Ecosyste.ms: Issues

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GitHub / sequana/lora issues and pull requests

#66 - checkm fails if there is space in the species name

Issue - State: open - Opened by cokelaer 8 months ago
Labels: bug

#66 - checkm fails if there is space in the species name

Issue - State: open - Opened by cokelaer 8 months ago
Labels: bug

#65 - add precommit, update flye container, small fixes

Pull Request - State: closed - Opened by cokelaer 11 months ago

#65 - add precommit, update flye container, small fixes

Pull Request - State: closed - Opened by cokelaer 11 months ago

#64 - rename workflows correctly

Pull Request - State: closed - Opened by cokelaer 11 months ago

#64 - rename workflows correctly

Pull Request - State: closed - Opened by cokelaer 11 months ago

#62 - Provide latest version of flye

Issue - State: closed - Opened by cokelaer 12 months ago - 1 comment

#62 - Provide latest version of flye

Issue - State: closed - Opened by cokelaer 12 months ago - 1 comment

#61 - add option to set sequana_coverage on

Issue - State: closed - Opened by cokelaer 12 months ago
Labels: enhancement

#61 - add option to set sequana_coverage on

Issue - State: closed - Opened by cokelaer 12 months ago
Labels: enhancement

#60 - Add multiqc,unicycler, update to use click

Pull Request - State: closed - Opened by cokelaer 12 months ago

#60 - Add multiqc,unicycler, update to use click

Pull Request - State: closed - Opened by cokelaer 12 months ago

#59 - Fixing CI workflow

Pull Request - State: closed - Opened by cokelaer about 1 year ago

#59 - Fixing CI workflow

Pull Request - State: closed - Opened by cokelaer about 1 year ago

#58 - add checkm software

Pull Request - State: closed - Opened by cokelaer about 1 year ago

#58 - add checkm software

Pull Request - State: closed - Opened by cokelaer about 1 year ago

#57 - cleanup .keras in Makefile

Issue - State: closed - Opened by cokelaer about 1 year ago

#57 - cleanup .keras in Makefile

Issue - State: closed - Opened by cokelaer about 1 year ago

#56 - set apptainers in the config

Issue - State: closed - Opened by cokelaer about 1 year ago

#56 - set apptainers in the config

Issue - State: closed - Opened by cokelaer about 1 year ago

#55 - set wrappers in the config

Issue - State: closed - Opened by cokelaer about 1 year ago

#55 - set wrappers in the config

Issue - State: closed - Opened by cokelaer about 1 year ago

#54 - get version from apptainer & update rulegraph

Pull Request - State: closed - Opened by ddesvillechabrol over 1 year ago - 1 comment

#54 - get version from apptainer & update rulegraph

Pull Request - State: closed - Opened by ddesvillechabrol over 1 year ago - 1 comment

#52 - set input for nanopore to fastq, fix min-rq type

Pull Request - State: closed - Opened by cokelaer over 1 year ago - 1 comment

#52 - set input for nanopore to fastq, fix min-rq type

Pull Request - State: closed - Opened by cokelaer over 1 year ago - 1 comment

#51 - some cleanup

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#51 - some cleanup

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#50 - Use poetry

Pull Request - State: closed - Opened by ddesvillechabrol over 1 year ago

#50 - Use poetry

Pull Request - State: closed - Opened by ddesvillechabrol over 1 year ago

#49 - move rulegraph inside main snakefile

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#49 - move rulegraph inside main snakefile

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#48 - rulegraph not created

Issue - State: closed - Opened by cokelaer over 1 year ago

#48 - rulegraph not created

Issue - State: closed - Opened by cokelaer over 1 year ago

#47 - replace denovo_tools by quast in apptainers

Issue - State: closed - Opened by cokelaer over 1 year ago

#47 - replace denovo_tools by quast in apptainers

Issue - State: closed - Opened by cokelaer over 1 year ago

#46 - add more containers and small refactoring

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#46 - add more containers and small refactoring

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#45 - add apptainers

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#45 - add apptainers

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#44 - Add polishing nanopore

Pull Request - State: closed - Opened by ddesvillechabrol over 2 years ago

#44 - Add polishing nanopore

Pull Request - State: closed - Opened by ddesvillechabrol over 2 years ago

#43 - add medaka_consensus & use profile

Pull Request - State: closed - Opened by ddesvillechabrol over 2 years ago

#43 - add medaka_consensus & use profile

Pull Request - State: closed - Opened by ddesvillechabrol over 2 years ago

#42 - Add polypolish

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 3 comments

#42 - Add polypolish

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 3 comments

#41 - scheme for integration of polishing step

Pull Request - State: closed - Opened by ddesvillechabrol over 2 years ago

#41 - scheme for integration of polishing step

Pull Request - State: closed - Opened by ddesvillechabrol over 2 years ago

#40 - Replace tailwindcss cdn with a builded one

Issue - State: open - Opened by ddesvillechabrol over 2 years ago
Labels: enhancement

#40 - Replace tailwindcss cdn with a builded one

Issue - State: open - Opened by ddesvillechabrol over 2 years ago
Labels: enhancement

