Nextflow stdout:

WARN: A process with name 'BCFTOOLS_STATS_FAMILY' is defined more than once in module script: /home/runner/work/nf-cmgg-germline/nf-cmgg-germline/./workflows/cmgg-germline.nf -- Make sure to not define the same function as process
ERROR ~ Error executing process > 'CMGG_CMGGGERMLINE:CMGGGERMLINE:INPUT_SPLIT_BEDTOOLS:BEDTOOLS_SPLIT (NA24385D2_NVQ_034)'

Caused by:
  Process `CMGG_CMGGGERMLINE:CMGGGERMLINE:INPUT_SPLIT_BEDTOOLS:BEDTOOLS_SPLIT (NA24385D2_NVQ_034)` terminated with an error exit status (1)

Command executed:

  bedtools \
      split \
       \
      -n null \
      -i NA24385D2_NVQ_034_intersect.bed \
      -p NA24385D2_NVQ_034
  
  cat <<-END_VERSIONS > versions.yml
  "CMGG_CMGGGERMLINE:CMGGGERMLINE:INPUT_SPLIT_BEDTOOLS:BEDTOOLS_SPLIT":
      bedtools: $(bedtools --version | sed -e "s/bedtools v//g")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error: num_chunks==0.
  
  
  Tool:    bedtools split
  Version: v2.31.1
  Summary: Split a Bed file.
  
  Usage:   bedtools split [OPTIONS] -i <bed> -n number-of-files
  
  Options: 
  	-i|--input (file)	BED input file (req'd).
  	-n|--number (int)	Number of files to create (req'd).
  	-p|--prefix (string)	Output BED file prefix.
  	-a|--algorithm (string) Algorithm used to split data.
  		* size (default): uses a heuristic algorithm to group the items
  		  so all files contain the ~ same number of bases
  		* simple : route records such that each split file has
  		  approximately equal records (like Unix split).
  
  	-h|--help		Print help (this screen).
  	-v|--version		Print version.
  
  
  Note: This programs stores the input BED records in memory.

Work dir:
  /home/runner/work/nf-cmgg-germline/nf-cmgg-germline/.nf-test/tests/4cd16ee0225696263163b852d9946cdd/work/de/a6213d05bea22839a40fef24d851a7

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

 -- Check '/home/runner/work/nf-cmgg-germline/nf-cmgg-germline/.nf-test/tests/4cd16ee0225696263163b852d9946cdd/meta/nextflow.log' file for details
Join mismatch for the following entries: 
- key=[id:NA24385D2_NVQ_034, sample:NA24385D2_NVQ_034, family:Proband_12345, vardict_min_af:null, family_count:2, type:cram] values= 
- key=[id:DNA049572, sample:DNA049572, family:Proband_12345, vardict_min_af:null, family_count:2, type:cram] values=


WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
ERROR ~ A DataflowVariable can only be assigned once. Use bind() to allow for equal values to be passed into already-bound variables.

 -- Check '/home/runner/work/nf-cmgg-germline/nf-cmgg-germline/.nf-test/tests/4cd16ee0225696263163b852d9946cdd/meta/nextflow.log' file for details
Nextflow stderr: