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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

Commits

Commits on Apr 26, 2024

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

  jfy133

  committed
  f7fceaf

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

  jfy133

  committed
  0778e58

Commits on Jun 28, 2024

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

  jfy133

  committed
  eb73ae6

• Continue customisation

  jfy133

  committed
  cc114f3

Commits on Jul 12, 2024

• More debugging

  jfy133

  committed
  37994df

Commits on Jul 19, 2024

• Get working function

  jfy133

  committed
  e07dc06

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

  jfy133

  committed
  c0f93d9

• Extract names properly

  jfy133

  committed
  de035ca

• Remove unnecesary code

  jfy133

  committed
  7890575

• Get working string check function!

  jfy133

  committed
  b795b9e

• TODO

  jfy133

  committed
  cac8152

Commits on Jul 20, 2024

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

  jfy133

  committed
  a8dcd64

• And get it back again

  jfy133

  committed
  56cba0c

Commits on Jul 22, 2024

• Sort output to ensure consistency

  jfy133

  committed
  0f12b21

• Sort file name only funciton

  jfy133

  committed
  d41aad9

Commits on Jul 26, 2024

• Start testing preprocessing

  jfy133

  committed
  61c4d24

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

  jfy133

  committed
  19db88c

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

  jfy133

  committed
  bcc3baf

• Backing up TODO notes

  jfy133

  committed
  0b58cf7

Commits on Aug 16, 2024

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

  jfy133

  committed
  eb4824e

Commits on Sep 20, 2024

• Finalise first test

  jfy133

  committed
  9ce930f

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

  jfy133

  authored
  5598eec

• Update tests to latest dev

  jfy133

  committed
  6362fa3

Commits on Oct 4, 2024

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

  jfy133

  committed
  61086b5

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

  jfy133

  committed
  9a56d48

• Start refactoring to use nft-utils

  jfy133

  committed
  bb12ca1

Commits on Oct 11, 2024

• fix qualimap output dir typo

  TCLamnidis

  committed
  87fafc5

• no sampleid in qualimap outdir

  TCLamnidis

  committed
  ef71d3b

Commits on Oct 18, 2024

• bump nft-utils version

  TCLamnidis

  committed
  a7fadc6

• start refactoring to use nft-utils

  TCLamnidis

  committed
  4baefaf

• update snapshot. Not sure it works yet.

  TCLamnidis

  committed
  8b7e950

Commits on Nov 8, 2024

• add preprocessing

  TCLamnidis

  committed
  2e5bf4f

Commits on Nov 29, 2024

• fix preprocessing checks

  TCLamnidis

  committed
  c204fe9

Commits on Nov 30, 2024

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

  TCLamnidis

  committed
  4efc86b

Commits on Dec 3, 2024

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

  TCLamnidis

  committed
  9f3611f

• reorder and add todos

  TCLamnidis

  committed
  6893eb6

• remove versions.ymls from snapshot

  TCLamnidis

  committed
  13a640c

Commits on Dec 4, 2024

• check bam names instead of content

  TCLamnidis

  committed
  5241ffc

• add ave_filtered_bam parameter to test profile

  TCLamnidis

  committed
  0dab178

• fix result pickup for bam filtering and deduplication

  TCLamnidis

  committed
  01850ad

Commits on Dec 6, 2024

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

  TCLamnidis

  committed
  42b3a47

• simplify bam_input_stats snapshot

  TCLamnidis

  committed
  0c6c8e3

• update snapshot

  TCLamnidis

  committed
  50ea5e1

• exclude unstable qualimap results.

  TCLamnidis

  committed
  997fb5b

Commits on Dec 11, 2024

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

  TCLamnidis

  committed
  82cb639

Commits on Dec 15, 2024

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

  TCLamnidis

  authored
  61f6285

Commits on Dec 20, 2024

• remove leftover todo

  TCLamnidis

  committed
  c0cd1eb

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

  TCLamnidis

  committed
  53d82b0

• add command legend, and align a bit more

  TCLamnidis

  committed
  5ed2b0b