BIMSBbioinfo / pigx_chipseq

Pipeline for Analysis of ChIP-Seq data

Home Page:http://bioinformatics.mdc-berlin.de/pigx/

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cryptic error when gtf annotation is missing

alexg9010 opened this issue · comments

When the gtf-file is not given, or commented, a cryptic error message is given.

test.yaml:

# ## ~~~~~~~~~~~~~~~~~~~~~~~~~LOCATIONS~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# ## This section needs to be adjusted to the planned analysis.   #
# ## ------------------------------------------------------------ #
 locations:
   input-dir: ./
   output-dir: ./output
   genome-file: ../dm_genome/Drosophila_melanogaster_sm_assembly6_chip.fa
#   spikein-file:
#   index-dir:
#   gff-file:
#
#
[..]
SyntaxError:
Input and output files have to be specified as strings or lists of strings.
  File "/gnu/store/1d1y4d7j8p4cnad7q9mswhbvs18falp6-pigx-chipseq-0.0.52/libexec/pigx_chipseq/Snake_ChIPseq.py", line 364, in <module>
  File "/gnu/store/1d1y4d7j8p4cnad7q9mswhbvs18falp6-pigx-chipseq-0.0.52/libexec/pigx_chipseq/Rules/Prepare_Annotation.py", line 11, in <module>