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Swtich singularity+conda setup to singularity setup for snakemake tasks #70

Merged
merged 25 commits into from
Apr 18, 2023
Merged

Swtich singularity+conda setup to singularity setup for snakemake tasks #70

merged 25 commits into from
Apr 18, 2023

Commits on Apr 8, 2023

  1. moving most rules away from conda to just container

    Manavalan Gajapathy committed Apr 8, 2023
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  2. fixes error in container path

    Manavalan Gajapathy committed Apr 8, 2023
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Commits on Apr 10, 2023

  1. refactors to remove wrapper dependency for multiqc

    Manavalan Gajapathy committed Apr 10, 2023
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  2. refactors samtools stats away from wrapper

    Manavalan Gajapathy committed Apr 10, 2023
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  3. refactors picard away from wrapper

    Manavalan Gajapathy committed Apr 10, 2023
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  4. fixes typo

    Manavalan Gajapathy committed Apr 10, 2023
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  5. adds container to picard_collect_multiple_metrics

    Manavalan Gajapathy committed Apr 10, 2023
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  6. removes container for mosdepth-plot as python is missing in there

    Manavalan Gajapathy committed Apr 10, 2023
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  7. fixes stupid bugs in picard rule

    Manavalan Gajapathy committed Apr 10, 2023
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  8. adds rule-level container instead of pipeline-level

    Manavalan Gajapathy committed Apr 10, 2023
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  9. removes old conda and wrapper directives from rules

    Manavalan Gajapathy committed Apr 10, 2023
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  10. removes unused conda envs

    Manavalan Gajapathy committed Apr 10, 2023
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  11. removes container as it can't be used with run directive

    Manavalan Gajapathy committed Apr 10, 2023
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  12. fixes wrong tool name in rule message

    Manavalan Gajapathy committed Apr 10, 2023
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  13. removes non-ascii spacing character - this caused error when swithced… 

    … to singularity in rule create_multiqc_config
    Manavalan Gajapathy committed Apr 10, 2023
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  14. uses mulled container instead of quac_watch conda env

    Manavalan Gajapathy committed Apr 10, 2023
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  15. removes quac-watch conda env

    Manavalan Gajapathy committed Apr 10, 2023
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  16. removes conda usage from snakemake cmd

    Manavalan Gajapathy committed Apr 10, 2023
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  17. updates docs on env type created

    Manavalan Gajapathy committed Apr 10, 2023
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  18. updates changelog

    Manavalan Gajapathy committed Apr 10, 2023
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  19. removes globally-defined singularity container

    Manavalan Gajapathy committed Apr 10, 2023
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  20. refactor rule aggregate_sample_rename_configs to use shell directive … 

    …instead of run to run the job in singularity container
    Manavalan Gajapathy committed Apr 10, 2023
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Commits on Apr 14, 2023

  1. adds github link

    Manavalan Gajapathy committed Apr 14, 2023
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  2. removes conda-create-envs-only section in docs

    Manavalan Gajapathy committed Apr 14, 2023
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  3. adds optional step to pull singularity images

    Manavalan Gajapathy committed Apr 14, 2023
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