From 886228c42d4c2c3586cc7fbeb7d2723d1790fa0a Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Tue, 29 Oct 2024 15:03:57 +0100 Subject: [PATCH 01/10] Try to fix RRA --- modules/local/mageck/graphrra.nf | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/modules/local/mageck/graphrra.nf b/modules/local/mageck/graphrra.nf index b22dfcee..cb0dafcc 100644 --- a/modules/local/mageck/graphrra.nf +++ b/modules/local/mageck/graphrra.nf @@ -27,11 +27,16 @@ process MAGECK_GRAPHRRA { #### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text. #### #### Orient a reference sequence according to reads orientation. + library(BiocFileCache) + bfc <- BiocFileCache("~/.cache/R/ExperimentHub") + library(ExperimentHub) + res <- bfcquery(bfc, "experimenthub.index.rds", field="rname", exact=TRUE) + bfcremove(bfc, rids=res\$rid) + eh = ExperimentHub() library(MAGeCKFlute) library(ggplot2) options(ggrepel.max.overlaps = Inf) - gdata = ReadRRA("$gene_summary") gdata <- transform(gdata, LogFDR = -log10(FDR)) png(filename = paste0("$meta.treatment","_vs_","$meta.reference","_scatterview.png"), width = 6, height = 4, units = "in", res = 300) @@ -60,6 +65,4 @@ process MAGECK_GRAPHRRA { writeLines(version_ggplot, f) close(f) """ - - } From 45eb416716bf25e053d8d5a0668d81660103245c Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Tue, 29 Oct 2024 15:26:15 +0100 Subject: [PATCH 02/10] Add singularity to the CI --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d9e783ad..4d07ea65 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -41,7 +41,7 @@ jobs: - "test_umis" - "test_screening_count_table" isMaster: - - ${{ github.base_ref == 'master' }} + - true # Exclude conda and singularity on dev exclude: - isMaster: false From 1ea9a9389d064ce228a995e2a182f22adbd0e0fc Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Tue, 29 Oct 2024 15:35:41 +0100 Subject: [PATCH 03/10] Add temp location --- modules/local/mageck/graphrra.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/mageck/graphrra.nf b/modules/local/mageck/graphrra.nf index cb0dafcc..f3b2bc07 100644 --- a/modules/local/mageck/graphrra.nf +++ b/modules/local/mageck/graphrra.nf @@ -33,6 +33,7 @@ process MAGECK_GRAPHRRA { res <- bfcquery(bfc, "experimenthub.index.rds", field="rname", exact=TRUE) bfcremove(bfc, rids=res\$rid) eh = ExperimentHub() + Sys.setenv(BIOMART_CACHE=tempdir()) library(MAGeCKFlute) library(ggplot2) From c6f5c194d72d9d485f3ebbeac84cab4c68a4db5f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 29 Oct 2024 16:10:00 +0000 Subject: [PATCH 04/10] try defining BIOMART_CACHE for mageck flute --- templates/template_fluteMLE.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/templates/template_fluteMLE.R b/templates/template_fluteMLE.R index 38abcdb0..f13383e1 100644 --- a/templates/template_fluteMLE.R +++ b/templates/template_fluteMLE.R @@ -7,10 +7,11 @@ # Required to fix corrupted cache from Singularity container library(BiocFileCache) bfc <- BiocFileCache("~/.cache/R/ExperimentHub") + library(ExperimentHub) res <- bfcquery(bfc, "experimenthub.index.rds", field="rname", exact=TRUE) bfcremove(bfc, rids=res\$rid) - library(ExperimentHub) eh = ExperimentHub() + Sys.setenv(BIOMART_CACHE=tempdir()) library(MAGeCKFlute) library(clusterProfiler) From 9f0de4f5658ba843774e77d7e319e09540b4b4bd Mon Sep 17 00:00:00 2001 From: medmaca Date: Fri, 1 Nov 2024 17:01:41 +0000 Subject: [PATCH 05/10] Modified to fix template_fluteMLE.R for Apptainer/Singularity --- templates/template_fluteMLE.R | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/templates/template_fluteMLE.R b/templates/template_fluteMLE.R index f13383e1..5ef753ad 100644 --- a/templates/template_fluteMLE.R +++ b/templates/template_fluteMLE.R @@ -4,15 +4,9 @@ #### #### graphs mageck MLE - # Required to fix corrupted cache from Singularity container - library(BiocFileCache) - bfc <- BiocFileCache("~/.cache/R/ExperimentHub") - library(ExperimentHub) - res <- bfcquery(bfc, "experimenthub.index.rds", field="rname", exact=TRUE) - bfcremove(bfc, rids=res\$rid) - eh = ExperimentHub() - Sys.setenv(BIOMART_CACHE=tempdir()) - + # Required to fix .cache issue with Singularity/Apptainer container + Sys.setenv(HOME = getwd()) + library(MAGeCKFlute) library(clusterProfiler) library(ggplot2) From 84a919a1f8f84589fe5058a90fc10489d260d99d Mon Sep 17 00:00:00 2001 From: medmaca Date: Thu, 7 Nov 2024 11:32:52 +0000 Subject: [PATCH 06/10] Modified graphrra.nf for Apptainer/Singularity. --- modules/local/mageck/graphrra.nf | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/modules/local/mageck/graphrra.nf b/modules/local/mageck/graphrra.nf index f3b2bc07..8c5e03fb 100644 --- a/modules/local/mageck/graphrra.nf +++ b/modules/local/mageck/graphrra.nf @@ -27,14 +27,7 @@ process MAGECK_GRAPHRRA { #### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text. #### #### Orient a reference sequence according to reads orientation. - library(BiocFileCache) - bfc <- BiocFileCache("~/.cache/R/ExperimentHub") - library(ExperimentHub) - res <- bfcquery(bfc, "experimenthub.index.rds", field="rname", exact=TRUE) - bfcremove(bfc, rids=res\$rid) - eh = ExperimentHub() - Sys.setenv(BIOMART_CACHE=tempdir()) - + Sys.setenv(HOME = getwd()) # Required for Singularity/Apptainer library(MAGeCKFlute) library(ggplot2) options(ggrepel.max.overlaps = Inf) From 39f5f5482293dabfa5c019afd1422b88dd4b887d Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Fri, 8 Nov 2024 08:50:18 +0100 Subject: [PATCH 07/10] pre commit --- templates/template_fluteMLE.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/template_fluteMLE.R b/templates/template_fluteMLE.R index 5ef753ad..b33ef5a9 100644 --- a/templates/template_fluteMLE.R +++ b/templates/template_fluteMLE.R @@ -6,7 +6,7 @@ # Required to fix .cache issue with Singularity/Apptainer container Sys.setenv(HOME = getwd()) - + library(MAGeCKFlute) library(clusterProfiler) library(ggplot2) From a7bc8296849b85a0b2a05ad0303228f39a2baaf6 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Fri, 8 Nov 2024 08:54:10 +0100 Subject: [PATCH 08/10] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e53dde61..36e44e7e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - 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 ([#192](https://github.com/nf-core/crisprseq/pull/192)) +- Add Singularity and Docker tests in the CI, also fix any issues users had when running MAGeCKFlute with Docker or Singularity. ([#214](https://github.com/nf-core/crisprseq/pull/214)) ### General From 5316dc94d36084e260a6c6215983189b954f16ac Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Fri, 8 Nov 2024 09:14:31 +0100 Subject: [PATCH 09/10] Add Matthew as a conntributer --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index e55f34a9..699e3753 100644 --- a/README.md +++ b/README.md @@ -136,6 +136,7 @@ We thank the following people for their extensive assistance in the development - [@jianhong](https://github.com/jianhong) - [@joannakraw](https://github.com/joannakraw) - [@mashehu](https://github.com/mashehu) +- [@medmaca](https://github.com/medmaca) - [@metinyazar](https://github.com/metinyazar) - [@msanvicente](https://github.com/msanvicente) - [@mschaffer-incyte](https://github.com/mschaffer-incyte) From 957b5f27b35e6e04e5e42e0ca7109b50cef95385 Mon Sep 17 00:00:00 2001 From: LaurenceKuhl Date: Fri, 8 Nov 2024 10:21:14 +0100 Subject: [PATCH 10/10] Update .github/workflows/ci.yml --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4d07ea65..d9e783ad 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -41,7 +41,7 @@ jobs: - "test_umis" - "test_screening_count_table" isMaster: - - true + - ${{ github.base_ref == 'master' }} # Exclude conda and singularity on dev exclude: - isMaster: false