From 2f32f10bd8ee5346bcf6aa171054e484d5e8691f Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Fri, 17 Jan 2025 11:23:13 +0000 Subject: [PATCH] Remove r from versions.yml --- modules/nf-core/shinyngs/app/environment.yml | 1 - .../shinyngs/staticdifferential/environment.yml | 1 - modules/nf-core/shinyngs/staticdifferential/main.nf | 1 - .../staticdifferential/tests/main.nf.test.snap | 6 +++--- .../shinyngs/staticexploratory/environment.yml | 1 - .../shinyngs/validatefomcomponents/environment.yml | 1 - .../nf-core/shinyngs/validatefomcomponents/main.nf | 1 - .../validatefomcomponents/tests/main.nf.test | 2 +- .../validatefomcomponents/tests/main.nf.test.snap | 12 ++++++------ 9 files changed, 10 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/shinyngs/app/environment.yml b/modules/nf-core/shinyngs/app/environment.yml index 1560b05add3..f98b8bf5493 100644 --- a/modules/nf-core/shinyngs/app/environment.yml +++ b/modules/nf-core/shinyngs/app/environment.yml @@ -3,4 +3,3 @@ channels: - bioconda dependencies: - bioconda::r-shinyngs=2.1.0 - - conda-forge::r-base=4.4.2 diff --git a/modules/nf-core/shinyngs/staticdifferential/environment.yml b/modules/nf-core/shinyngs/staticdifferential/environment.yml index 1560b05add3..f98b8bf5493 100644 --- a/modules/nf-core/shinyngs/staticdifferential/environment.yml +++ b/modules/nf-core/shinyngs/staticdifferential/environment.yml @@ -3,4 +3,3 @@ channels: - bioconda dependencies: - bioconda::r-shinyngs=2.1.0 - - conda-forge::r-base=4.4.2 diff --git a/modules/nf-core/shinyngs/staticdifferential/main.nf b/modules/nf-core/shinyngs/staticdifferential/main.nf index 516f166f694..01a1593d03d 100644 --- a/modules/nf-core/shinyngs/staticdifferential/main.nf +++ b/modules/nf-core/shinyngs/staticdifferential/main.nf @@ -47,7 +47,6 @@ process SHINYNGS_STATICDIFFERENTIAL { cat <<-END_VERSIONS > versions.yml "${task.process}": - r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))") END_VERSIONS """ diff --git a/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap b/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap index 338b87d80e0..1242be467b1 100644 --- a/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap +++ b/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap @@ -74,10 +74,10 @@ ] ], "2": [ - "versions.yml:md5,45c5f38af38a536b8a0869946c746adf" + "versions.yml:md5,f2e3d411d3d82796173bcce72c30c20e" ], "versions": [ - "versions.yml:md5,45c5f38af38a536b8a0869946c746adf" + "versions.yml:md5,f2e3d411d3d82796173bcce72c30c20e" ], "volcanos_html": [ [ @@ -109,6 +109,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T20:13:33.841282396" + "timestamp": "2025-01-17T11:10:38.36289072" } } \ No newline at end of file diff --git a/modules/nf-core/shinyngs/staticexploratory/environment.yml b/modules/nf-core/shinyngs/staticexploratory/environment.yml index 1560b05add3..f98b8bf5493 100644 --- a/modules/nf-core/shinyngs/staticexploratory/environment.yml +++ b/modules/nf-core/shinyngs/staticexploratory/environment.yml @@ -3,4 +3,3 @@ channels: - bioconda dependencies: - bioconda::r-shinyngs=2.1.0 - - conda-forge::r-base=4.4.2 diff --git a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml index 1560b05add3..f98b8bf5493 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml +++ b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml @@ -3,4 +3,3 @@ channels: - bioconda dependencies: - bioconda::r-shinyngs=2.1.0 - - conda-forge::r-base=4.4.2 diff --git a/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/modules/nf-core/shinyngs/validatefomcomponents/main.nf index fda2933ce79..0605a623439 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/main.nf +++ b/modules/nf-core/shinyngs/validatefomcomponents/main.nf @@ -40,7 +40,6 @@ process SHINYNGS_VALIDATEFOMCOMPONENTS { cat <<-END_VERSIONS > versions.yml "${task.process}": - r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))") END_VERSIONS """ diff --git a/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test b/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test index e52224d46be..570465e9383 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test +++ b/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test @@ -62,7 +62,7 @@ nextflow_process { file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/Mus_musculus.anno.tsv", checkIfExists:true) ] input[2] = [['id':'SRP254919'], - file("params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.yaml", checkIfExists:true) + file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.yaml", checkIfExists:true) ] """ } diff --git a/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap b/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap index 13f4ee61814..a10c17a2714 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap +++ b/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap @@ -35,7 +35,7 @@ ] ], "4": [ - "versions.yml:md5,27850ec80be9f3b7aa6c8a19b2d60617" + "versions.yml:md5,a2d30e2d652938fb225e7cf251606893" ], "assays": [ [ @@ -70,7 +70,7 @@ ] ], "versions": [ - "versions.yml:md5,27850ec80be9f3b7aa6c8a19b2d60617" + "versions.yml:md5,a2d30e2d652938fb225e7cf251606893" ] } ], @@ -78,7 +78,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T20:09:27.110985279" + "timestamp": "2025-01-17T11:12:21.151359039" }, "stub": { "content": [ @@ -197,7 +197,7 @@ ] ], "4": [ - "versions.yml:md5,27850ec80be9f3b7aa6c8a19b2d60617" + "versions.yml:md5,a2d30e2d652938fb225e7cf251606893" ], "assays": [ [ @@ -232,7 +232,7 @@ ] ], "versions": [ - "versions.yml:md5,27850ec80be9f3b7aa6c8a19b2d60617" + "versions.yml:md5,a2d30e2d652938fb225e7cf251606893" ] } ], @@ -240,6 +240,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-16T20:04:03.89610247" + "timestamp": "2025-01-17T11:20:18.658397016" } } \ No newline at end of file