From 4673818562b8578c145c9278fabdb75963f2a052 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Tue, 20 Aug 2024 16:00:55 +0200 Subject: [PATCH 1/4] Test --- CHANGELOG.md | 1 + README.md | 2 ++ .../crisprcleanr/normalize/crisprcleanr-normalize.diff | 8 ++++++-- modules/nf-core/crisprcleanr/normalize/main.nf | 3 ++- 4 files changed, 11 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8fafb666..2feb0c4c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fix cutadapt 3' and 5' no such variable found bug ([#187](https://github.com/nf-core/crisprseq/pull/187)) - Fix design matrix bug that introduced dots instead of a hyphen ([#190](https://github.com/nf-core/crisprseq/pull/190)) - Make output of FluteMLE optional as when some pathways produce bugs some channels are then empty ([#190](https://github.com/nf-core/crisprseq/pull/190)) +- Fix a typo in crisprcleanr/normalize, when a user inputs a file ### Deprecated diff --git a/README.md b/README.md index 99859c3e..efb18385 100644 --- a/README.md +++ b/README.md @@ -134,6 +134,8 @@ We thank the following people for their extensive assistance in the development - [@SusiJo](https://github.com/SusiJo) - [@joannakraw](https://github.com/joannakraw) - [@metinyazar](https://github.com/metinyazar) +- [@metinyazar](https://github.com/metinyazar) +- [@bolenala](https://github.com/bolenala) ## Contributions and Support diff --git a/modules/nf-core/crisprcleanr/normalize/crisprcleanr-normalize.diff b/modules/nf-core/crisprcleanr/normalize/crisprcleanr-normalize.diff index daa9446f..c3438e19 100644 --- a/modules/nf-core/crisprcleanr/normalize/crisprcleanr-normalize.diff +++ b/modules/nf-core/crisprcleanr/normalize/crisprcleanr-normalize.diff @@ -1,4 +1,7 @@ Changes in module 'nf-core/crisprcleanr/normalize' +'modules/nf-core/crisprcleanr/normalize/environment.yml' is unchanged +'modules/nf-core/crisprcleanr/normalize/meta.yml' is unchanged +Changes in 'crisprcleanr/normalize/main.nf': --- modules/nf-core/crisprcleanr/normalize/main.nf +++ modules/nf-core/crisprcleanr/normalize/main.nf @@ -8,12 +8,15 @@ @@ -18,7 +21,7 @@ Changes in module 'nf-core/crisprcleanr/normalize' path "versions.yml", emit: versions when: -@@ -26,20 +29,48 @@ +@@ -26,20 +29,49 @@ """ #!/usr/bin/env Rscript library(CRISPRcleanR) @@ -51,7 +54,8 @@ Changes in module 'nf-core/crisprcleanr/normalize' + rownames(library) = library[,1] + library = library[order(rownames(library)),] + library = library[,-1] -+ count_file_to_normalize <- count_file ++ names(count_file)[names(count_file) == 'Gene'] <- 'gene' ++ count_file_to_normalize <- count_file %>% dplyr::select(sgRNA, gene, everything()) + } + + normANDfcs <- ccr.NormfoldChanges(Dframe=count_file_to_normalize,saveToFig = FALSE,min_reads=${min_reads},EXPname="${prefix}", libraryAnnotation=library,display=FALSE) diff --git a/modules/nf-core/crisprcleanr/normalize/main.nf b/modules/nf-core/crisprcleanr/normalize/main.nf index d8969379..07f286f2 100644 --- a/modules/nf-core/crisprcleanr/normalize/main.nf +++ b/modules/nf-core/crisprcleanr/normalize/main.nf @@ -55,7 +55,8 @@ process CRISPRCLEANR_NORMALIZE { rownames(library) = library[,1] library = library[order(rownames(library)),] library = library[,-1] - count_file_to_normalize <- count_file + names(count_file)[names(count_file) == 'Gene'] <- 'gene' + count_file_to_normalize <- count_file %>% dplyr::select(sgRNA, gene, everything()) } normANDfcs <- ccr.NormfoldChanges(Dframe=count_file_to_normalize,saveToFig = FALSE,min_reads=${min_reads},EXPname="${prefix}", libraryAnnotation=library,display=FALSE) From b52ee8febc3643c7df9292722d3d06629acec1a6 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Tue, 20 Aug 2024 16:04:37 +0200 Subject: [PATCH 2/4] Update PR number --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2feb0c4c..eac1d11b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fix cutadapt 3' and 5' no such variable found bug ([#187](https://github.com/nf-core/crisprseq/pull/187)) - Fix design matrix bug that introduced dots instead of a hyphen ([#190](https://github.com/nf-core/crisprseq/pull/190)) - Make output of FluteMLE optional as when some pathways produce bugs some channels are then empty ([#190](https://github.com/nf-core/crisprseq/pull/190)) -- Fix a typo in crisprcleanr/normalize, when a user inputs a file +- Fix a typo in crisprcleanr/normalize, when a user inputs a file ([#192](https://github.com/nf-core/crisprseq/pull/192)) ### Deprecated From 0d6cfc4aa3f3902963fbb8ca25542c0c3854f0dc Mon Sep 17 00:00:00 2001 From: LaurenceKuhl Date: Tue, 20 Aug 2024 19:50:41 +0200 Subject: [PATCH 3/4] Update README.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index efb18385..9fb8bffa 100644 --- a/README.md +++ b/README.md @@ -134,7 +134,6 @@ We thank the following people for their extensive assistance in the development - [@SusiJo](https://github.com/SusiJo) - [@joannakraw](https://github.com/joannakraw) - [@metinyazar](https://github.com/metinyazar) -- [@metinyazar](https://github.com/metinyazar) - [@bolenala](https://github.com/bolenala) ## Contributions and Support From 671ca2ff101d0de9642a88dd33fa7e62ea6ffcb9 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Wed, 21 Aug 2024 09:22:22 +0200 Subject: [PATCH 4/4] Alphabetically sort the order --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 9fb8bffa..6841ca44 100644 --- a/README.md +++ b/README.md @@ -126,15 +126,15 @@ Main developers: We thank the following people for their extensive assistance in the development of this pipeline: - [@alan-tracey](https://github.com/alan-tracey) +- [@bolenala](https://github.com/bolenala) - [@ggabernet](https://github.com/ggabernet) - [@jianhong](https://github.com/jianhong) +- [@joannakraw](https://github.com/joannakraw) - [@mashehu](https://github.com/mashehu) +- [@metinyazar](https://github.com/metinyazar) - [@msanvicente](https://github.com/msanvicente) - [@mschaffer-incyte](https://github.com/mschaffer-incyte) - [@SusiJo](https://github.com/SusiJo) -- [@joannakraw](https://github.com/joannakraw) -- [@metinyazar](https://github.com/metinyazar) -- [@bolenala](https://github.com/bolenala) ## Contributions and Support