null, absoluteThreshold:null, maxMatches:null, evaluationmode:null] values=


Join mismatch for the following entries: key=[id:freebayes, caller:freebayes, vartype:small, subsample:null, normshift:null, normdist:null, normsizediff:null, maxdist:null, pctsize:null, pctseq:null, pctovl:null, refdist:null, chunksize:null, dup_to_ins:null, typeignore:null, bpDistance:null, percentThreshold:null, absoluteThreshold:null, maxMatches:null, evaluationmode:null] values=


ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

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