├── .github └── workflows │ └── stubtest.yml ├── .gitignore ├── Dockerfile ├── README.md ├── configs ├── atlas.config ├── ceres.config ├── custom.config ├── publishdir.config ├── sge.config └── slurm.config ├── docs ├── Case_01.md ├── Case_02.md ├── Case_03.md ├── FAQ.md ├── GenomeScope2_online.pdf ├── Install.md ├── README.md ├── _config.yml ├── atlas_run.txt ├── case1_reports │ ├── report.step1.html │ ├── report.step2.html │ ├── timeline.step1.html │ └── timeline.step2.html ├── case3_reports │ ├── report.step1.html │ ├── report.step2.html │ ├── timeline.step1.html │ └── timeline.step2.html ├── imgs │ ├── Figure01.svg │ └── FigureS01.svg ├── reference │ └── README.md ├── report.html ├── report_atlas.html ├── report_ceres.html ├── timeline.html ├── timeline_atlas.html └── timeline_ceres.html ├── environment.yml ├── main.nf ├── modules ├── arrow.nf ├── busco.nf ├── freebayes.nf ├── helper_functions.nf ├── purge_dups.nf └── qv.nf ├── nextflow.config ├── other_dependencies.yml ├── submit_nf.slurm └── templates └── reshape_arrow.sh /.github/workflows/stubtest.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/.github/workflows/stubtest.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | env 2 | * 3 | *~ 4 | .* -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/Dockerfile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/README.md -------------------------------------------------------------------------------- /configs/atlas.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/configs/atlas.config -------------------------------------------------------------------------------- /configs/ceres.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/configs/ceres.config -------------------------------------------------------------------------------- /configs/custom.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/configs/custom.config -------------------------------------------------------------------------------- /configs/publishdir.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/configs/publishdir.config -------------------------------------------------------------------------------- /configs/sge.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/configs/sge.config -------------------------------------------------------------------------------- /configs/slurm.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/configs/slurm.config -------------------------------------------------------------------------------- /docs/Case_01.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/Case_01.md -------------------------------------------------------------------------------- /docs/Case_02.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/Case_02.md -------------------------------------------------------------------------------- /docs/Case_03.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/Case_03.md -------------------------------------------------------------------------------- /docs/FAQ.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/FAQ.md -------------------------------------------------------------------------------- /docs/GenomeScope2_online.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/GenomeScope2_online.pdf -------------------------------------------------------------------------------- /docs/Install.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/Install.md -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/_config.yml -------------------------------------------------------------------------------- /docs/atlas_run.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/atlas_run.txt -------------------------------------------------------------------------------- /docs/case1_reports/report.step1.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/case1_reports/report.step1.html -------------------------------------------------------------------------------- /docs/case1_reports/report.step2.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/case1_reports/report.step2.html -------------------------------------------------------------------------------- /docs/case1_reports/timeline.step1.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/case1_reports/timeline.step1.html -------------------------------------------------------------------------------- /docs/case1_reports/timeline.step2.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/case1_reports/timeline.step2.html -------------------------------------------------------------------------------- /docs/case3_reports/report.step1.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/case3_reports/report.step1.html -------------------------------------------------------------------------------- /docs/case3_reports/report.step2.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/case3_reports/report.step2.html -------------------------------------------------------------------------------- /docs/case3_reports/timeline.step1.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/case3_reports/timeline.step1.html -------------------------------------------------------------------------------- /docs/case3_reports/timeline.step2.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/case3_reports/timeline.step2.html -------------------------------------------------------------------------------- /docs/imgs/Figure01.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/imgs/Figure01.svg -------------------------------------------------------------------------------- /docs/imgs/FigureS01.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/imgs/FigureS01.svg -------------------------------------------------------------------------------- /docs/reference/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/reference/README.md -------------------------------------------------------------------------------- /docs/report.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/report.html -------------------------------------------------------------------------------- /docs/report_atlas.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/report_atlas.html -------------------------------------------------------------------------------- /docs/report_ceres.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/report_ceres.html -------------------------------------------------------------------------------- /docs/timeline.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/timeline.html -------------------------------------------------------------------------------- /docs/timeline_atlas.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/timeline_atlas.html -------------------------------------------------------------------------------- /docs/timeline_ceres.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/docs/timeline_ceres.html -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/environment.yml -------------------------------------------------------------------------------- /main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/main.nf -------------------------------------------------------------------------------- /modules/arrow.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/modules/arrow.nf -------------------------------------------------------------------------------- /modules/busco.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/modules/busco.nf -------------------------------------------------------------------------------- /modules/freebayes.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/modules/freebayes.nf -------------------------------------------------------------------------------- /modules/helper_functions.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/modules/helper_functions.nf -------------------------------------------------------------------------------- /modules/purge_dups.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/modules/purge_dups.nf -------------------------------------------------------------------------------- /modules/qv.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/modules/qv.nf -------------------------------------------------------------------------------- /nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/nextflow.config -------------------------------------------------------------------------------- /other_dependencies.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/other_dependencies.yml -------------------------------------------------------------------------------- /submit_nf.slurm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/submit_nf.slurm -------------------------------------------------------------------------------- /templates/reshape_arrow.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/isugifNF/polishCLR/HEAD/templates/reshape_arrow.sh --------------------------------------------------------------------------------