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vpc-ccg / pamir

Discovery and Genotyping of Novel Sequence Insertions in Many Sequenced Individuals
BSD 3-Clause "New" or "Revised" License
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Pamir.sh requiring centromer parameter is inconsistent with README #46

Closed Krannich479 closed 4 years ago

Krannich479 commented 4 years ago

Hi, I am using your latest pamir.sh (commit f49e0b8795a47e640eee7307fe6eaa7c0b690964, of May 29th 2020) as follows: /path/to/pamir/pamir.sh --configfile /path/to/config.yaml -j 16 and receive an error about the centromer parameter:

Running Pamir (f49e0b8)
snakemake(5.9.1)... OK 
samtools(1.9)... OK 
bedtools(2.29.2)... OK 
mrsfast(3.4.1)... OK 
bwa(0.7.17)... OK 
repeatmasker(4.0.9)... OK, Version not checked.
AssertionError in line 7 of /path/to/pamir/pamir/Snakefile:
centromeres is a mandatory field in config
  File "/path/to/pamir/pamir/Snakefile", line 25, in <module>
  File "/path/to/pamir/pamir/Snakefile", line 7, in cfg_mandatory

According to your README, the centromer parameter is not mandatory and I also prefer not to exclude regions. Is this possibly just an easy fix of un-setting a mandatory flag somewhere?

fhach commented 4 years ago

@Krannich479 it should be addressed today.

fhach commented 4 years ago

@Krannich479 You may check the master branch. make clean && make

Krannich479 commented 4 years ago

That seems solved to me. Thanks!