Fix: chip input issue #135
Merged
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
CChahrour
added a commit
that referenced
this pull request
Feb 7, 2024
* Fix slurm preset (#118) * require snakemake<8 * fix escape character and whitespace errors * Delete setup.cfg file * fix: split peak call rules * tests: added all peak call methods to atac test * Update output file paths in alignment_post_processing.smk * Update file paths in hub.smk * fix: updated wildcards for bigBed files * Refactor test_seqnado_config_creation function and add missing options to config_atac.yml * Update config file for chip sequencing * fix: seqnado-design * chore: removed commented code * Fix file path in lanceotron_no_input rule * Fix metadata and experiment creation in DesignIP class * Fix symlink_files function to handle both paired and single-end assays * Add log and wrapper for fastqc_raw_single rule * update config if ucsc is null * Fix config (#119) * remove split fastq from config and all rules * clean up config and fix spelling of indices * remove test config files * update default heatmap options * return to config but with small changes * refactor config.py * fix typo in config.py * use indices consistently for genome indices * update config process in docs * add entrypoint and chmod profile (#122) * Feature add config rerun (#126) * add option to rerun config * update config docs with rerun * move sigularity fix to faq in docs (#127) * feat(pipeline): handle failed peak calls (#131) * fix: add validate peaks rule * Add get_peak_files function to retrieve peak files based on assay type * fix(pipeline): inputs not used for peak call (#132) * Develop (#128) * Fix slurm preset (#118) * require snakemake<8 * fix escape character and whitespace errors * Delete setup.cfg file * fix: split peak call rules * tests: added all peak call methods to atac test * Update output file paths in alignment_post_processing.smk * Update file paths in hub.smk * fix: updated wildcards for bigBed files * Refactor test_seqnado_config_creation function and add missing options to config_atac.yml * Update config file for chip sequencing * fix: seqnado-design * chore: removed commented code * Fix file path in lanceotron_no_input rule * Fix metadata and experiment creation in DesignIP class * Fix symlink_files function to handle both paired and single-end assays * Add log and wrapper for fastqc_raw_single rule * update config if ucsc is null * Fix config (#119) * remove split fastq from config and all rules * clean up config and fix spelling of indices * remove test config files * update default heatmap options * return to config but with small changes * refactor config.py * fix typo in config.py * use indices consistently for genome indices * update config process in docs * add entrypoint and chmod profile (#122) * Feature add config rerun (#126) * add option to rerun config * update config docs with rerun * move sigularity fix to faq in docs (#127) --------- Co-authored-by: alsmith <[email protected]> * fix: "f" missing for all get_control_X functions. Whoops... * fix: multiple errors with get_control_X files * fix: removed touch sentinel * fix: && removed at end of lines * fix: make blank file if peak calls fail * fix: validate peaks wrong param supplied --------- Co-authored-by: Catherine Chahrour <[email protected]> * Fix: chip input issue (#135) * fix symlinking issue for input fastq files --------- Co-authored-by: alsmith <[email protected]> Co-authored-by: Alastair Smith <[email protected]>
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.
No description provided.