sequana/sequana-wrappers issues and pull requests

#49 - Adding trinity_quantify (using kallisto)

Pull Request - State: closed - Opened by khourhin almost 3 years ago - 1 comment

#48 - set depth log & multiqc params as optional

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

#48 - set depth log & multiqc params as optional

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

#47 - fix copy_requirements

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

#46 - Adding Trinity/Hmmer + tests

Pull Request - State: closed - Opened by khourhin almost 3 years ago - 1 comment

#46 - Adding Trinity/Hmmer + tests

Pull Request - State: closed - Opened by khourhin almost 3 years ago - 1 comment

#45 - Add blast stub and adapt bowtie2 wrapper

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

#45 - Add blast stub and adapt bowtie2 wrapper

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

#44 - Add mark duplicates and macs3

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

#44 - Add mark duplicates and macs3

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

#43 - wrapper mark_duplicates to be added

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

#43 - wrapper mark_duplicates to be added

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

#42 - Digital normalisation

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

#42 - Digital normalisation

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

#41 - add digital normalisation

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

#41 - add digital normalisation

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

#40 - update test for sequana_coverage

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

#40 - update test for sequana_coverage

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

#39 - Fix missing gbk

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

#39 - Fix missing gbk

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

#38 - Fix Bowtie2 wrapper and add SAF support for featureCounts

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

#38 - Fix Bowtie2 wrapper and add SAF support for featureCounts

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

#37 - Update wrappers docs

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

#36 - Check value to avoid pathlib default

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

#36 - Check value to avoid pathlib default

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

#35 - Wrappers documentation

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

#35 - Wrappers documentation

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

#34 - refacto rulegraph & add local files links

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

#34 - refacto rulegraph & add local files links

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

#33 - Documentation

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

#32 - in sequana_coverage rule, use the standalone instead of python code

Issue - State: closed - Opened by cokelaer about 3 years ago - 1 comment
Labels: enhancement

#32 - in sequana_coverage rule, use the standalone instead of python code

Issue - State: closed - Opened by cokelaer about 3 years ago - 1 comment
Labels: enhancement

#31 - Variant related

Pull Request - State: closed - Opened by cokelaer over 3 years ago - 1 comment

#31 - Variant related

Pull Request - State: closed - Opened by cokelaer over 3 years ago - 1 comment

#30 - wrapper: macs3

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

#30 - wrapper: macs3

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

#29 - wrapper: homer

Issue - State: open - Opened by cokelaer over 3 years ago

#29 - wrapper: homer

Issue - State: open - Opened by cokelaer over 3 years ago

#28 - wrappers: add_read_group + snpeff_add_locus , etc

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

#28 - wrappers: add_read_group + snpeff_add_locus , etc

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

#27 - Update CI action

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

#27 - Update CI action

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

#26 - Feature counts and bowtie updates

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

#26 - Feature counts and bowtie updates

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

#25 - Feature counts and bowtie updates

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

#25 - Feature counts and bowtie updates

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

#24 - Doc

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

#24 - Doc

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

#23 - wrapper feature counts

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

#23 - wrapper feature counts

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

#22 - Add fastq stats and fixes

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

#22 - Add fastq stats and fixes

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

#21 - Fix consistency bwa/bowtie + add minimap2

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

#21 - Fix consistency bwa/bowtie + add minimap2

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

#20 - add minimap2

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

#20 - add minimap2

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

#19 - bowtie/bowtie2/bwa consistency

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

#18 - add bwa wrapper and tests

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

#18 - add bwa wrapper and tests

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

#17 - add files for bowtie1 build wrapper

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

#17 - add files for bowtie1 build wrapper

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

#16 - more wrappers: conda/bowti1

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

#16 - more wrappers: conda/bowti1

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

#15 - add bcl2fastq recipe

Pull Request - State: closed - Opened by cokelaer over 3 years ago - 6 comments

#15 - add bcl2fastq recipe

Pull Request - State: closed - Opened by cokelaer over 3 years ago - 6 comments

#14 - Inconsistency for options params

Issue - State: closed - Opened by ddesvillechabrol over 3 years ago - 1 comment

#14 - Inconsistency for options params

Issue - State: closed - Opened by ddesvillechabrol over 3 years ago - 1 comment

#13 - Compression

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

#13 - Compression

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

#12 - rules from sequana to integrate (possibly)

Issue - State: open - Opened by cokelaer over 3 years ago

#12 - rules from sequana to integrate (possibly)

Issue - State: open - Opened by cokelaer over 3 years ago

#11 - update doc

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

#11 - update doc

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

#10 - Falco

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

#10 - Falco

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

#9 - Wrappers to make compatible with previous sequana pipelines

Issue - State: closed - Opened by khourhin over 3 years ago

#9 - Wrappers to make compatible with previous sequana pipelines

Issue - State: closed - Opened by khourhin over 3 years ago

#8 - Adding snakemake wrappers

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

#8 - Adding snakemake wrappers

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

#7 - Fastqc

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

#7 - Fastqc

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

#6 - Wrappers to include

Issue - State: closed - Opened by khourhin over 3 years ago

#5 - import snakemake busco wrapper

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

#4 - remove maxThreads option if grid is used

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

#3 - Update .github/workflow/main.yml

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

#2 - Add canu wrapper

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

#1 - Setup git actions & tests

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

GitHub / sequana/sequana-wrappers issues and pull requests