Commits · 92935da48497f2834404a9eb62e436eb73fcb167 · ESB / ONT_pilot_gitlab · GitLab

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Jul 13, 2020
- 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
- mv config/sbatch.sh to sub-folder Zymo-GridION-EVEN-BB-SN · 931d24db
  Valentina Galata authored 4 years ago
  
  931d24db
- Merge branch 'cleanup' of... · 345e3f67
  Valentina Galata authored 4 years ago
  
  Merge branch 'cleanup' of ssh://git-r3lab-server.uni.lu:8022/susheel.busi/ont_pilot_gitlab into cleanup Adding Susheel's changes for the mock sample (config files)
  345e3f67
- i don't know what I'm doing · 8b0e2efd
  Susheel Busi authored 4 years ago
  
  8b0e2efd
- updated slurm file for MOCK run · 6ccd4acc
  Susheel Busi authored 4 years ago
  
  6ccd4acc
- updated sbatch file for MOCK run · f6f57407
  Susheel Busi authored 4 years ago
  
  f6f57407
Jul 08, 2020
- mv not used scripts in workflow/ to a backup folder · fb600249
  Valentina Galata authored 4 years ago
  
  fb600249
- updated sbatch.sh for GDB · 2362a407
  Valentina Galata authored 4 years ago
  
  2362a407
- added slurm.yaml for Zymo-GridION-EVEN-BB-SN; rm not used configs · c6afa55b
  Valentina Galata authored 4 years ago
  
  c6afa55b
Jul 07, 2020
- slurm.yaml file updated for Zymo-MOCK-EVEN sample increasing time limit for bwa_mem_assembly · 82fd036f
  Susheel Busi authored 4 years ago
  
  82fd036f
- Issue #48 - exporting PERL5LIB issue fixed for casc · 4d2e96cd
  Susheel Busi authored 4 years ago
  
  4d2e96cd
- Merge branch 'cleanup' of https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab into cleanup · 721983a9
  Susheel Busi authored 4 years ago
  
  721983a9
- rm symlink in polishing_lr_medaka · 40b1be70
  Valentina Galata authored 4 years ago
  
  40b1be70
Jul 02, 2020
- report: minor changed in cdhit figure · c33301f8
  Valentina Galata authored 4 years ago
  
  c33301f8
- report: cdhit figure; rm not used/old scripts · 3472b20a
  Valentina Galata authored 4 years ago
  
  3472b20a
- report: diamond: fig w/o log10 and zoomed in (issue #22 ) · a19c935c
  Valentina Galata authored 4 years ago
  
  a19c935c
- workflow: rm partial gene counts rule from analysis (issue #50 ) · 95f70fe7
  Valentina Galata authored 4 years ago
  
  95f70fe7
- report: update for diamond/prodigal figures · d935fc15
  Valentina Galata authored 4 years ago
  
  d935fc15
- report: added total/partial gene counts (prodigal) (issue #50 ) · 347a86b8
  Valentina Galata authored 4 years ago
  
  347a86b8
- report: diamond query/subject length ratio (issue #22 ) · d876006c
  Valentina Galata authored 4 years ago
  
  d876006c
- report: added pct values to mappability barplots (issue #23 ) · 62dc23c4
  Valentina Galata authored 4 years ago
  
  62dc23c4
- Merge branch 'cleanup' of https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab into cleanup · 7ef88cb9
  Susheel Busi authored 4 years ago
  
  7ef88cb9