Commits · 3b208403c75a3d1e4c843b53de65a5b90c1f51b6 · LBMC / nextflow · GitLab

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Feb 04, 2021
- docker: add deeptools 3.5.0 · 3b208403
  Laurent Modolo authored 4 years ago
  
  3b208403
- solution_RNASeq.nf: update command to launch pipe · 015419e5
  Laurent Modolo authored 4 years ago
  
  015419e5
- nextfow.config: update base default version · cfd71a7d
  Laurent Modolo authored 4 years ago
  
  cfd71a7d
- docker: add ucsc:407 · 81ab1116
  Laurent Modolo authored 4 years ago
  
  81ab1116
- 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
- samtools: fix flagstats cmd · ebb5cb65
  Laurent Modolo authored 4 years ago
  
  ebb5cb65
- samtools: change label for bam_stats · 42f56bde
  Laurent Modolo authored 4 years ago
  
  42f56bde
- samtools: add bam_stats process · a4d4bdb9
  Laurent Modolo authored 4 years ago
  
  a4d4bdb9
Jan 27, 2021
- nextflow.config: add memory limits · ebecfb6d
  Laurent Modolo authored 4 years ago
  
  ebecfb6d
- picard: fix uper memory limit to 30GB · 41f34c15
  Laurent Modolo authored 4 years ago
  
  41f34c15
- picard: fix bams var in main.nf · 988c4020
  Laurent Modolo authored 4 years ago
  
  988c4020
Jan 25, 2021
- bedtools: add bam_id val · 9cc39469
  Laurent Modolo authored 4 years ago
  
  9cc39469
- samtools: fix filter_bam_mapped · e3a42082
  Laurent Modolo authored 4 years ago
  
  e3a42082
- bedtools: bam_to_fastq emits tuple · 30d17edc
  Laurent Modolo authored 4 years ago
  
  30d17edc
- bedtools: fix bam_to_fastq script · 8338d66f
  Laurent Modolo authored 4 years ago
  
  8338d66f
- bedtools: fix tags · 5d11f90e
  Laurent Modolo authored 4 years ago
  
  5d11f90e
- samtools: fix catched bams names · 9f34d846
  Laurent Modolo authored 4 years ago
  
  9f34d846
- samtools: fix samtools version · a8e8560a
  Laurent Modolo authored 4 years ago
  
  a8e8560a
- bedtools: fix output value name for bam_to_fastq_pairedend · 2e62b247
  Laurent Modolo authored 4 years ago
  
  2e62b247
- bedtools: change bam_to_fastq_pairedend name to be more consistant · 41651a7a
  Laurent Modolo authored 4 years ago
  
  41651a7a
- fix input and output for bedtools and samtools · 8bebb4a1
  Laurent Modolo authored 4 years ago
  
  8bebb4a1
- bedtools: add bam to fastq convertion · 70c7d906
  Laurent Modolo authored 4 years ago
  
  70c7d906
- samtools: nf_module add mapped and unmapped filter · de331fa7
  Laurent Modolo authored 4 years ago
  
  de331fa7
- sratoolkit: rename main module · ce4c569e
  Laurent Modolo authored 4 years ago
  
  ce4c569e
- nf_module: sratoolkit add DSL2 · 5bc80c3d
  Laurent Modolo authored 4 years ago
  
  5bc80c3d
Jan 22, 2021
- nf_modules: add deeptools to DSL2 · 7b298e92
  Laurent Modolo authored 4 years ago
  
  7b298e92
- nf_modules: add sambamba to DSL2 · 94c41f30
  Laurent Modolo authored 4 years ago
  
  94c41f30
- nf_modules: add samtools DSL2 · 3de89ded
  Laurent Modolo authored 4 years ago
  
  3de89ded
- nf_modules: add picard · a3d3e95b
  Laurent Modolo authored 4 years ago
  
  a3d3e95b
- nf_modules: multiqc add DSL2 · fe874785
  Laurent Modolo authored 4 years ago
  
  fe874785
- nf_modules: fastqc add DSL2 · f172f456
  Laurent Modolo authored 4 years ago
  
  f172f456
- nf_modules: masc2 add DSL2 · a12e9229
  Laurent Modolo authored 4 years ago
  
  a12e9229
- nf_modules: add bowtie to DSL2 · 829ff319
  Laurent Modolo authored 4 years ago
  
  829ff319