Ecosyste.ms: Issues

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GitHub / karel-brinda/miniphy issues and pull requests

#36 - Update conda, envs, and directories

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#35 - Add param to config indicating whether Snakemake should use conda

Issue - State: closed - Opened by karel-brinda over 1 year ago - 1 comment
Labels: enhancement

#35 - Add param to config indicating whether Snakemake should use conda

Issue - State: closed - Opened by karel-brinda over 1 year ago - 1 comment
Labels: enhancement

#33 - Format

Pull Request - State: closed - Opened by leoisl over 1 year ago - 5 comments

#33 - Format

Pull Request - State: closed - Opened by leoisl over 1 year ago - 5 comments

#32 - Update README

Pull Request - State: closed - Opened by leoisl over 1 year ago

#32 - Update README

Pull Request - State: closed - Opened by leoisl over 1 year ago

#31 - Make this pipeline configurable

Pull Request - State: closed - Opened by leoisl almost 2 years ago - 31 comments

#30 - Workflow clean up and reproducibility

Pull Request - State: closed - Opened by leoisl almost 2 years ago - 1 comment

#30 - Workflow clean up and reproducibility

Pull Request - State: closed - Opened by leoisl almost 2 years ago - 1 comment

#29 - K-mer counting should use only 1 snakemake thread and max number of cores

Issue - State: closed - Opened by karel-brinda over 3 years ago - 8 comments

#29 - K-mer counting should use only 1 snakemake thread and max number of cores

Issue - State: closed - Opened by karel-brinda over 3 years ago - 8 comments

#28 - Show filename in case of the "Unknown suffix" error

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: enhancement

#27 - Input files should be relative to the list of files

Issue - State: closed - Opened by karel-brinda over 3 years ago - 2 comments
Labels: enhancement, wontfix

#26 - MissingInputException: Missing input files for rule symlink_nw_tree

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: bug

#26 - MissingInputException: Missing input files for rule symlink_nw_tree

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: bug

#25 - Updates from the O2 cluster

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#25 - Updates from the O2 cluster

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#24 - Dont use dirs as outputs

Issue - State: open - Opened by karel-brinda over 3 years ago - 1 comment
Labels: enhancement

#24 - Dont use dirs as outputs

Issue - State: open - Opened by karel-brinda over 3 years ago - 1 comment
Labels: enhancement

#23 - Add support for custom trees

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#22 - Choice between txt (simpl) and fa as a configuration param

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: enhancement, wontfix

#22 - Choice between txt (simpl) and fa as a configuration param

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: enhancement, wontfix

#21 - Release and include a new version of ProPhyle with propagation without BWT

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement

#20 - Add detailed batch stats (for individual samples/records)

Issue - State: open - Opened by karel-brinda over 3 years ago - 1 comment
Labels: enhancement

#19 - Add file sizes to the output stats

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement

#19 - Add file sizes to the output stats

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement

#18 - Post-propagation input files resolved incorrectly

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: bug

#17 - In dry run (-n), Snakemake is trying to load the node list before it exists

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: bug

#16 - Input gz decompression doesn't work

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: bug

#15 - Underscores in file names confuse the pipeline

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: bug

#15 - Underscores in file names confuse the pipeline

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: bug

#14 - Aggregate statistics

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#14 - Aggregate statistics

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#13 - Add histogram and clns summary

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#13 - Add histogram and clns summary

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#12 - Standardize trees

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#12 - Standardize trees

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#11 - Always use binary tree with a root

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: bug

#10 - Add a possibility of using custom trees

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement

#9 - Add k-mer histograms and seq summaries

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#9 - Add k-mer histograms and seq summaries

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#8 - Add configuration

Issue - State: closed - Opened by karel-brinda over 3 years ago - 1 comment
Labels: enhancement

#7 - Split results to results and intermediate

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement

#7 - Split results to results and intermediate

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement

#6 - Add k-mer propagation using ProPhyle

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#6 - Add k-mer propagation using ProPhyle

Pull Request - State: closed - Opened by karel-brinda over 3 years ago

#5 - Support properly dir outputs

Issue - State: closed - Opened by karel-brinda over 3 years ago - 3 comments
Labels: enhancement

#5 - Support properly dir outputs

Issue - State: closed - Opened by karel-brinda over 3 years ago - 3 comments
Labels: enhancement

#4 - Add summarizing sequences from a list of files

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement

#4 - Add summarizing sequences from a list of files

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement

#3 - Add global stats aggregation

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement

#2 - Add k-mer counting (from list of fa/txt files)

Issue - State: closed - Opened by karel-brinda over 3 years ago
Labels: enhancement