fix(pipeline): inputs not used for peak call #132
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* 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]>
…151/SeqNado into fix-no-inputs-used-for-peak-call
alsmith151
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Feb 5, 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]> --------- Co-authored-by: alsmith <[email protected]> Co-authored-by: Alastair Smith <[email protected]>
CChahrour
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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]>
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