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Heya, I've just created a <PR> for a bug that occu...
# sarek_dev
j
Heya, I've just created a PR for a bug that occurs when using GATK.GRCh37 for the genome, which links to an igenomes interval file in GATK-style .list format. I was wondering if you wanted this fix, or instead just update the s3 intervals file?
👀 1
m
Thanks Julian, I'll have a look
Just wondering, have you tried passing the intervals to the GATK4_INTERVALLISTTOBED process?
j
I have not but I looked at the GATK documentation before and it looked like its only IntervalList -> BED
m
OK
How about adding an extra if statement in local/create_intervals_bed then?
j
create_intervals_bed already has an if statement (the last one) that deals with the gatk-style .list format, but for the intervals_combined part I got the error:
Copy code
ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_Sarek)'

Caused by:
  Process `NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_Sarek)` terminated with an error exit status (1)


Command executed:

  FILE_TYPE=$(htsfile wgs_calling_regions_Sarek.list)
  
  case "$FILE_TYPE" in
      *BGZF-compressed*)
          [ '$(basename wgs_calling_regions_Sarek.list)' != '$(basename wgs_calling_regions_Sarek.bed.gz)' ] && ln -s wgs_calling_regions_Sarek.list wgs_calling_regions_Sarek.bed.gz ;;
      *gzip-compressed*)
          [ "$(basename wgs_calling_regions_Sarek.list)" == "$(basename wgs_calling_regions_Sarek.bed.gz)" ] && echo "Input and output names cannot be the same" && exit 1
          bgzip -d -c -@ 1 wgs_calling_regions_Sarek.list | bgzip -c  -@ 1 > wgs_calling_regions_Sarek.bed.gz ;;
      *bzip2-compressed*)
          bzcat wgs_calling_regions_Sarek.list | bgzip -c  -@ 1 > wgs_calling_regions_Sarek.bed.gz ;;
      *XZ-compressed*)
          xzcat wgs_calling_regions_Sarek.list | bgzip -c  -@ 1 > wgs_calling_regions_Sarek.bed.gz ;;
      *)
          bgzip -c  -@ 1 wgs_calling_regions_Sarek.list > wgs_calling_regions_Sarek.bed.gz ;;
  esac
  
  tabix -@ 1   -f wgs_calling_regions_Sarek.bed.gz

Command exit status:
  1

Command output:
  (empty)

Command error:
  [E::get_intv] Failed to parse TBX_GENERIC: was wrong -p [type] used?
  The offending line was: "1:1-121485432"
  tbx_index_build3 failed: wgs_calling_regions_Sarek.bed.gz
👀 1
But yeh that error happens if there is no LIST_TO_BED conversion (similar to how the GATK4_INTERVALLISTTOBED process works). Let me know if you want it this way and I can upload the .list/.intervals files to test-data, or whether you want to just change the s3 igenomes file to a .bed/.interval_list
m
I'll check with @Rike Hanssen what we think might be the best solution
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