WIP: Checkpoint snakefile
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added 1 commit
- 10ce73e6 - updated rules and workflows for running assembly with spades and mmseq comparisons
added 1 commit
- 87b28001 - updated mmseq plot scripts - working finally
added 1 commit
- f37ddcf7 - included scripts for mmseq plotting with metaspades
added 1 commit
- 73dd1bc8 - fixed awk error in the mmseq prepare files script
added 1 commit
- b97e0104 - fixed the metaspades overlap with mmseq plotting
added 1 commit
- 0b5d4048 - created new ANALYSIS_RULES and workflow for incorporating the cd-hit and quast analyses
added 1 commit
- 1ad79bf6 - updated the overal snakefiles including the with the ANALYSIS_RULES
added 1 commit
- ecdc09d4 - adding the script for coverage plots and the PLOT RULES created by CCL
added 1 commit
- 9cdb8210 - added rules for mappability_index and estimating unique_mapped_reads from BAM files
added 1 commit
- f0e70006 - added the CRISPR related environments, rules and modified the workflows and...
added 1 commit
- 2717c181 - cleaned up path exporting for rule/ANALYSIS_RULES and added to the config/CONFIG.yaml file
added 1 commit
- 51c5727f - edited the to fix the snakemake error - try # 14 million and one
added 1 commit
- e98663ed - fixed the path for the minced_CRISPR_output.txt file, and also fixed the CASC issue
added 1 commit
- aeb752cd - removing the date flag from CASC shell due to errors
added 19 commits
- 32df69ba - added plasflow (issue #28 (closed)): includes important updates of config and snakemake files
- 69406c10 - added .gitignore
- 5a7350e8 - added rgi (issue #29 (closed))
- 2ab9da0b - made FAA temp in rgi input rules; other minor changes (issue #29 (closed))
- 1e8401ff - config/import clean-up: analysis
- c574d4e1 - config/import clean-up: analysis
- 3ae1c1cc - config/import clean-up: assembly annotation
- 4bc62cb2 - config/import clean-up: assembly annotation
- 3b6ed7ed - config/import clean-up: binning
- 2f3f06fd - config/import clean-up: binning
- 5db187d4 - config/import clean-up: checkpoint assembly annotation
- a4b878ef - config/import clean-up: mapping
- e45e1d93 - config/import clean-up: metaT
- fb908557 - config/import clean-up: mmseq
- be7ed38b - config/import clean-up: plot
- 39b63d3e - config/import clean-up: taxonomy
- 00d122a1 - config/import clean-up
- ac10becd - config/import clean-up
- 1a42ca25 - Merge branch 'checkpoint_snakefile_VG' into 'checkpoint_snakefile'
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