Ecosyste.ms: Issues

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GitHub / sequana/rnaseq issues and pull requests

#47 - Update summary, pin sequana to use new plots

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

#46 - fix regressionm update pyproject

Pull Request - State: closed - Opened by cokelaer about 2 months ago

#45 - plot feature counts does not appear

Issue - State: closed - Opened by cokelaer 5 months ago
Labels: bug

#44 - Fix the default rRNA

Pull Request - State: closed - Opened by cokelaer 7 months ago - 1 comment

#42 - rRNA is set to empty string (regression)

Issue - State: closed - Opened by cokelaer 10 months ago
Labels: bug

#41 - Fix typo for multiqc bowtie2 paired reports

Pull Request - State: closed - Opened by cokelaer 10 months ago

#41 - Fix typo for multiqc bowtie2 paired reports

Pull Request - State: closed - Opened by cokelaer 10 months ago

#40 - change aligner -> aligner_choice to be sequanix comptabible

Issue - State: open - Opened by cokelaer 10 months ago
Labels: enhancement

#40 - change aligner -> aligner_choice to be sequanix comptabible

Issue - State: closed - Opened by cokelaer 10 months ago
Labels: enhancement

#39 - Fix bowtie1 regression (log).

Pull Request - State: closed - Opened by cokelaer 10 months ago - 1 comment

#39 - Fix bowtie1 regression (log).

Pull Request - State: closed - Opened by cokelaer 10 months ago - 1 comment

#38 - add rnaseqc container and update rseqc

Pull Request - State: closed - Opened by cokelaer 10 months ago - 1 comment

#38 - add rnaseqc container and update rseqc

Pull Request - State: closed - Opened by cokelaer 10 months ago - 1 comment

#37 - Refactorisation to use click

Pull Request - State: closed - Opened by cokelaer 10 months ago

#35 - Fix Annotation plot, add new expression plot

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

#34 - plot showing most expressed genes

Issue - State: closed - Opened by cokelaer almost 1 year ago - 1 comment
Labels: enhancement

#34 - plot showing most expressed genes

Issue - State: closed - Opened by cokelaer almost 1 year ago - 1 comment
Labels: enhancement

#34 - plot showing most expressed genes

Issue - State: closed - Opened by cokelaer almost 1 year ago - 1 comment
Labels: enhancement

#33 - fastp multiqc shows only 1 sample

Issue - State: closed - Opened by cokelaer almost 1 year ago - 1 comment
Labels: bug

#33 - fastp multiqc shows only 1 sample

Issue - State: closed - Opened by cokelaer almost 1 year ago - 1 comment
Labels: bug

#32 - Fixes #31 and #15

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

#32 - Fixes #31 and #15

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

#32 - Fixes #31 and #15

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

#31 - add option to not perform rRNA

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

#31 - add option to not perform rRNA

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

#31 - add option to not perform rRNA

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

#30 - Fix options not used in star_mapping

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

#30 - Fix options not used in star_mapping

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

#30 - Fix options not used in star_mapping

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

#29 - update new apptainer for graphviz

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

#28 - ashr required in new analysis. Need a new singularity

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

#28 - ashr required in new analysis. Need a new singularity

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

#28 - ashr required in new analysis. Need a new singularity

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

#27 - Fixing CI action (apptainer)

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

#27 - Fixing CI action (apptainer)

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

#26 - table in HTML reports limited to 20 comparisons

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

#26 - table in HTML reports limited to 20 comparisons

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

#26 - table in HTML reports limited to 20 comparisons

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

#25 - move containers in the config file

Pull Request - State: closed - Opened by cokelaer almost 2 years ago - 1 comment

#25 - move containers in the config file

Pull Request - State: closed - Opened by cokelaer almost 2 years ago - 1 comment

#25 - move containers in the config file

Pull Request - State: closed - Opened by cokelaer almost 2 years ago - 1 comment

#24 - update workflow to use fastp wrapper

Pull Request - State: closed - Opened by cokelaer almost 2 years ago - 1 comment

#24 - update workflow to use fastp wrapper

Pull Request - State: closed - Opened by cokelaer almost 2 years ago - 1 comment

#24 - update workflow to use fastp wrapper

Pull Request - State: closed - Opened by cokelaer almost 2 years ago - 1 comment

#23 - Improve output table csv file per comparison

Issue - State: open - Opened by khourhin almost 2 years ago - 1 comment
Labels: enhancement

#23 - Improve output table csv file per comparison

Issue - State: open - Opened by khourhin almost 2 years ago
Labels: enhancement

#22 - Fix python3.8 and 3.9 requirements

Pull Request - State: closed - Opened by cokelaer almost 2 years ago

#22 - Fix python3.8 and 3.9 requirements

Pull Request - State: closed - Opened by cokelaer almost 2 years ago

#21 - rnadiff directory should be cleaned from deset previous results when rerun with --force

