Commits · ad8474e6577d8999e0ab99d9aaf039a38c306c58 · Xavier Grand / ChIPster

Feb 18, 2021
- fastp: fix output to capture json files · ad8474e6
  Laurent Modolo authored 4 years ago
  
  ad8474e6
- add multiqc 1.9 · 819684ce
  Laurent Modolo authored 4 years ago
  
  819684ce
- fastp: add json output for multiqc · 9cc57a97
  Laurent Modolo authored 4 years ago
  
  9cc57a97
- multiqc: fix typo :7 · 6faa2900
  Laurent Modolo authored 4 years ago
  
  6faa2900
- macs2: fix mfold option · 8c295a37
  Laurent Modolo authored 4 years ago
  
  8c295a37
- multiqc: add publishDir · 00e1e797
  Laurent Modolo authored 4 years ago
  
  00e1e797
- bedtools: add merge_bed process · 9ec0803c
  Laurent Modolo authored 4 years ago
  
  9ec0803c
- fastp: add fastp 0.20.1 · 5b444810
  Laurent Modolo authored 4 years ago
  
  5b444810
- macs2: rm mfold param · d115c1c1
  Laurent Modolo authored 4 years ago
  
  d115c1c1
- macs2: fix macs call cmd · 88b5f2d5
  Laurent Modolo authored 4 years ago
  
  88b5f2d5
- macs2.nf: fix processes to match macs3 · 7d01e0e0
  Laurent Modolo authored 4 years ago
  
  7d01e0e0
- macs3: add mfold option · d41a1c90
  Laurent Modolo authored 4 years ago
  
  d41a1c90
- macs3: fix gsize parameter · 4f37c0be
  Laurent Modolo authored 4 years ago
  
  4f37c0be
- macs3: change queue option to mono_cpus · 558ec8ce
  Laurent Modolo authored 4 years ago
  
  558ec8ce
- macs3: fix call-summits option · 2f8070de
  Laurent Modolo authored 4 years ago
  
  2f8070de
- macs3: test new syntax for options · bd7dec8f
  Laurent Modolo authored 4 years ago
  
  bd7dec8f
- macs3: fix call cmd · c4218fde
  Laurent Modolo authored 4 years ago
  
  c4218fde
- macs3: add default gsize · 62e7c32c
  Laurent Modolo authored 4 years ago
  
  62e7c32c
- macs3: fix file names · 8d12bcf2
  Laurent Modolo authored 4 years ago
  
  8d12bcf2
- macs3: fix awk cmd · eab763e8
  Laurent Modolo authored 4 years ago
  
  eab763e8
- macs3: add main.nf · 0d885dcd
  Laurent Modolo authored 4 years ago
  
  0d885dcd
Feb 17, 2021
- gatk3: add new processes · 1207cdab
  Laurent Modolo authored 4 years ago
  
  1207cdab
- gatk3: fix variant calling · eddc374c
  Laurent Modolo authored 4 years ago
  
  eddc374c
- samtools: modify output name of merge_multi_bam · cd23e1e3
  Laurent Modolo authored 4 years ago
  
  cd23e1e3
- samtools: add process to merge multiple bam · ff5c7a24
  Laurent Modolo authored 4 years ago
  
  ff5c7a24
Feb 15, 2021
- fix bwa indexing · 21f39466
  Laurent Modolo authored 4 years ago
  
  21f39466
- typo in gatk3 to DSL2 · 23755281
  Laurent Modolo authored 4 years ago
  
  23755281
- add gatk3 to DSL2 · 4a115a8a
  Laurent Modolo authored 4 years ago
  
  4a115a8a
- update picard samtools and bwa for DSL2 · 7a17de40
  Laurent Modolo authored 4 years ago
  
  7a17de40
Feb 10, 2021
- nf_modules: add ucsc bg to bw fix output · 59f8cb0a
  Laurent Modolo authored 4 years ago
  
  59f8cb0a
- nf_modules: add ucsc bg to bw sorting step · b16d01fc
  Laurent Modolo authored 4 years ago
  
  b16d01fc
- nf_modules: add ucsc bg to bw · b0f22ec2
  Laurent Modolo authored 4 years ago
  
  b0f22ec2
Feb 04, 2021
- nf_modules: add bam to bedgraph and change deeptools version · ef37d983
  Laurent Modolo authored 4 years ago
  
  ef37d983
Feb 03, 2021
- nf_module: remove publishDir instruction · ed7fec13
  Laurent Modolo authored 4 years ago
  
  ed7fec13
- fastqc: main.nf cleanup code · 0a08b991
  Laurent Modolo authored 4 years ago
  
  0a08b991
- samtools: main.nf clarify bam_index output1 · b9d4fdda
  Laurent Modolo authored 4 years ago
  
  b9d4fdda
- samtools: test for indexing · ed50e0a0
  Laurent Modolo authored 4 years ago
  
  ed50e0a0
Jan 29, 2021
- nf_modules: update output tuple to handle list as file_id · 28a831bf
  Laurent Modolo authored 4 years ago
  
  28a831bf
- samtools: change file_id to bam.simpleName · 0dff7e33
  Laurent Modolo authored 4 years ago
  
  0dff7e33
- docker: add samtools v1.11 · 962ac77e
  Laurent Modolo authored 4 years ago
  
  962ac77e