Commits · 950ec4b3756118ae48c33c7671fa2b4526de3c58 · LBMC / nextflow

Aug 19, 2021
- emase-zero: use g2tr instean of tr2g · 950ec4b3
  Laurent Modolo authored 3 years ago
  
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  950ec4b3
- kb: add g2t process · 734051f9
  Laurent Modolo authored 3 years ago
  
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  734051f9
Aug 18, 2021
- emase-zero: change ${bin} argument · 451b7da0
  Laurent Modolo authored 3 years ago
  
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  451b7da0
Aug 17, 2021
- gatk4: add samtools bam index · 607bf264
  Laurent Modolo authored 3 years ago
  
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  607bf264
- alntools: fix tsv output :20 · 7eeb7d90
  Laurent Modolo authored 3 years ago
  
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  7eeb7d90
Aug 16, 2021
- Merge branch 'crey02-master-patch-25149' into 'master' · 9489f360
  Laurent Modolo authored 3 years ago
  
  Crey02 master patch 25149 See merge request !24
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  9489f360
Jul 23, 2021
- alntools: redirect stderr to report file · 8be11d56
  Laurent Modolo authored 3 years ago
  
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  8be11d56
Jul 21, 2021
- macs2: set default qvalue to 0.99 · 6ddf33f5
  Laurent Modolo authored 3 years ago
  
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  6ddf33f5
- kb: create a correction step for the t2g.txt messed with by kb · 5dc7c7f8
  Laurent Modolo authored 3 years ago
  
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  5dc7c7f8
- kb: add clean t2g script in count processes · c3a4c54e
  Laurent Modolo authored 3 years ago
  
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  c3a4c54e
Jul 19, 2021
- kb: change sort option for t2g · 3f8b847c
  Laurent Modolo authored 3 years ago
  
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  3f8b847c
- kb: create a backup of t2g.txt as kb rewrite it · 72580e6b
  Laurent Modolo authored 3 years ago
  
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  72580e6b
Jul 15, 2021
- kb: remove gffutils buggy dependency for t2g.txt construction · 57bdbc31
  Laurent Modolo authored 3 years ago
  
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  57bdbc31
Jul 13, 2021
- kb: go back to working 0.26.0 version · a9f4a856
  Laurent Modolo authored 3 years ago
  
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  a9f4a856
Jul 09, 2021
- gffread: remove empty line · 0d30c103
  Laurent Modolo authored 3 years ago
  
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  0d30c103
- kb: update to 0.26.3 · f7a50522
  Laurent Modolo authored 3 years ago
  
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  f7a50522
Jul 05, 2021
- kb: fix cardinality for split() step · 0c461dac
  Laurent Modolo authored 3 years ago
  
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  0c461dac
Jul 02, 2021
- mlepetit/nextflow-Maxime · 45be888a
  Laurent Modolo authored 3 years ago
  
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  45be888a
Jun 30, 2021
- kb: change --lamano option into --workflow lamano · 32c4ad6c
  Laurent Modolo authored 3 years ago
  
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  32c4ad6c
Jun 29, 2021
- bioawk: fix fasta2transcriptslength process · 6925f9d0
  Laurent Modolo authored 3 years ago
  
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  6925f9d0
- kb: fix missing line :330 · 87abd17d
  Laurent Modolo authored 3 years ago
  
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  87abd17d
Jun 28, 2021
- gatk4: rename _out option for gvcf · 22455a05
  Laurent Modolo authored 3 years ago
  
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  22455a05
- gatk4: add gvcf to variant_calling_out · 5eae8fe1
  Laurent Modolo authored 3 years ago
  
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  5eae8fe1
Jun 24, 2021
- docker: add htseq 0.13.5 · ed5b2f47
  Laurent Modolo authored 3 years ago
  
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  ed5b2f47
Jun 22, 2021
- gatk4: change file_prefix definition to handle Map · 2e4cc629
  Laurent Modolo authored 3 years ago
  
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  2e4cc629
Jun 21, 2021
- gatk4: remove map only usefull for testing · d42ded32
  Laurent Modolo authored 3 years ago
  
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  d42ded32
Jun 17, 2021
- gatk4: working variant calling pipeline · 2dcade89
  Laurent Modolo authored 3 years ago
  
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  2dcade89
Jun 04, 2021
- mutliqc: add flatten step · 3808033c
  Laurent Modolo authored 3 years ago
  
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  3808033c
- bowtie2: fix switch :67 · c05b8c6a
  Laurent Modolo authored 3 years ago
  
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- multiqc: fix process name · 3cd8d74f
  Laurent Modolo authored 3 years ago
  
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- multiqc: add comments on usage · 1ae0c21d
  Laurent Modolo authored 3 years ago
  
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  1ae0c21d
- multiqc: add workflow to perform report channel cleanning · 84b2ae0e
  Laurent Modolo authored 3 years ago
  
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  84b2ae0e
- cleanup DSL1 test.sh · 2150d981
  Laurent Modolo authored 3 years ago
  
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  2150d981
- switcth to nextflow DSL2 · cc2d49f6
  Laurent Modolo authored 3 years ago
  
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  cc2d49f6
Jun 02, 2021
- kb: add velocity workflow · 753be570
  Laurent Modolo authored 3 years ago
  
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  753be570
- gatk4: fix include path · 179127d0
  Laurent Modolo authored 3 years ago
  
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  179127d0
- gatk4: fix include path · 78ed7b01
  Laurent Modolo authored 3 years ago
  
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  78ed7b01
- fix emit: for named workflow · 92e0e00a
  Laurent Modolo authored 3 years ago
  
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  92e0e00a
- add example of variant calling with gatk4 · e363dd6f
  Laurent Modolo authored 3 years ago
  
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  e363dd6f
- bwa: add mapping workflow · 6f67c65c
  Laurent Modolo authored 3 years ago
  
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  6f67c65c