Code

Adding stubs at all level#1335

Code

Merged

maxulysse merged 42 commits intonf-core:devnf-core/rnaseq:devfrom maxulysse:stubs_everywheremaxulysse/nf-core_rnaseq:stubs_everywhereCopy head branch name to clipboardAug 21, 2024

+18,829-4,788

Commits

Commits on Jul 3, 2024

• stub for align_star + a single snapshot match per test

  maxulysse

  committed
  0620d21

  Copy full SHA for 0620d21

• add stubs + code polish + Harshil align

  maxulysse

  committed
  573ca90

  Copy full SHA for 573ca90

• add stub

  maxulysse

  committed
  3efcb84

  Copy full SHA for 3efcb84

• update all nf-core modules and subworkflows and do not include tags

  maxulysse

  committed
  345d1f8

  Copy full SHA for 345d1f8

• simplify snapshot for stub

  maxulysse

  committed
  eb08f2f

  Copy full SHA for eb08f2f

• add stubs for subworkflow local quantify_rsem

  maxulysse

  committed
  c956f6f

  Copy full SHA for c956f6f

• update default snapshot

  maxulysse

  committed
  bf5797f

  Copy full SHA for bf5797f

Commits on Jul 4, 2024

• add plugin

  maxulysse

  committed
  37780ad

  Copy full SHA for 37780ad

• update all subworkflows

  maxulysse

  committed
  150ac0b

  Copy full SHA for 150ac0b

• do not snapshot fastq in stub

  maxulysse

  committed
  9fd07da

  Copy full SHA for 9fd07da

• pipeline level stub

  maxulysse

  committed
  2cdeea1

  Copy full SHA for 2cdeea1

• fix stub test for prepare_genome

  maxulysse

  committed
  3c78a6a

  Copy full SHA for 3c78a6a

• update all subworkflows

  maxulysse

  committed
  c572fc0

  Copy full SHA for c572fc0

Commits on Jul 5, 2024

• correctly align

  maxulysse

  committed
  df9efba

  Copy full SHA for df9efba

Commits on Jul 9, 2024

• update all modules

  maxulysse

  committed
  bc7d7a5

  Copy full SHA for bc7d7a5

Commits on Jul 11, 2024

• use seqera containers

  maxulysse

  committed
  b78a653

  Copy full SHA for b78a653

Commits on Jul 12, 2024

• Merge branch 'dev' into stubs_everywhere

  maxulysse

  authored
  98cf1fa

  Copy full SHA for 98cf1fa

• update all modules/subworkflows + remove tags

  maxulysse

  committed
  8759ed7

  Copy full SHA for 8759ed7

• update snapshot

  maxulysse

  committed
  5c1db07

  Copy full SHA for 5c1db07

Commits on Jul 16, 2024

• Merge branch 'dev' into stubs_everywhere

  maxulysse

  authored
  3c9250d

  Copy full SHA for 3c9250d

Commits on Jul 22, 2024

• Merge branch 'dev' into stubs_everywhere

  maxulysse

  authored
  8052b6b

  Copy full SHA for 8052b6b

• update nf-test to 0.9.0

  maxulysse

  committed
  8b28fee

  Copy full SHA for 8b28fee

• sort

  maxulysse

  committed
  3eaf7a4

  Copy full SHA for 3eaf7a4

• update all modules/subworkflows + remove tags

  maxulysse

  committed
  86bac63

  Copy full SHA for 86bac63

• remove tags

  maxulysse

  committed
  ee285c8

  Copy full SHA for ee285c8

• keep card 3.1.1 that does not break CI due to weird RG

  maxulysse

  committed
  88286cd

  Copy full SHA for 88286cd

• update snapshot

  maxulysse

  committed
  f5adb7a

  Copy full SHA for f5adb7a

• update snapshot

  maxulysse

  committed
  d1c19be

  Copy full SHA for d1c19be

• update all modules + subworkflows / remove tags + path markduplicates

  maxulysse

  committed
  f94beb3

  Copy full SHA for f94beb3

• update snapshots

  maxulysse

  committed
  784aeb2

  Copy full SHA for 784aeb2

• update stringtie_stringtie

  maxulysse

  committed
  30afc0e

  Copy full SHA for 30afc0e

• update snapshots for fastq_align_hisat2

  maxulysse

  committed
  58cee58

  Copy full SHA for 58cee58

• add proper stubs and tests for local star_*_igenomes modules

  maxulysse

  committed
  586058b

  Copy full SHA for 586058b

Commits on Aug 16, 2024

• Merge branch 'dev' into stubs_everywhere

  maxulysse

  committed
  32a6440

  Copy full SHA for 32a6440

• proper sha for module bedtools/genomecov

  maxulysse

  committed
  f77e714

  Copy full SHA for f77e714

• update samtools/stats module + rm tags

  maxulysse

  committed
  200d4bd

  Copy full SHA for 200d4bd

Commits on Aug 20, 2024

• Merge branch 'dev' into stubs_everywhere

  maxulysse

  authored
  34fecc9

  Copy full SHA for 34fecc9

• clean up stub tests

  maxulysse

  committed
  3088bde

  Copy full SHA for 3088bde

• Merge branch 'dev' into stubs_everywhere

  maxulysse

  authored
  a0499c8

  Copy full SHA for a0499c8

• update CHANGELOG

  maxulysse

  committed
  56539ac

  Copy full SHA for 56539ac

• update snapshot

  maxulysse

  committed
  a68cb69

  Copy full SHA for a68cb69

Commits on Aug 21, 2024

• update snapshot

  maxulysse

  committed
  1b34d1e

  Copy full SHA for 1b34d1e