Merge changes from main into hotfix #338
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* services.json modified in order to properly delete fitrimmed fastq les in assembly annotation * self.service_samples modified in order to properly get list of service samples * assembly files to delete modified in services.json * services.json updated with mtbseq service info * Modified purge_files function for avoiding repeated files in files_to_delete list * Modified purge_files function for avoiding repeated files in files_to_delete list * Relocated self.rename() method usage for _DEL renaming of purged folders. Now it is called when self.option = rename_nocopy * delete_rename() function renamed to just delete() * self.option rename_nocopy renamed to rename * Reverted lasts commits * Reverted some weird changes... * Relocated self.rename() method usage for _DEL renaming of purged folders * Renamed self.delete_rename() method. Now is self.delete() * rename_nocopy option modified in just rename * files to delete added to services.json for rnaseq service * Updated CHANGELOG * fixed linting * Fixed linting
* Added @click.pass_context before autoclean_sftp function * Updated CHANGELOG.md * removed tatus file
…og_viralrecon. (#282) * Updated CHANGELOG.md * removed tatus file * Corrected singularity-images path when updating pangolin database * Updated Changelog * Added line break after prompted input * Updated CHANGELOG
…rly find trimmed reads from bacass pipeline
…r to properly find trimmed reads from bacass pipeline
… is included in the RESULTS folder
…/multiqc/ html reports
…iles to the service folder
Develop merge for 2.2.0 release
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Automatically created pull request to merge changes from main into hotfix.