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Created with Raphaël 2.2.016Oct2Jun13Mar715Feb27Jan16Dec151228Nov252314Oct9Sep65118Jul121Apr21Feb1514112Nov27Apr8711Feb1016Sep74127Jul2120230Jun25242322171615928May2720Apr15Update env_scripts_python.yaml: remove unused channelmastermasterconfig_template: correction of the first commentdocs(changelog): update change in v1.3.01.3.01.3.0fix(write_demultiplex_files.py): correct mkdirrefactor: simplifying the codedocs(scripts/write_demultiplex_files.py): correct a commentrefactor: replace "singularity" by "container" (Deprecated singularity directive)prepare_spygen.R: delete an unnecessary line of codefix(prepare_spygen.R): remove the extra '_' in CNEG and POOL samplesfix(prepare_spygen.R): remove the extra '_' in CNEG and Pool samplesdevelopdevelopfix(write_demultiplex_files.py): The first sample of all_samples is now analysedstyle(config_template): fix typostyle(config_template): fix typombruno-master-p…mbruno-master-patch-33133Merge branch 'master' of https://gitlab.mbb.cnrs.fr/edna/snakemake_rapidrun_obitoolsfix(clean_pcrerr_samples): fix obiclean error when empty input filefix(obitools_envs): conda env creation too longrefactor(rules, config): rename some subfolders keysMerge branch 'develop'style(Snakefile): fix typostatus(Snakefile): Developement to Productiondocs(readme): update Quick Start in README.mddocs(changelog): update change log with 1.3.0refactor(config_template): add commentremove(envs/fastqsplitter_envs.yaml): unused conda envRemove old config filesRemove unused rulesrefactor(split_fastq.smk): replace fastqsplitter by seqkit split2feat: change input and ouptut pathsstyle(Snakefile): remove empty linesUpdate README: remove slack linkstyle(Snakemake): Add commentsfix(checkpoint): problem with empty filesrefactor(table_assigned_sequences.smk): add {projet} and {marker} in output file namefix(ngsfilter.smk): MissingOutputExceptionfix(ngsfilter.smk): ValueError: malformed node or stringfix(get_targets): no longer returns the same file multiple timesUpdate samples_to_runs.smkfeat(prepare_spygen): create all_samples.csv (required in the config file)Reverting to cdfa6fca1.2.01.2.0commom.smk: remove print in get_internal_samples + remove commented function