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Remove inefficient basic file handling pipeline steps #505

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adamrtalbot opened this issue Sep 7, 2023 · 0 comments
Open

Remove inefficient basic file handling pipeline steps #505

adamrtalbot opened this issue Sep 7, 2023 · 0 comments
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enhancement New feature or request

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adamrtalbot commented Sep 7, 2023 •
edited

Description of feature

The following processes do nothing but unpack tars or handle files. We can remove some or all of them to make the pipeline much more efficient:

  • ADJUST_MAXBIN2_EXT
  • BUSCO_DB_PREPARATION
  • BUSCO_SAVE_DOWNLOAD
  • CAT_DB_GENERATE
  • CAT_DB
  • CAT_SUMMARY
  • CENTRIFUGE_DB_PREPARATION
  • GTDBTK_DB_PREPARATION
  • KRAKEN2_DB_PREPARATION
  • KRONA_DB
  • POOL_PAIRED_READS
  • POOL_SINGLE_READS
  • RENAME_POSTDASTOOL
  • RENAME_PREDASTOOL

All of these steps can be handled with Nextflow. They may require upstream changes in nf-core/modules.

The following processes could be simplified, altered or perhaps removed but will have to be checked on a case-by-case basis:

  • CAT
  • COMBINE_TSV
  • CONVERT_DEPTHS
  • QUAST_BINS_SUMMARY
  • SPADESHYBRID
  • TIARA_CLASSIFY

Related issues:
@adamrtalbot adamrtalbot added the enhancement New feature or request label Sep 7, 2023
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