#39 - Add Polypolish

Issue - State: closed - Opened by ddesvillechabrol over 2 years ago
Labels: enhancement

#39 - Add Polypolish

Issue - State: closed - Opened by ddesvillechabrol over 2 years ago
Labels: enhancement

#38 - Add Homopolish

Issue - State: closed - Opened by ddesvillechabrol over 2 years ago - 1 comment
Labels: enhancement

#38 - Add Homopolish

Issue - State: closed - Opened by ddesvillechabrol over 2 years ago - 1 comment
Labels: enhancement

#37 - Add Medaka

Issue - State: closed - Opened by ddesvillechabrol over 2 years ago
Labels: enhancement

#37 - Add Medaka

Issue - State: closed - Opened by ddesvillechabrol over 2 years ago
Labels: enhancement

#36 - Busco v5.3

Issue - State: open - Opened by ddesvillechabrol over 2 years ago
Labels: bug

#36 - Busco v5.3

Issue - State: open - Opened by ddesvillechabrol over 2 years ago
Labels: bug

#35 - Use tailwind instead of bulma

Pull Request - State: closed - Opened by ddesvillechabrol over 2 years ago

#35 - Use tailwind instead of bulma

Pull Request - State: closed - Opened by ddesvillechabrol over 2 years ago

#34 - Create summary page

Pull Request - State: closed - Opened by ddesvillechabrol almost 3 years ago

#34 - Create summary page

Pull Request - State: closed - Opened by ddesvillechabrol almost 3 years ago

#33 - Blast only contig subset

Pull Request - State: closed - Opened by ddesvillechabrol almost 3 years ago

#33 - Blast only contig subset

Pull Request - State: closed - Opened by ddesvillechabrol almost 3 years ago

#32 - polishing tool for nanopore

Issue - State: closed - Opened by cokelaer almost 3 years ago
Labels: enhancement

#32 - polishing tool for nanopore

Issue - State: closed - Opened by cokelaer almost 3 years ago
Labels: enhancement

#31 - Improvement to the UI , small HTML change, multiqc modules added

Pull Request - State: closed - Opened by cokelaer almost 3 years ago - 1 comment
Labels: enhancement

#31 - Improvement to the UI , small HTML change, multiqc modules added

Pull Request - State: closed - Opened by cokelaer almost 3 years ago - 1 comment
Labels: enhancement

#30 - limit blast to first 100 contigs ?

Issue - State: closed - Opened by cokelaer almost 3 years ago
Labels: enhancement

#29 - include eukaryotes/prokaryotes option compulsary

Issue - State: closed - Opened by cokelaer almost 3 years ago
Labels: enhancement

#29 - include eukaryotes/prokaryotes option compulsary

Issue - State: closed - Opened by cokelaer almost 3 years ago
Labels: enhancement

#28 - links towards sequana_coverage and quast

Issue - State: closed - Opened by cokelaer almost 3 years ago
Labels: enhancement

#28 - links towards sequana_coverage and quast

Issue - State: closed - Opened by cokelaer almost 3 years ago
Labels: enhancement

#27 - update canu options & add circlator force option

Pull Request - State: closed - Opened by ddesvillechabrol almost 3 years ago

#27 - update canu options & add circlator force option

Pull Request - State: closed - Opened by ddesvillechabrol almost 3 years ago

#26 - missing seqtk in requirements

Issue - State: closed - Opened by cokelaer almost 3 years ago

#26 - missing seqtk in requirements

Issue - State: closed - Opened by cokelaer almost 3 years ago

#25 - fix rulegraph & setup.py

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago

#25 - fix rulegraph & setup.py

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago

#24 - imporvements in the main script

Issue - State: closed - Opened by cokelaer about 3 years ago
Labels: enhancement

#24 - imporvements in the main script

Issue - State: closed - Opened by cokelaer about 3 years ago
Labels: enhancement

#23 - Fixing #22, #21 and #20

Pull Request - State: closed - Opened by cokelaer about 3 years ago

#23 - Fixing #22, #21 and #20

Pull Request - State: closed - Opened by cokelaer about 3 years ago

#22 - add the rulegraph rule

Issue - State: closed - Opened by cokelaer about 3 years ago

#22 - add the rulegraph rule

Issue - State: closed - Opened by cokelaer about 3 years ago

#21 - config minimap2 section change asm20 to map-pb

Issue - State: closed - Opened by cokelaer about 3 years ago

#21 - config minimap2 section change asm20 to map-pb

Issue - State: closed - Opened by cokelaer about 3 years ago

#19 - fix pipeline using input_directory

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago

#19 - fix pipeline using input_directory

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago

#18 - Add flye assembler

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago

#18 - Add flye assembler

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago

#17 - Add flye

Issue - State: closed - Opened by ddesvillechabrol about 3 years ago
Labels: enhancement

#17 - Add flye

Issue - State: closed - Opened by ddesvillechabrol about 3 years ago
Labels: enhancement

#16 - add merge data after ccs generation

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago - 1 comment

#16 - add merge data after ccs generation

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago - 1 comment

#15 - Add ci fix requirements

Pull Request - State: closed - Opened by cokelaer about 3 years ago