Code

Add metawrap (from tools-au)#5936

Code

Merged

bgruening merged 45 commits intogalaxyproject:maingalaxyproject/tools-iuc:mainfrom TomHarrop:port_metawrapTomHarrop/tools-iuc:port_metawrapCopy head branch name to clipboardApr 11, 2024

+269

Commits

Commits on Apr 8, 2024

• working binning, requires singularity hack

  TomHarrop

  committed
  c4c538f

• working output collection -> test

  TomHarrop

  committed
  187e805

• try smaller test data

  TomHarrop

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  1dc1ad0

• working test. add params

  TomHarrop

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  3724ad7

• add shed and help text

  TomHarrop

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  2c8d5bd

• rename shed file

  TomHarrop

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  091998c

• catch contig and stat outputs

  TomHarrop

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  63b3501

• start wrapper

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  bb47577

• rebase deleted macros

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  c359bea

• add test output

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  cc9279f

• fix DB location, add parameter test

  TomHarrop

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  4a08143

• checkm database in package. don't need to set

  TomHarrop

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  490d0b7

• move Snakefile

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  a569bc5

• investigate symlink

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  558eb74

• use discover_datasets for recursive search

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  0c99617

• true

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  182259c

• tidy whitespace

  TomHarrop

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  66228df

• fix repo link

  TomHarrop

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  3041a85

• try smaller subset

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  027a654

• try single test

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  46560e6

• only run a single test to reduce time

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  2283502

• rename test input

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  3e3fb20

• make sure PR.yaml is using the right biocontainer

  TomHarrop

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  bf5c011

• make sure PR.yaml is using the right biocontainer

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  99840ef

• Revert "make sure PR.yaml is using the right biocontainer"

  Show description for 8bc0e70
  TomHarrop

  committed
  8bc0e70

• Revert "make sure PR.yaml is using the right biocontainer"

  Show description for f331186
  TomHarrop

  committed
  f331186

• try to request less RAM

  TomHarrop

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  f2684d1

• Mem parameter is ignored by component pplacer

  TomHarrop

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  3cb659f

• Revert RAM

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  acde1fa

• tidy up snakefile

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  cf2a2f9

• metadata for toolshed

  TomHarrop

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  c3d3cc9

• exclude extras

  TomHarrop

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  a760eb6

Commits on Apr 9, 2024

• port metawrap

  TomHarrop

  committed
  17bfdfa

• lint

  TomHarrop

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  2ee00a3

• update quoting

  TomHarrop

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  a009168

• try quick to reduce RAM usage

  TomHarrop

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  a13e757

• conditional quick

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  85f8bec

• tidy up ram test

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  09dd66f

• use hidden param to run tests

  TomHarrop

  committed
  2e3e354

• Update tools/metawrapmg/.shed.yml

  Show description for e0198ac
  

  TomHarrop

  and

  bgruening

  authored
  e0198ac

• Merge branch 'port_metawrap' of github.com:TomHarrop/tools-iuc into port_metawrap

  TomHarrop

  committed
  4f27b78

• test main output

  TomHarrop

  committed
  616ab57

• Update tools/metawrapmg/.shed.yml

  Show description for 1acf766
  

  TomHarrop

  and

  bebatut

  authored
  1acf766

• remove fasta.gz handling

  TomHarrop

  committed
  4c1a76e

• remove visible from collection output

  TomHarrop

  committed
  555992c