Ecosyste.ms: Issues

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GitHub / nf-core/crisprseq issues and pull requests

#78 - add metromap targeted modifications

Pull Request - State: open - Opened by mirpedrol about 1 year ago - 1 comment

#77 - Important! Template update for nf-core/tools v2.10

Pull Request - State: open - Opened by nf-core-bot about 1 year ago

#76 - fix modules bwa_index and bowtie2_build after module update

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

#75 - Report plots docs

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

#74 - Add more report plots

Pull Request - State: closed - Opened by mirpedrol about 1 year ago - 3 comments

#73 - Targeted pipeline does not work with BWA

Issue - State: closed - Opened by npatel-ah about 1 year ago - 2 comments
Labels: bug

#72 - template based edits are always zero and way to increase sensitivity

Issue - State: open - Opened by npatel-ah about 1 year ago - 4 comments
Labels: enhancement

#71 - example file for `--rra_contrasts`

Issue - State: open - Opened by zhouzhendiao about 1 year ago
Labels: bug

#70 - Dont save reference files and other intermediate output files

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

#69 - Rename merging summary

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

#68 - if count_table given don't ask for input or library

Issue - State: open - Opened by LaurenceKuhl over 1 year ago
Labels: bug

#67 - Don't stash unexistent files

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

#66 - Fix resume

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

#65 - Remove samtools/faidx

Pull Request - State: closed - Opened by mirpedrol over 1 year ago - 2 comments

#64 - Extend multiqc report

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

#63 - Add --control-sgrna parameter for megeck count

Issue - State: open - Opened by zhouzhendiao over 1 year ago - 2 comments
Labels: enhancement

#61 - ERROR ~ No such variable: ch_library

Issue - State: open - Opened by zhouzhendiao over 1 year ago - 3 comments
Labels: bug

#60 - Add BAGEL2 functionality

Pull Request - State: open - Opened by LaurenceKuhl over 1 year ago - 2 comments

#59 - Integrate Bagel2

Issue - State: open - Opened by LaurenceKuhl over 1 year ago
Labels: enhancement

#58 - Use `Channel.fromSamplesheet()` from `nf-validation` plugin

Pull Request - State: closed - Opened by mirpedrol over 1 year ago - 2 comments

#57 - Bump dev version

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

#56 - fix bug full_test

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

#55 - Add test_screening_full.config in the config file

Pull Request - State: closed - Opened by LaurenceKuhl over 1 year ago - 2 comments

#54 - Run test_Targeted when using `-profile test`

Pull Request - State: closed - Opened by mirpedrol over 1 year ago - 2 comments

#53 - Use `Channel.fromSamplesheet()` from `nf-validation`

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

#52 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#51 - Release review

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

#50 - remove profile aws_tower

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

#49 - Improve metro map

Issue - State: open - Opened by mirpedrol over 1 year ago
Labels: enhancement

#48 - Split AWS fulltests in two separate files

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

#47 - Add mageck and crisprcleanr in the citations

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

#46 - UMI steps to subworkflows

Issue - State: open - Opened by mirpedrol over 1 year ago
Labels: enhancement, good-first-issue

#45 - Add new parameters `--reference` and `--protospacer`

Pull Request - State: closed - Opened by mirpedrol over 1 year ago - 2 comments

#44 - Release review

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

#43 - Is there a way to specify a common reference genome and run the analysis without protospacer

Issue - State: closed - Opened by npatel-ah over 1 year ago - 3 comments
Labels: enhancement

#42 - Improve docs

Pull Request - State: closed - Opened by mirpedrol over 1 year ago - 3 comments

#41 - Dev > Master for v2.0.0

Pull Request - State: closed - Opened by LaurenceKuhl over 1 year ago - 2 comments

#40 - modify readme

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

#39 - use new github style of dark mode images

Pull Request - State: closed - Opened by mashehu over 1 year ago - 2 comments

#38 - bump version to 2.0.0 and update changelog

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

#37 - Full screening config file for aws

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

#36 - fix image links

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

#35 - add tube map

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

#34 - move sub-docs into subdirectories

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

#33 - crisprcleanr output added in the main.nf and docs

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

#32 - Review Docs from #30

Pull Request - State: closed - Opened by mirpedrol over 1 year ago - 2 comments

#31 - change name of certain params for more clarity

Pull Request - State: closed - Opened by LaurenceKuhl over 1 year ago - 2 comments

#30 - Add screening analysis

Pull Request - State: closed - Opened by LaurenceKuhl over 1 year ago - 3 comments

#29 - Add documentation

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

#28 - Add nf-test

Issue - State: open - Opened by mirpedrol over 1 year ago
Labels: enhancement

#27 - Merge workflows targeted & screening

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

#26 - tiny markdown fixes

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

#25 - alias all includes of MINIMAP2_ALIGN

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

#24 - Add UMI clustering

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

#23 - Replace System.exit(1)

Issue - State: closed - Opened by mirpedrol over 1 year ago - 2 comments
Labels: bug

#22 - Adding functional genomics

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

#21 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#20 - Alignment subworkflows

Issue - State: open - Opened by mirpedrol over 1 year ago
Labels: enhancement, good-first-issue

#19 - UMI extraction

Issue - State: open - Opened by mirpedrol over 1 year ago
Labels: enhancement

#18 - Reduce cigar parser R script

Issue - State: open - Opened by mirpedrol over 1 year ago
Labels: enhancement

#17 - Add mock samples

Issue - State: open - Opened by mirpedrol over 1 year ago
Labels: enhancement

#16 - Add UMIs

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

#15 - Add spikes functionality

Issue - State: open - Opened by mirpedrol over 1 year ago
Labels: enhancement

#14 - Add Zenodo DOI master -> dev

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

#13 - Bump to 1.1dev

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

#12 - Bump to v1.0

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

#11 - bump to v1.0

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

#10 - dump to v1.0

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

#9 - Changes to include indels and templates count recovery

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

#8 - Apply changes from code review

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

#7 - bump version to 1.0

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

#6 - Template processes only run when a template is provided

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

#5 - First release

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

#4 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 2 comments

#3 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#2 - Important! Template update for nf-core/tools v2.6

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 2 comments

#1 - First version of the pipeline

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