sorting scripts depending on their function #28
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We can push this on dev if you want to but as long as #23 isn't fixed I won't accept this on our master branch!
README.md
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| When the enviroment is created, set the variable 'path_env' in the configuration file as the path to it. | ||
| Every other dependency will be automatically installed by Nextflow using conda. For that a new conda enviroment will be created, which can be found in the from Nextflow created work directory after the first pipeline run. | ||
| It is **not** required to create and activate the enviroment from the yaml-file beforehand. | ||
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| **Important Note:** For conda the channel bioconda needs to be set as highest priority! This is required due to two differnt packages with the same name in different channels. For the pipeline the package jellyfish from the channel bioconda is needed and **NOT** the jellyfisch package from the channel conda-forge! |
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Wanted to merge with dev... Missed to change it while creating the request. The base is now dev. |
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I have posted several questions to the output gtf format #29, though I don't think that it could change something, if create_gtf is working with all paths, still I would wait and test it beforehand |
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@anastasiia this only affects the script build in nextflow. It won't affect the script itself. |
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the scripts are sorted very well! Still I would rely on what @HendrikSchultheis says about merging
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I would push it on dev! Because every path of the scripts changes. I fear that its going to cause a lot of problems if we change the files by other pull requests and then move them to a different location by accepting this pull request. I do not how how git manages this. |
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If this is really only about the new folder structure in /bin we should merge this. |
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We can't we should have waited with your pull request. I do not know how to solve this conflict now. |
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I broke my old Branch trying to resolve this conflict. |
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Can't you just merge dev into estmiated_motifs and update those files? |
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Let's try. |
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It worked. |
I had to create a new branch and redo the work because i totally broke my old one.
Sorted all scripts in sub-folders depending on their function.
Tested it as far as i could. Run does not complete because of issue #23.
create_gtf is working! Which is one of the more sensitive scripts if it comes to changing paths.