Issue - State: closed - Opened by cokelaer almost 2 years ago - 1 comment
Labels: enhancement

#20 - remove upset plot if only one comparison is available

Issue - State: closed - Opened by cokelaer almost 2 years ago - 1 comment
Labels: question

#20 - remove upset plot if only one comparison is available

Issue - State: closed - Opened by cokelaer almost 2 years ago - 1 comment
Labels: question

#19 - Fix strand balance automatic selection bug

Pull Request - State: closed - Opened by cokelaer about 2 years ago - 1 comment
Labels: bug

#19 - Fix strand balance automatic selection bug

Pull Request - State: closed - Opened by cokelaer about 2 years ago - 1 comment
Labels: bug

#19 - Fix strand balance automatic selection bug

Pull Request - State: closed - Opened by cokelaer about 2 years ago - 1 comment
Labels: bug

#18 - config file not configure properly for sequanix

Issue - State: closed - Opened by cokelaer about 2 years ago - 1 comment
Labels: bug

#18 - config file not configure properly for sequanix

Issue - State: closed - Opened by cokelaer about 2 years ago - 1 comment
Labels: bug

#17 - Update CI and switch branch from master to main

Pull Request - State: closed - Opened by cokelaer about 2 years ago - 1 comment

#17 - Update CI and switch branch from master to main

Pull Request - State: closed - Opened by cokelaer about 2 years ago - 1 comment

#16 - Fixing CI

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

#16 - Fixing CI

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

#16 - Fixing CI

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

#15 - pipeline does not work if fastp rule is deactivate

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

#15 - pipeline does not work if fastp rule is deactivate

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

#14 - gene HTML tables are sometimes not appearing

Issue - State: closed - Opened by khourhin over 2 years ago - 1 comment

#14 - gene HTML tables are sometimes not appearing

Issue - State: closed - Opened by khourhin over 2 years ago - 1 comment

#14 - gene HTML tables are sometimes not appearing

Issue - State: closed - Opened by khourhin over 2 years ago - 1 comment

#13 - Update Readme to 0.15.1 (bowtie2 align wrapper update)

Pull Request - State: closed - Opened by khourhin over 2 years ago - 1 comment

#13 - Update Readme to 0.15.1 (bowtie2 align wrapper update)

Pull Request - State: closed - Opened by khourhin over 2 years ago - 1 comment

#12 - Error in rnaseq.rules

Issue - State: closed - Opened by PierreL-B over 2 years ago - 2 comments

#12 - Error in rnaseq.rules

Issue - State: closed - Opened by PierreL-B over 2 years ago - 2 comments

#12 - Error in rnaseq.rules

Issue - State: closed - Opened by PierreL-B over 2 years ago - 2 comments

#11 - error in bowtie2_index.rules

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

#11 - error in bowtie2_index.rules

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

#11 - error in bowtie2_index.rules

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

#10 - multiple feature counts

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment
Labels: enhancement

#10 - multiple feature counts

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment
Labels: enhancement

#10 - multiple feature counts

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment
Labels: enhancement

#9 - simplify start_mapping rule

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment

#9 - simplify start_mapping rule

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment

#9 - simplify start_mapping rule

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment

#8 - seg fault star mapping

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment
Labels: bug

#8 - seg fault star mapping

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment
Labels: bug

#8 - seg fault star mapping

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment
Labels: bug

#7 - Error in indexing : do not create SAIndex output file

Issue - State: closed - Opened by PierreL-B almost 4 years ago - 2 comments

#7 - Error in indexing : do not create SAIndex output file

Issue - State: closed - Opened by PierreL-B almost 4 years ago - 2 comments

#7 - Error in indexing : do not create SAIndex output file

Issue - State: closed - Opened by PierreL-B almost 4 years ago - 2 comments

#6 - large memory required in onsuccess when creating files from GFF file

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment

#6 - large memory required in onsuccess when creating files from GFF file

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment

#6 - large memory required in onsuccess when creating files from GFF file

Issue - State: closed - Opened by cokelaer almost 4 years ago - 1 comment

#5 - tolerance argument in get_most_probable_strand_consensus() function

Issue - State: closed - Opened by PierreL-B almost 4 years ago - 1 comment

#5 - tolerance argument in get_most_probable_strand_consensus() function

Issue - State: closed - Opened by PierreL-B almost 4 years ago - 1 comment

#5 - tolerance argument in get_most_probable_strand_consensus() function

Issue - State: closed - Opened by PierreL-B almost 4 years ago - 1 comment

#4 - pre-fill parameters related to indexing

Issue - State: closed - Opened by cokelaer about 4 years ago - 1 comment

#4 - pre-fill parameters related to indexing

Issue - State: closed - Opened by cokelaer about 4 years ago - 1 comment