Commits · cb0e17b290aba0d1e5d8128011fd65fc20460782 · ESB / ONT_pilot_gitlab · GitLab

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Jul 23, 2020
- updated GDB contig files · cb0e17b2
  Valentina Galata authored 4 years ago
  
  cb0e17b2
- adjusted annotation step (issue #66 , not tested yet) · 4d60da61
  Valentina Galata authored 4 years ago
  
  4d60da61
- cleanup: replace out/err log by log; changed params for metaquast · 57bd9934
  Valentina Galata authored 4 years ago
  
  57bd9934
- cleanup: replace out/err log by log · 5fbb942a
  Valentina Galata authored 4 years ago
  
  5fbb942a
- added contig filtering (not adjusted yet) (issue #66 ) · 73b62b1d
  Valentina Galata authored 4 years ago
  
  73b62b1d
Jul 22, 2020
- report update (incl metat polished assemblies) (issue #52 ) · 680d8114
  Valentina Galata authored 4 years ago
  
  680d8114
- cleaned up GDB config · c20052fd
  Valentina Galata authored 4 years ago
  
  c20052fd
- updated GDB config files · 4ee61449
  Valentina Galata authored 4 years ago
  
  4ee61449
- assembly polishing w/ racon and metat (issue #52 ) · 7778266f
  Valentina Galata authored 4 years ago
  
  7778266f
Jul 20, 2020
- added notes (short scripts etc.) incl. scripts for issue #65 · ea06388a
  Valentina Galata authored 4 years ago
  
  ea06388a
- cleanup: rm backup files · 411efdef
  Valentina Galata authored 4 years ago
  
  411efdef
- report: added diamond density plot · 3bf391ef
  Valentina Galata authored 4 years ago
  
  3bf391ef
Jul 17, 2020
- added mash screen analysis (issue #64 ) · 04c4ddd4
  Valentina Galata authored 4 years ago
  
  04c4ddd4
- updated slurm.yaml for GIS20: longer runtime for mapping_assembly_uniq · e12bfc99
  Valentina Galata authored 4 years ago
  
  e12bfc99
Jul 16, 2020
- updated configs: updated mapping rule names in slurm configs; other minor changes · b97da7d9
  Valentina Galata authored 4 years ago
  
  b97da7d9
Jul 14, 2020
- updated configs for ganges dataset (issue #60 ) · 6a052006
  Valentina Galata authored 4 years ago
  
  6a052006
- forgot to rm mapping and coverage from assembly step · d6f1b932
  Valentina Galata authored 4 years ago
  
  d6f1b932
Jul 13, 2020
- updated ganges config files; fixed a bug in init.smk and basecalling.smk · 708d8bf5
  Valentina Galata authored 4 years ago
  
  708d8bf5
- updated ganges config.yaml (merged); changed how input files are linked · a538f7b8
  Valentina Galata authored 4 years ago
  
  a538f7b8
- changed how input files are linked · 91629224
  Valentina Galata authored 4 years ago
  
  91629224
- updated ganges config.yaml · 7d13fd2c
  Valentina Galata authored 4 years ago
  
  7d13fd2c
- config files etc for ganges sample · 92935da4
  Susheel Busi authored 4 years ago
  
  92935da4
- added configs for GIS20 (issue #57 ) · ee9d2237
  Valentina Galata authored 4 years ago
  
  ee9d2237
- minor changes in sbatch.sh (GDB, Zymo) · 6809a185
  Valentina Galata authored 4 years ago
  
  6809a185
- renamed in config/: Zymo-GridION-EVEN-BB-SN to Zymo · 8d46c000
  Valentina Galata authored 4 years ago
  
  8d46c000
- report: added mash figure (ssiue #59 ) · 9356b17e
  Valentina Galata authored 4 years ago
  
  9356b17e
- updated fastqc.yaml · 86830543
  Valentina Galata authored 4 years ago
  
  86830543
- updated gitignore · 67f2f168
  Valentina Galata authored 4 years ago
  
  67f2f168
- changed init: fixed a bug in init.smk (issue #56 ) · bff8c0dd
  Valentina Galata authored 4 years ago
  
  bff8c0dd
- changed init: fixed a bug in init.smk (issue #56 ) · ec1816ee
  Valentina Galata authored 4 years ago
  
  ec1816ee
- changed init: fixed a bug and rm unsed file (issue #56 ) · 88ea9a0d
  Valentina Galata authored 4 years ago
  
  88ea9a0d
- changed init: LR can have FASTQ (instead of FAST5); updated configs (issue... · e41852d5
  Valentina Galata authored 4 years ago
  
  changed init: LR can have FASTQ (instead of FAST5); updated configs (issue #56); other minor changes
  e41852d5
- updated config.yaml for GDB and mock · b5ad0b08
  Valentina Galata authored 4 years ago
  
  b5ad0b08
- init.smk for workflow and workflow_report · 0171c350
  Valentina Galata authored 4 years ago
  
  0171c350
Jul 10, 2020
- updated mash rules (issue #58 ) · 3f9425a4
  Valentina Galata authored 4 years ago
  
  3f9425a4
Jul 09, 2020
- added mash analysis (issue #58 ) · e08b0f30
  Valentina Galata authored 4 years ago
  
  e08b0f30
- added circ_contigs_fasta.py (issue #53 ); added kraken2 (tax) (issue #55 ) · 334acc25
  Valentina Galata authored 4 years ago
  
  334acc25
- blast-based analysis: find putative circ contigs (issue #53 ) · 1ebb366e
  Valentina Galata authored 4 years ago
  
  1ebb366e
- report: exclude metat if no data provided · 8e79f28c
  Valentina Galata authored 4 years ago
  
  8e79f28c
- updated Zymo-GridION-EVEN-BB-SN/sbatch.sh · abc1d13b
  Valentina Galata authored 4 years ago
  
  abc1d13b