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tgen / jetstream_resources

Collection of scripts and README files tracking the source and generation of reference genomes and annotation files
MIT License
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Add automatic mappability file creation for suncity #35

Closed ChristopheLegendre closed 4 years ago

ChristopheLegendre commented 4 years ago

I have added a script create_mappability_file.sh to automatically capture GRCh37-single-read Umap K100 mappability file for GATK CNV. I also updated the suncity_resources.ini by adding a variable pointing to the expected compressed bed file.

ChristopheLegendre commented 4 years ago
  1. I deleted it from my side; should not have happened.
  2. module load is also present other files such as increate_sexCheck_SNP_list.sh. I thought it was ok to put it. --> I removed the line and now check for the presence of gatk tool in the user's PATH. That may imply that the variable GATK_MODULE in the ini file should not be defined.
  3. OK. line 35 updated
  4. README added
  5. I split the line 24. Though I think it was more elegant and shorter to have it in one line.
PedalheadPHX commented 4 years ago

@ChristopheLegendre Can you add Lines 4-35 from the phoenix_resources.ini to the suncity_resources.ini. Then you can wrap the if statement in the ENVIROMENT variable, and still use module load locally, I didn't realize you could check for things the path so I'd still do that in the else section. See the new salmon script for an example (https://github.com/tgen/jetstream_resources/blob/master/phoenix/create_salmon_index.sh)

ChristopheLegendre commented 4 years ago

lines added to suncity_resources.ini file and script updated accordingly