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Add nf-test#1063

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jfy133 wants to merge 49 commits intodevnf-core/eager:devfrom nf-test-conversionnf-core/eager:nf-test-conversionCopy head branch name to clipboard

+1,044-3

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Commits on Apr 26, 2024

• Add general structure, and generate (not working!) snapshot for basic test profile

  jfy133

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  f7fceaf

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• Try adding an ignore zip system, doesn't work atm though...

  jfy133

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Commits on Jun 28, 2024

• Merge branch 'dev' into nf-test-conversionMerge in from dev

  jfy133

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  eb73ae6

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• Continue customisation

  jfy133

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Commits on Jul 12, 2024

• More debugging

  jfy133

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Commits on Jul 19, 2024

• Get working function

  jfy133

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  e07dc06

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• Get working function properly, and start integrating into snapshot: problem with collection/name not working

  jfy133

  committed
  c0f93d9

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• Extract names properly

  jfy133

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• Remove unnecesary code

  jfy133

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• Get working string check function!

  jfy133

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• TODO

  jfy133

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Commits on Jul 20, 2024

• Update MQC so works on gitpod, try to re-add original getAllFilesFromDir (but not working - no md5swum?!)

  jfy133

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  a8dcd64

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• And get it back again

  jfy133

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Commits on Jul 22, 2024

• Sort output to ensure consistency

  jfy133

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• Sort file name only funciton

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Commits on Jul 26, 2024

• Start testing preprocessing

  jfy133

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• Merge branch 'dev' into nf-test-conversion

  jfy133

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  19db88c

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• Start adding preprocessing dir but diff not working so can't ser variability

  jfy133

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  bcc3baf

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• Backing up TODO notes

  jfy133

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Commits on Aug 16, 2024

• Final snapshots, need to double check all files are covered but I think so

  jfy133

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Commits on Sep 20, 2024

• Finalise first test

  jfy133

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• Merge branch 'dev' into nf-test-conversion

  jfy133

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  5598eec

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• Update tests to latest dev

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Commits on Oct 4, 2024

• Merge branch 'dev' into nf-test-conversion

  jfy133

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• Merge branch 'dev' into nf-test-conversion

  jfy133

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  9a56d48

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• Start refactoring to use nft-utils

  jfy133

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Commits on Oct 11, 2024

• fix qualimap output dir typo

  TCLamnidis

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  87fafc5

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• no sampleid in qualimap outdir

  TCLamnidis

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  ef71d3b

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Commits on Oct 18, 2024

• bump nft-utils version

  TCLamnidis

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  a7fadc6

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• start refactoring to use nft-utils

  TCLamnidis

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  4baefaf

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• update snapshot. Not sure it works yet.

  TCLamnidis

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  8b7e950

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Commits on Nov 8, 2024

• add preprocessing

  TCLamnidis

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Commits on Nov 29, 2024

• fix preprocessing checks

  TCLamnidis

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Commits on Nov 30, 2024

• Merge remote-tracking branch 'origin/dev' into nf-test-conversion

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Commits on Dec 3, 2024

• Merge remote-tracking branch 'origin/dev' into nf-test-conversion

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  9f3611f

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• reorder and add todos

  TCLamnidis

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  6893eb6

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• remove versions.ymls from snapshot

  TCLamnidis

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Commits on Dec 4, 2024

• check bam names instead of content

  TCLamnidis

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• add ave_filtered_bam parameter to test profile

  TCLamnidis

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• fix result pickup for bam filtering and deduplication

  TCLamnidis

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Commits on Dec 6, 2024

• add final_bams,mapstats. fix mapping. remove old code

  TCLamnidis

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  42b3a47

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• simplify bam_input_stats snapshot

  TCLamnidis

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  0c6c8e3

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• update snapshot

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• exclude unstable qualimap results.

  TCLamnidis

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Commits on Dec 11, 2024

• Check existence of Multiqc output files. reorder tests to match alphanumeric ordering of directories in output

  TCLamnidis

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Commits on Dec 15, 2024

• Merge branch 'dev' into nf-test-conversion

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Commits on Dec 20, 2024

• remove leftover todo

  TCLamnidis

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• Merge branch 'nf-test-conversion' of github.com:nf-core/eager into nf-test-conversion

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• add command legend, and align a bit more

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