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Refactor pipeline filtering, create params flags for tools #148

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Refactor pipeline filtering, create params flags for tools #148

wants to merge 40 commits into from

Commits on Mar 28, 2024

  1. feat: flag for busco

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    slsevilla committed Mar 28, 2024
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  2. refactor: change filtering for failed samples CDCgov#147

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    slsevilla committed Mar 28, 2024
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Commits on Mar 31, 2024

  1. refactor: ica handling CDCgov#149

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  2. refactor: updating new ica handling CDCgov#149

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  3. refactor: handling errors, ica handling, filtering CDCgov#147 CDCgov#149

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  4. refactor: check ica param is as expected 149

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  5. refactor: create ncbi_excel_creation flag CDCgov#150

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  6. refactor: filtering strategy bbduk CDCgov#147

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  7. chore: fix meta tuple called

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  8. refactor: move fastp variables to config CDCgov#150

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  9. refactor: ica handling, filtering CDCgov#147 CDCgov#149

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  10. refactor: ica handling CDCgov#147

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  11. refactor: ica handling, filtering CDCgov#147 CDCgov#149

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  12. refactor: fastqc ica handling, filtering CDCgov#147 CDCgov#149

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Commits on Apr 1, 2024

  1. refactor: move kraken params to config CDCgov#150

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  2. refactor: krakenbh handle ica and terra CDCgov#149

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    slsevilla committed Apr 1, 2024
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  3. refactor: kraken subwf and modules for ica, reorg wf calls CDCgov#149

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  4. refactor: add check for terra parms CDCgov#151

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  5. refactor: add param for extended_qc CDCgov#151

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    slsevilla committed Apr 1, 2024
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  6. refactor: spades for ica CDCgov#149

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  7. refactor: spades wf modules for ica CDCgov#149

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  8. refactor: rename_headers for ica CDCgov#149

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    slsevilla committed Apr 1, 2024
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  9. refactor: ica, output file handling CDCgov#149

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    slsevilla committed Apr 1, 2024
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Commits on Apr 3, 2024

  1. refactor: create extended_qc variable CDCgov#151

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    slsevilla committed Apr 3, 2024
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  2. refactor: filtering CDCgov#147

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    slsevilla committed Apr 3, 2024
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  3. refactor: move filtering to workflow level CDCgov#147

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    slsevilla committed Apr 3, 2024
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  4. refactor: scaffolds samplesshet ica CDCgov#149

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  5. refactor: kraken2 makereport, top mash hits ica CDCgov#149

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  6. refactor: phoenix wf filtering, ica CDCgov#147 CDCgov#149

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  7. refactor: determine taxaID, fast ani ica CDCgov#149

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  8. refactor: mlst ica CDCgov#149

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    slsevilla committed Apr 3, 2024
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  9. refactor: mlst, amrfinder for terra, ica CDCgov#149

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  10. refactor: summary lines ica CDCgov#149

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    slsevilla committed Apr 3, 2024
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Commits on Apr 4, 2024

  1. chore: fix missed ica flag

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    slsevilla committed Apr 4, 2024
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  2. refactor: summary lines ica CDCgov#149

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    slsevilla committed Apr 4, 2024
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  3. feat: flags for execution CDCgov#153

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    slsevilla committed Apr 4, 2024
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  4. refactor: griphin ica CDCgov#149

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    slsevilla committed Apr 4, 2024
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Commits on Apr 9, 2024

  1. chore: unblock expected outputs

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    slsevilla committed Apr 9, 2024
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  2. chore: unblock griphin, outputs

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    slsevilla committed Apr 9, 2024
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  3. docs: changes added to log

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    slsevilla committed Apr 9, 2024
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