things needed in the backend

[ajle96]

• logging
• automated indexing for genome table?
• change index function
• use flock to prevent multiple cwl_creater.py run
• a workflow parser to generate graph
• make metadata from conditions table
• crontab
• add genome path to self.conf
• hisat2 with different tags depending on downstream analysis
• Use root dir to resolve abs location of cwl scripts in programs.py (put root dir to repo in conf then get root dir in each function)
• Use self.file_names to get the list of file names instead of the keys of input_files. 1) to be safe 2) save some processing time
• folder

try to stick to 80 characters per line :)

[tonyyzy]

@ajle96 let me know which part you need me to do :)

[ajle96]

just a place to save all the things, add here new things

[tonyyzy]

Actually, if multiple aligners are used, and both sam will be passed to htseq_count then htseq_prepare will be written to workflow twice. htseq_prepare only need be called once for a single workflow as it only depends on gtf annotation file.

…

On Mon, 18 Feb 2019, 6:35 pm ajle96 ***@***.*** wrote: just a place to save all the things, add here new things — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#65 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AlLb-eGhfHf8_tpRRbHrHLxRUaDciRlqks5vOvJrgaJpZM4bBQ8K> .

[ajle96]

Then let's have it wrapped in a workflow. It's the quickest option @FilipeJesus can this be done?