V1.12rc #416
Open
V1.12rc #416
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
- Removed the unused r1-only=False parameter in the render_r1_r2() function in both the rnaseq and chipseq Snakefiles\n- Changed the name of 'r1_only' function to 'render_r1_only' in both Snakefiles to make the name more intuitive and updated the rest of the files accordingly
Fixed render_r1_r2 function(s) in Snakefiles
Move `strand_arg` assignment from the `run` block to the `params` block so that `--rerun-trigger` will detect changes to strandedness configuration and re-run those rules
Make strand_arg a param
Add lib.postprocess.utils.extract_from_zip function, used for extracting -- and then immediately gzipping -- a file from within a downloaded zip. Include reference config for Plodia interpunctella
Just a small mistake Co-authored-by: Ryan Dale <[email protected]>
* Change SRA fastq directory Change the directory where SRA fastq files are downloaded and add the 'orig_filename' column to the config object for each sample so that the rest of the workflow works correctly * Make code more elegant Change a nested for-loop implementation in patters_targets.py to a more elegant one-line solution and clean up some code in Snakefile * improve helper.fill_patterns add check when combining by `zip` to ensure values are all same length add more doctests --------- Co-authored-by: Ryan Dale <[email protected]>
ucsc might be blocking circle-ci given the licenseing requirements of chainfiles
this tool was last updated in 2017, and has incompatibilites with recent numpy.
* Have STAR use disk memory for its temporary files. * handle cases where $TMPDIR is not set --------- Co-authored-by: Ryan Dale <[email protected]>
* GAT no longer used, remove from requirements * don't pin python * pin snakemake >8 * update env.yml * update snakefiles and lib to reflect changes in snakemake 8 * rm --bias for kallisto, which was causing segfaults * rm --reason for snakemake 8 * disable colocalization workflow
After further testing it turns out Biowulf will not accept this temporary directory unless it is further specified.
It'll be mysterious if it does fail but probably not necessary to take up quite so much space for those temp files.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
params:directive, letting jobs re-run if strandedness changed in config. Previously, rules needed to be manually re-run after changing strandedness in config.lcdbwf::vargenes_heatmap()function