Commits · 9489f360f17061ec141a870ff34f8070e2b8f8f6 · LBMC / nextflow

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
  9489f360
Jul 23, 2021
- alntools: redirect stderr to report file · 8be11d56
  Laurent Modolo authored 3 years ago
  
  8be11d56
Jul 21, 2021
- macs2: set default qvalue to 0.99 · 6ddf33f5
  Laurent Modolo authored 3 years ago
  
  6ddf33f5
- kb: create a correction step for the t2g.txt messed with by kb · 5dc7c7f8
  Laurent Modolo authored 3 years ago
  
  5dc7c7f8
- kb: add clean t2g script in count processes · c3a4c54e
  Laurent Modolo authored 3 years ago
  
  c3a4c54e
Jul 19, 2021
- kb: change sort option for t2g · 3f8b847c
  Laurent Modolo authored 3 years ago
  
  3f8b847c
- kb: create a backup of t2g.txt as kb rewrite it · 72580e6b
  Laurent Modolo authored 3 years ago
  
  72580e6b
Jul 15, 2021
- kb: remove gffutils buggy dependency for t2g.txt construction · 57bdbc31
  Laurent Modolo authored 3 years ago
  
  57bdbc31
Jul 13, 2021
- kb: go back to working 0.26.0 version · a9f4a856
  Laurent Modolo authored 3 years ago
  
  a9f4a856
Jul 09, 2021
- gffread: remove empty line · 0d30c103
  Laurent Modolo authored 3 years ago
  
  0d30c103
- kb: update to 0.26.3 · f7a50522
  Laurent Modolo authored 3 years ago
  
  f7a50522
Jul 05, 2021
- kb: fix cardinality for split() step · 0c461dac
  Laurent Modolo authored 3 years ago
  
  0c461dac
Jul 02, 2021
- mlepetit/nextflow-Maxime · 45be888a
  Laurent Modolo authored 3 years ago
  
  45be888a
Jun 30, 2021
- kb: change --lamano option into --workflow lamano · 32c4ad6c
  Laurent Modolo authored 3 years ago
  
  32c4ad6c
Jun 29, 2021
- bioawk: fix fasta2transcriptslength process · 6925f9d0
  Laurent Modolo authored 3 years ago
  
  6925f9d0
- kb: fix missing line :330 · 87abd17d
  Laurent Modolo authored 3 years ago
  
  87abd17d
Jun 28, 2021
- gatk4: rename _out option for gvcf · 22455a05
  Laurent Modolo authored 3 years ago
  
  22455a05
- gatk4: add gvcf to variant_calling_out · 5eae8fe1
  Laurent Modolo authored 3 years ago
  
  5eae8fe1
Jun 24, 2021
- docker: add htseq 0.13.5 · ed5b2f47
  Laurent Modolo authored 3 years ago
  
  ed5b2f47
Jun 22, 2021
- gatk4: change file_prefix definition to handle Map · 2e4cc629
  Laurent Modolo authored 3 years ago
  
  2e4cc629
Jun 21, 2021
- gatk4: remove map only usefull for testing · d42ded32
  Laurent Modolo authored 3 years ago
  
  d42ded32
Jun 17, 2021
- gatk4: working variant calling pipeline · 2dcade89
  Laurent Modolo authored 3 years ago
  
  2dcade89
Jun 04, 2021
- mutliqc: add flatten step · 3808033c
  Laurent Modolo authored 3 years ago
  
  3808033c
- bowtie2: fix switch :67 · c05b8c6a
  Laurent Modolo authored 3 years ago
  
  c05b8c6a
- multiqc: fix process name · 3cd8d74f
  Laurent Modolo authored 3 years ago
  
  3cd8d74f
- multiqc: add comments on usage · 1ae0c21d
  Laurent Modolo authored 3 years ago
  
  1ae0c21d
- multiqc: add workflow to perform report channel cleanning · 84b2ae0e
  Laurent Modolo authored 3 years ago
  
  84b2ae0e
- cleanup DSL1 test.sh · 2150d981
  Laurent Modolo authored 3 years ago
  
  2150d981
- switcth to nextflow DSL2 · cc2d49f6
  Laurent Modolo authored 3 years ago
  
  cc2d49f6
Jun 02, 2021
- kb: add velocity workflow · 753be570
  Laurent Modolo authored 3 years ago
  
  753be570
- gatk4: fix include path · 179127d0
  Laurent Modolo authored 3 years ago
  
  179127d0
- gatk4: fix include path · 78ed7b01
  Laurent Modolo authored 3 years ago
  
  78ed7b01
- fix emit: for named workflow · 92e0e00a
  Laurent Modolo authored 3 years ago
  
  92e0e00a
- add example of variant calling with gatk4 · e363dd6f
  Laurent Modolo authored 3 years ago
  
  e363dd6f
- bwa: add mapping workflow · 6f67c65c
  Laurent Modolo authored 3 years ago
  
  6f67c65c
Jun 01, 2021
- gatk4: first version of new variant calling workflow · 94772e16
  Laurent Modolo authored 3 years ago
  
  94772e16
May 31, 2021
- emase-zero: remove collect() :20 · d22860c2
  Laurent Modolo authored 3 years ago
  
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- emaze: change input to follow change to t2g in kb main.nf · 9293f190
  Laurent Modolo authored 3 years ago
  
  9293f190
May 28, 2021
- kb: working marseq quantif pipeline · d448ef6a
  Laurent Modolo authored 3 years ago
  
  d448ef6a
May 26, 2021
- emaze: change imput from gtf to fasta to compute transcript length · 4eef1122
  Laurent Modolo authored 3 years ago
  
  4eef1122