processing QC metrics error

@YiLiu6240 sorry one more. I think this is down to the VCF file format changing. Using code commit 177aa4b3170d984c704384cc47309162edc4fbe9

Command

docker run \
--rm \
-v /data:/data \
--cpus="1" \
mrbase-report-module:177aa4b3170d984c704384cc47309162edc4fbe9 \
Rscript render_gwas_report.R \
/data/igd/IEU-b-1/IEU-b-1_data.vcf.gz \
--refdata /data/ref/1kg_v3_nomult.bcf \
--output_dir . \
--n_cores 1

Output

ml18692@ieu-db-interface:~/v3$ bash report.sh 
2019-09-25 15:52:29 INFO::Config:
2019-09-25 15:52:29 INFO::input: /data/igd/IEU-b-1/IEU-b-1_data.vcf.gz
  id: IEU-b-1_data
  output_dir: .
  bcf_file: /data/igd/IEU-b-1/IEU-b-1_data.vcf.gz
  refdata: /data/ref/1kg_v3_nomult.bcf
  metadata_file: ./metadata.json
  qc_metrics_file: ./qc_metrics.json
  report_file: ./IEU-b-1_data_report.html
  intermediates_dir: ./intermediate
  rmd_intermediates_dir: ./intermediate/rmd_intermediate_files
  n_cores: 1
  no_report: FALSE
  reuse: FALSE
2019-09-25 15:52:29 INFO::Reading data...
Lines   total/split/realigned/skipped:  9/0/0/0
2019-09-25 15:53:13 INFO::Reading data done.
# A tibble: 6 x 12
  CHROM    POS ID    REF   ALT    EFFECT     SE   PVAL PVAL_ztest    AF
  <int>  <int> <chr> <chr> <chr>   <dbl>  <dbl>  <dbl>      <dbl> <dbl>
1    10 9.96e6 rs47… A     G     -0.0037 0.0052 0.716      0.477  0.509
2    10 9.96e6 rs47… C     T     -0.0033 0.0052 0.775      0.526  0.509
3    10 9.96e6 rs12… G     T     -0.0035 0.0052 0.739      0.501  0.509
4    10 1.00e8 rs73… A     G     -0.0099 0.0054 0.0400     0.0668 0.679
5    10 1.00e8 rs73… A     G     -0.0084 0.0054 0.0843     0.120  0.679
6    10 1.00e8 rs70… C     T     -0.0075 0.0067 0.269      0.263  0.219
# ... with 2 more variables: AF_reference <dbl>, N <int>
2019-09-25 15:53:13 INFO::Processing metadata...
2019-09-25 15:53:13 INFO::Processing metadata done.
2019-09-25 15:53:13 INFO::Processing qc metrics...
Error in if (!is.null(top_hits) || nrow(top_hits) > 0) { : 
  missing value where TRUE/FALSE needed
Calls: do.call ... <Anonymous> -> splice_if -> probe -> map_lgl -> qc__se_n_r2
In addition: Warning messages:
1: `lang()` is deprecated as of rlang 0.2.0.
Please use `call2()` instead.
This warning is displayed once per session. 
2: `new_overscope()` is deprecated as of rlang 0.2.0.
Please use `new_data_mask()` instead.
This warning is displayed once per session. 
3: `overscope_eval_next()` is deprecated as of rlang 0.2.0.
Please use `eval_tidy()` with a data mask instead.
This warning is displayed once per session. 
4: `is_lang()` is deprecated as of rlang 0.2.0.
Please use `is_call()` instead.
This warning is displayed once per session. 
5: `mut_node_car()` is deprecated as of rlang 0.2.0.
This warning is displayed once per session. 
6: The `printer` argument is deprecated as of rlang 0.3.0.
This warning is displayed once per session. 
Execution halted

MRCIEU / opengwas-reports

processing QC metrics error #21