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fix: chip input issue #136

Merged
merged 24 commits into from
Feb 7, 2024
Merged

fix: chip input issue #136

merged 24 commits into from
Feb 7, 2024

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CChahrour
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CChahrour and others added 24 commits January 24, 2024 15:06
* require snakemake<8

* fix escape character and whitespace errors
alignment_post_processing.smk
add missing options to config_atac.yml
class
and single-end assays
* 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 option to rerun config

* update config docs with rerun
* fix: add validate peaks rule

* Add get_peak_files function to retrieve peak files based on assay type
* 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 symlinking issue for input fastq files
@CChahrour CChahrour merged commit f9f1da5 into master Feb 7, 2024
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2 participants