Commits · 87abd17d77bf85c235111b046b6b4096cfe0bb46 · Xavier Grand / ChIPster

Jun 29, 2021
- 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
  
  d22860c2
- 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
- alntools: separate transcript length computation · 6231fc3f
  Laurent Modolo authored 3 years ago
  
  6231fc3f
May 25, 2021
- gffread: add awk cmd to remove duplicated transcript · c355cfa8
  Laurent Modolo authored 3 years ago
  
  c355cfa8
May 21, 2021
- gffread: add -x and -M option · d62c64d2
  Laurent Modolo authored 3 years ago
  
  d62c64d2
- gffread: add -x option · b9a27794
  Laurent Modolo authored 3 years ago
  
  b9a27794
May 20, 2021
- gffread: add main.nf · 3dd05762
  Laurent Modolo authored 3 years ago
  
  3dd05762
May 18, 2021
- bowtie2: change file_id handling · 192fef09
  Laurent Modolo authored 3 years ago
  
  192fef09
May 17, 2021
- kb: fix missing \ at end of lines · 5a367584
  Laurent Modolo authored 3 years ago
  
  5a367584
May 11, 2021
- cutadapt: update output name and capture · cb215113
  Laurent Modolo authored 3 years ago
  
  cb215113
- cutadapt: update to last contributing guide version · 5af36606
  Laurent Modolo authored 3 years ago
  
  5af36606
May 10, 2021
- alntools: try fix for bam bai · 451c10bb
  Laurent Modolo authored 3 years ago
  
  451c10bb
May 07, 2021
- kb: remove view() · 972e601e
  Laurent Modolo authored 3 years ago
  
  972e601e
- flexi_splitter: split computation per plate · 1852fe84
  Laurent Modolo authored 3 years ago
  
  1852fe84
- flexi_splitter: fix tag :25 · 1d80497e
  Laurent Modolo authored 3 years ago
  
  1d80497e
- flexi_splitter: fixed group_fastq process · b92686a4
  Laurent Modolo authored 3 years ago
  
  b92686a4
May 06, 2021
- alntools: remove chunck option · 6cc2e1a8
  Laurent Modolo authored 3 years ago
  
  6cc2e1a8