VEP complains about the Cache directory not found

[ranijames]

Dear All,
First of all, I thank you for the pipeline written for VEP. I am new to nextflow and trying to use some established/published pipelines. I have been using your repo for testing the nextflow pipeline using VEP. Pretty much the same code without using the scheduler. Now I am ruing into an issue while trying to execute the nextflow pipeline.
For example, I am trying to run the whole pipeline as following, without the processes for vcf_to_tsv and for split_VEP_fields.
So this is how I am running the pipeline,
./nextflow run main.nf -resume –ref_fa /home/Alva.Rani/vep_data/input/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa --ref_fai /path/to/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.fai

After following all other steps as mentioned in the README. And, here is what I it is throwing me,

N E X T F L O W  ~  version 19.01.0
Launching `main.nf` [elated_poincare] - revision: 8131ab3472
WARN: There's no process matching config selector: vcf_to_tsv
~~~~~~~ VEP Pipeline ~~~~~~~
* Project dir:        /home/Alva.Rani/scripts/test_next/vep-annotation-nf
* Launch dir:         /home/Alva.Rani/scripts/test_next/vep-annotation-nf
* Work dir:           /home/Alva.Rani/scripts/test_next/vep-annotation-nf/work
* Profile:            standard
* Script name:        main.nf
* Script ID:          8131ab3472413dd12f18afd6ddd67642
* Container engine:   docker
* Workflow session:   1465a194-dbbe-4507-8ed5-61592daeaf36
* Nextflow run name:  elated_poincare
* Nextflow version:   19.01.0, build 5050 (22-01-2019 11:19 UTC)
* Launch command:
nextflow run main.nf -resume –ref_fa /home/Alva.Rani/vep_data/input/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa --ref_fai /path/to/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.fai

[warm up] executor > local
[skipping] Stored process > download_ref
[d5/ee2143] Submitted process > vep (Normal1.VarScan2.indel.filtered)
[0d/c968e7] Submitted process > vep (Normal1.HaplotypeCaller.NA.filtered)
[ed/f59e6f] Submitted process > vep (Tumor1.LoFreq.NA.filtered)
[5f/88b4bc] Submitted process > vep (Normal1.VarScan2.snp.filtered)
[e6/aa9e12] Submitted process > vep (Tumor1.VarScan2.snp.filtered)
[d2/ba9b32] Submitted process > vep (Tumor1.HaplotypeCaller.NA.filtered)
[2b/092961] Submitted process > vep (Normal1.LoFreq.NA.filtered)
[7f/8ce161] Submitted process > vep (Tumor1.VarScan2.indel.filtered)
[1d/b48ade] Submitted process > vep (Tumor1_Normal1.LoFreqSomatic.snvs.NA.filtered)
ERROR ~ Error executing process > 'vep (Normal1.VarScan2.indel.filtered)'

Caused by:
  Process `vep (Normal1.VarScan2.indel.filtered)` terminated with an error exit status (2)

Command executed:

  vep     --offline     --assembly "/home/Alva.Rani/scripts/test_next/vep-annotation-nf/ref/homo_sapiens_vep_96_GRCh37"     --fasta "input.2"     --hgvs     --hgvsg     --protein     --symbol     --ccds     --canonical     --biotype     --pubmed     -i "Normal1.VarScan2.indel.filtered.vcf"     --format vcf     -o "Normal1.VarScan2.indel.filtered.vep.vcf"     --vcf

Command exit status:
  2

Command output:
  (empty)

Command error:
  Possible precedence issue with control flow operator at /conda/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
  
  -------------------- EXCEPTION --------------------
  **MSG: ERROR: Cache directory /root/.vep/homo_sapiens not found**
  
  STACK Bio::EnsEMBL::VEP::CacheDir::dir /conda/share/ensembl-vep-96.0-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311
  STACK Bio::EnsEMBL::VEP::CacheDir::init /conda/share/ensembl-vep-96.0-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227
  STACK Bio::EnsEMBL::VEP::CacheDir::new /conda/share/ensembl-vep-96.0-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
  STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /conda/share/ensembl-vep-96.0-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115
  STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /conda/share/ensembl-vep-96.0-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91
  STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /conda/share/ensembl-vep-96.0-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175
  STACK Bio::EnsEMBL::VEP::Runner::init /conda/share/ensembl-vep-96.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm:123
  STACK Bio::EnsEMBL::VEP::Runner::run /conda/share/ensembl-vep-96.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm:194
  STACK toplevel /conda/bin/vep:218
  Date (localtime)    = Fri Mar 27 15:32:02 2020
  Ensembl API version = 96
  ---------------------------------------------------

Work dir:
  /home/Alva.Rani/scripts/test_next/vep-annotation-nf/work/d5/ee2143ec3b58ab914810914e7b1611

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
WARN: Killing pending tasks (8)

The nextflow version I am using is 19.01.1 and the OS is Ubuntu 18.04.3 LTS. Any suggestions or help is greatly appreciated. I have no idea what is that thing I am doing wrong. In the ref I have the
homo_sapiens_vep_96_GRCh37 folder with files in it.

Thank You!