gtf2bed.py iGenomes incompatibility

[sisterdot]

Hey!

thanks for starting this project!

i was testing pipeline

nf-core/slamseq v1.0.0
Container: singularity - nfcore/slamseq:1.0.0

• starting it with --genome GRCh38:

Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf

i am getting the error:

Error executing process > 'gtf2bed (genes.gtf)'
Caused by:
  Process `gtf2bed (genes.gtf)` terminated with an error exit status (1)

Command executed:

  gtf2bed.py genes.gtf | sort -k1,1 -k2,2n > genes.3utr.bed

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "gtf2bed.py", line 223, in <module>
      lastCDSIndexInExon = exonRank.index(lastCDS)
  AttributeError: 'dict_keys' object has no attribute 'index'

• lets try --genome GRCm38

Staging foreign file: s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf

i am getting the error:

gtf2bed.py", line 50, in <module>
      key, value = attribute.split(' ')
  ValueError: too many values to unpack (expected 2)

• lets try --genome mm10

Staging foreign file: s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf

gtf2bed.py", line 223, in <module>
      lastCDSIndexInExon = exonRank.index(lastCDS)
  AttributeError: 'dict_keys' object has no attribute 'index'

• lets try --genome hg38

Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf

that works !

BR!