From add08063c1e057ef5a741b5ab68dce5654085764 Mon Sep 17 00:00:00 2001 From: luisas Date: Tue, 29 Oct 2024 12:27:10 +0100 Subject: [PATCH 01/13] modules --- .../stimulus/transform/environment.yml | 19 ++++++ modules/nf-core/stimulus/transform/main.nf | 43 +++++++++++++ modules/nf-core/stimulus/transform/meta.yml | 53 ++++++++++++++++ .../stimulus/transform/tests/main.nf.test | 63 +++++++++++++++++++ .../nf-core/stimulus/transform/tests/tags.yml | 2 + 5 files changed, 180 insertions(+) create mode 100644 modules/nf-core/stimulus/transform/environment.yml create mode 100644 modules/nf-core/stimulus/transform/main.nf create mode 100644 modules/nf-core/stimulus/transform/meta.yml create mode 100644 modules/nf-core/stimulus/transform/tests/main.nf.test create mode 100644 modules/nf-core/stimulus/transform/tests/tags.yml diff --git a/modules/nf-core/stimulus/transform/environment.yml b/modules/nf-core/stimulus/transform/environment.yml new file mode 100644 index 00000000000..e390f437f30 --- /dev/null +++ b/modules/nf-core/stimulus/transform/environment.yml @@ -0,0 +1,19 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::python=3.12 + - conda-forge::pytorch=2.4.1 + - conda-forge::matplotlib=3.9.2 + - conda-forge::pandas=2.2.3 + - conda-forge::polars=1.9.0 + - conda-forge::ray-core=2.37.0 + - conda-forge::safetensors=0.4.5 + - conda-forge::scikit-learn=1.5.2 + # NOTE https://github.com/nf-core/modules/issues/5814 + - pip: + # this will not lint, it fails the check with 1 equal sign + # and crashes tools with 2 + - stimulus-py=0.0.9 \ No newline at end of file diff --git a/modules/nf-core/stimulus/transform/main.nf b/modules/nf-core/stimulus/transform/main.nf new file mode 100644 index 00000000000..d54fe7fa36e --- /dev/null +++ b/modules/nf-core/stimulus/transform/main.nf @@ -0,0 +1,43 @@ +process STIMULUS_TRANSFORM { + tag "$meta.id" + label 'process_medium' + container "docker.io/mathysgrapotte/stimulus-py:latest" + + input: + tuple val(meta), path(transform_json) + path(csv) + + output: + tuple val(meta), path("${prefix}.csv"), emit: csv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def STIMULUS_VER = '0.0.9' + """ + stimulus-transform-csv -c ${csv} -j ${transform_json} -o ${prefix}.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + Python: \$(python --version | cut -d ' ' -f 2) + Stimulus-py: ${STIMULUS_VER} + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def STIMULUS_VER = '0.0.9' // container not used in stub, change manually + """ + touch ${meta.id}_modelcheck.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + Python: \$(python --version | cut -d ' ' -f 2) + Stimulus-py: ${STIMULUS_VER} + END_VERSIONS + """ +} diff --git a/modules/nf-core/stimulus/transform/meta.yml b/modules/nf-core/stimulus/transform/meta.yml new file mode 100644 index 00000000000..f7388dcd805 --- /dev/null +++ b/modules/nf-core/stimulus/transform/meta.yml @@ -0,0 +1,53 @@ +--- +name: "stimulus_transform" +description: Use stimulus-py package to transform the data. +keywords: + - deeplearning + - noise + - preprocessing +tools: + - "stimulus": + description: "Python package for processing deep learning models" + homepage: "https://github.com/mathysgrapotte/stimulus-py" + documentation: "https://github.com/mathysgrapotte/stimulus-py" + tool_dev_url: "https://github.com/mathysgrapotte/stimulus-py" + doi: "" + licence: "MIT" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + + - transform_json: + type: file + description: Json file with the transformation instructions + pattern: "*.json" + + - - csv: + type: file + description: Csv file to be transformed + pattern: "*.csv" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + + - csv: + type: file + description: CSV file with the transformed data + pattern: "*.csv" + +authors: + - "@luisas" +maintainers: + - "@luisas" diff --git a/modules/nf-core/stimulus/transform/tests/main.nf.test b/modules/nf-core/stimulus/transform/tests/main.nf.test new file mode 100644 index 00000000000..67cc4a99920 --- /dev/null +++ b/modules/nf-core/stimulus/transform/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process STIMULUS_TRANSFORM" + script "../main.nf" + process "STIMULUS_TRANSFORM" + + tag "modules" + tag "modules_nfcore" + tag "stimulus" + tag "stimulus/transform" + + test("test") { + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/experiment_config.json", checkIfExists: true) + ] + input[1] = [ + file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv", checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/experiment_config.json", checkIfExists: true) + ] + input[1] = [ + file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv", checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/stimulus/transform/tests/tags.yml b/modules/nf-core/stimulus/transform/tests/tags.yml new file mode 100644 index 00000000000..bca743d0094 --- /dev/null +++ b/modules/nf-core/stimulus/transform/tests/tags.yml @@ -0,0 +1,2 @@ +stimulus/transform: + - "modules/nf-core/stimulus/transform/**" From b6d56c08407ac94f855f28f5bdb49dd9f765bbf5 Mon Sep 17 00:00:00 2001 From: luisas Date: Tue, 29 Oct 2024 12:47:04 +0100 Subject: [PATCH 02/13] update --- modules/nf-core/stimulus/transform/meta.yml | 39 +++++++++++---------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/modules/nf-core/stimulus/transform/meta.yml b/modules/nf-core/stimulus/transform/meta.yml index f7388dcd805..c25186decde 100644 --- a/modules/nf-core/stimulus/transform/meta.yml +++ b/modules/nf-core/stimulus/transform/meta.yml @@ -12,14 +12,14 @@ tools: documentation: "https://github.com/mathysgrapotte/stimulus-py" tool_dev_url: "https://github.com/mathysgrapotte/stimulus-py" doi: "" - licence: "MIT" + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` - transform_json: type: file @@ -31,21 +31,22 @@ input: description: Csv file to be transformed pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - csv: - type: file - description: CSV file with the transformed data - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - csv: + type: file + description: CSV file with the transformed data + pattern: "*.csv" + + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" From 4d93f4399badfd26a8e28ab875f1c672bbe672db Mon Sep 17 00:00:00 2001 From: luisas Date: Tue, 29 Oct 2024 12:56:29 +0100 Subject: [PATCH 03/13] fix lint --- .../stimulus/transform/environment.yml | 2 +- modules/nf-core/stimulus/transform/meta.yml | 27 +++++++++---------- 2 files changed, 14 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/stimulus/transform/environment.yml b/modules/nf-core/stimulus/transform/environment.yml index e390f437f30..0365a812ecf 100644 --- a/modules/nf-core/stimulus/transform/environment.yml +++ b/modules/nf-core/stimulus/transform/environment.yml @@ -16,4 +16,4 @@ dependencies: - pip: # this will not lint, it fails the check with 1 equal sign # and crashes tools with 2 - - stimulus-py=0.0.9 \ No newline at end of file + - stimulus-py=0.0.9 diff --git a/modules/nf-core/stimulus/transform/meta.yml b/modules/nf-core/stimulus/transform/meta.yml index c25186decde..7e569b3e58f 100644 --- a/modules/nf-core/stimulus/transform/meta.yml +++ b/modules/nf-core/stimulus/transform/meta.yml @@ -20,7 +20,6 @@ input: description: | Groovy Map containing sample information e.g. `[ id:'sample1' ]` - - transform_json: type: file description: Json file with the transformation instructions @@ -32,21 +31,21 @@ input: pattern: "*.csv" output: - csv: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - csv: - type: file - description: CSV file with the transformed data - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - csv: + type: file + description: CSV file with the transformed data + pattern: "*.csv" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" From 3101547661e342be23108913ff136ef7bc7adf13 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 29 Oct 2024 13:26:03 +0000 Subject: [PATCH 04/13] fix tests --- modules/nf-core/stimulus/transform/main.nf | 5 +- modules/nf-core/stimulus/transform/meta.yml | 1 - .../stimulus/transform/tests/main.nf.test | 12 ++-- .../transform/tests/main.nf.test.snap | 68 +++++++++++++++++++ 4 files changed, 75 insertions(+), 11 deletions(-) create mode 100644 modules/nf-core/stimulus/transform/tests/main.nf.test.snap diff --git a/modules/nf-core/stimulus/transform/main.nf b/modules/nf-core/stimulus/transform/main.nf index d54fe7fa36e..314146977f6 100644 --- a/modules/nf-core/stimulus/transform/main.nf +++ b/modules/nf-core/stimulus/transform/main.nf @@ -16,7 +16,7 @@ process STIMULUS_TRANSFORM { script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def STIMULUS_VER = '0.0.9' """ stimulus-transform-csv -c ${csv} -j ${transform_json} -o ${prefix}.csv @@ -30,9 +30,10 @@ process STIMULUS_TRANSFORM { stub: def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" def STIMULUS_VER = '0.0.9' // container not used in stub, change manually """ - touch ${meta.id}_modelcheck.log + touch ${meta.id}.csv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/stimulus/transform/meta.yml b/modules/nf-core/stimulus/transform/meta.yml index 7e569b3e58f..48b12e2efc9 100644 --- a/modules/nf-core/stimulus/transform/meta.yml +++ b/modules/nf-core/stimulus/transform/meta.yml @@ -11,7 +11,6 @@ tools: homepage: "https://github.com/mathysgrapotte/stimulus-py" documentation: "https://github.com/mathysgrapotte/stimulus-py" tool_dev_url: "https://github.com/mathysgrapotte/stimulus-py" - doi: "" licence: ["MIT"] input: diff --git a/modules/nf-core/stimulus/transform/tests/main.nf.test b/modules/nf-core/stimulus/transform/tests/main.nf.test index 67cc4a99920..195cc6fa69c 100644 --- a/modules/nf-core/stimulus/transform/tests/main.nf.test +++ b/modules/nf-core/stimulus/transform/tests/main.nf.test @@ -12,14 +12,12 @@ nextflow_process { test("test") { when { process { - """ + """ input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/experiment_config.json", checkIfExists: true) ] - input[1] = [ - file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv", checkIfExists: true), - ] + input[1] = file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv", checkIfExists: true) """ } } @@ -39,14 +37,12 @@ nextflow_process { when { process { - """ + """ input[0] = [ [ id:'test'], // meta map file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/experiment_config.json", checkIfExists: true) ] - input[1] = [ - file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv", checkIfExists: true), - ] + input[1] = file(params.modules_testdata_base_path + "../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv", checkIfExists: true) """ } } diff --git a/modules/nf-core/stimulus/transform/tests/main.nf.test.snap b/modules/nf-core/stimulus/transform/tests/main.nf.test.snap new file mode 100644 index 00000000000..ea1ee38038f --- /dev/null +++ b/modules/nf-core/stimulus/transform/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "test": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv:md5,854ec944dfaa7e6b10ad4f080aee3125" + ] + ], + "1": [ + "versions.yml:md5,1531e9ca7e4e3b3489aa1932a9e14003" + ], + "csv": [ + [ + { + "id": "test" + }, + "test.csv:md5,854ec944dfaa7e6b10ad4f080aee3125" + ] + ], + "versions": [ + "versions.yml:md5,1531e9ca7e4e3b3489aa1932a9e14003" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-29T13:24:04.435440394" + }, + "test - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,1531e9ca7e4e3b3489aa1932a9e14003" + ], + "csv": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1531e9ca7e4e3b3489aa1932a9e14003" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-29T13:24:17.732637128" + } +} \ No newline at end of file From 19d5f2985421c2177330fe4124f5973a7fbe155c Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 29 Oct 2024 13:55:21 +0000 Subject: [PATCH 05/13] fix meta --- modules/nf-core/stimulus/transform/meta.yml | 27 +++++++++++---------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/stimulus/transform/meta.yml b/modules/nf-core/stimulus/transform/meta.yml index 48b12e2efc9..f5a7ced9a1d 100644 --- a/modules/nf-core/stimulus/transform/meta.yml +++ b/modules/nf-core/stimulus/transform/meta.yml @@ -1,4 +1,3 @@ ---- name: "stimulus_transform" description: Use stimulus-py package to transform the data. keywords: @@ -12,6 +11,7 @@ tools: documentation: "https://github.com/mathysgrapotte/stimulus-py" tool_dev_url: "https://github.com/mathysgrapotte/stimulus-py" licence: ["MIT"] + identifier: "" input: - - meta: @@ -21,31 +21,32 @@ input: e.g. `[ id:'sample1' ]` - transform_json: type: file - description: Json file with the transformation instructions - pattern: "*.json" - + description: | + Json file with the transformation instructions + pattern: ".json" - - csv: type: file - description: Csv file to be transformed - pattern: "*.csv" + description: | + Csv file to be transformed + pattern: ".csv" output: - csv: - meta: type: map description: | Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - csv: + e.g. `[ id:'sample1' ]` + - "${prefix}.csv": type: file - description: CSV file with the transformed data - pattern: "*.csv" - + description: | + Transformed CSV file + pattern: ".csv" - versions: - versions.yml: type: file - description: File containing software versions + description: | + File containing software versions pattern: "versions.yml" - authors: - "@luisas" maintainers: From 8e79f35922a48b450352e1811e78a1d7ecbc7ed6 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 29 Oct 2024 13:58:45 +0000 Subject: [PATCH 06/13] update --- modules/nf-core/stimulus/transform/environment.yml | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/stimulus/transform/environment.yml b/modules/nf-core/stimulus/transform/environment.yml index 0365a812ecf..fbf5fe9b102 100644 --- a/modules/nf-core/stimulus/transform/environment.yml +++ b/modules/nf-core/stimulus/transform/environment.yml @@ -1,19 +1,13 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - conda-forge::python=3.12 - - conda-forge::pytorch=2.4.1 - conda-forge::matplotlib=3.9.2 - conda-forge::pandas=2.2.3 - conda-forge::polars=1.9.0 + - conda-forge::python=3.12 + - conda-forge::pytorch=2.4.1 - conda-forge::ray-core=2.37.0 - conda-forge::safetensors=0.4.5 - conda-forge::scikit-learn=1.5.2 - # NOTE https://github.com/nf-core/modules/issues/5814 - - pip: - # this will not lint, it fails the check with 1 equal sign - # and crashes tools with 2 - - stimulus-py=0.0.9 From d5130e00cc391d4e4b25366b5abbf65f503d2d07 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 29 Oct 2024 13:59:36 +0000 Subject: [PATCH 07/13] update --- modules/nf-core/stimulus/transform/meta.yml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/stimulus/transform/meta.yml b/modules/nf-core/stimulus/transform/meta.yml index f5a7ced9a1d..a6913791814 100644 --- a/modules/nf-core/stimulus/transform/meta.yml +++ b/modules/nf-core/stimulus/transform/meta.yml @@ -1,18 +1,16 @@ name: "stimulus_transform" description: Use stimulus-py package to transform the data. keywords: - - deeplearning - - noise - - preprocessing + - machine learning + - neural network + - unit test tools: - "stimulus": - description: "Python package for processing deep learning models" + description: "Stochastic Testing and Input Manipulation for Unbiased Learning Systems" homepage: "https://github.com/mathysgrapotte/stimulus-py" documentation: "https://github.com/mathysgrapotte/stimulus-py" tool_dev_url: "https://github.com/mathysgrapotte/stimulus-py" licence: ["MIT"] - identifier: "" - input: - - meta: type: map From 2aaa082fb9a3610757418c3a86146a9a62feb751 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 29 Oct 2024 14:34:26 +0000 Subject: [PATCH 08/13] increase memory --- memory.config | 3 +++ modules/nf-core/stimulus/transform/tests/main.nf.test | 5 ++++- 2 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 memory.config diff --git a/memory.config b/memory.config new file mode 100644 index 00000000000..4e7d43d1d5f --- /dev/null +++ b/memory.config @@ -0,0 +1,3 @@ +process{ + memory = "6.GB" +} diff --git a/modules/nf-core/stimulus/transform/tests/main.nf.test b/modules/nf-core/stimulus/transform/tests/main.nf.test index 195cc6fa69c..521f90a607e 100644 --- a/modules/nf-core/stimulus/transform/tests/main.nf.test +++ b/modules/nf-core/stimulus/transform/tests/main.nf.test @@ -10,6 +10,9 @@ nextflow_process { tag "stimulus/transform" test("test") { + + config "./memory.config" + when { process { """ @@ -32,7 +35,7 @@ nextflow_process { } test("test - stub") { - + config "./memory.config" options "-stub" when { From 77cfbaa913cdc3206cc25afc6357c9bfd8f8fd0a Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 29 Oct 2024 14:35:31 +0000 Subject: [PATCH 09/13] increase memory --- memory.config => modules/nf-core/stimulus/transform/memory.config | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename memory.config => modules/nf-core/stimulus/transform/memory.config (100%) diff --git a/memory.config b/modules/nf-core/stimulus/transform/memory.config similarity index 100% rename from memory.config rename to modules/nf-core/stimulus/transform/memory.config From 24f375c4988375f4214005a0b9078aa02a9afe1c Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 29 Oct 2024 14:35:48 +0000 Subject: [PATCH 10/13] increase memory --- modules/nf-core/stimulus/transform/memory.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/stimulus/transform/memory.config b/modules/nf-core/stimulus/transform/memory.config index 4e7d43d1d5f..d21ca74ea32 100644 --- a/modules/nf-core/stimulus/transform/memory.config +++ b/modules/nf-core/stimulus/transform/memory.config @@ -1,3 +1,3 @@ process{ - memory = "6.GB" + memory = "12.GB" } From b97fddc5f18b8274a28463ca379b31f67445f47a Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 29 Oct 2024 15:05:21 +0000 Subject: [PATCH 11/13] fix config place --- modules/nf-core/stimulus/transform/{ => tests}/memory.config | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename modules/nf-core/stimulus/transform/{ => tests}/memory.config (100%) diff --git a/modules/nf-core/stimulus/transform/memory.config b/modules/nf-core/stimulus/transform/tests/memory.config similarity index 100% rename from modules/nf-core/stimulus/transform/memory.config rename to modules/nf-core/stimulus/transform/tests/memory.config From 8dcbdc7fb4e14fc96ad3e211c0d32df8674862ed Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Wed, 30 Oct 2024 12:28:28 +0100 Subject: [PATCH 12/13] Update modules/nf-core/stimulus/transform/main.nf Co-authored-by: alessiovignoli <45239231+alessiovignoli@users.noreply.github.com> --- modules/nf-core/stimulus/transform/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/stimulus/transform/main.nf b/modules/nf-core/stimulus/transform/main.nf index 314146977f6..98e4499d821 100644 --- a/modules/nf-core/stimulus/transform/main.nf +++ b/modules/nf-core/stimulus/transform/main.nf @@ -24,7 +24,7 @@ process STIMULUS_TRANSFORM { cat <<-END_VERSIONS > versions.yml "${task.process}": Python: \$(python --version | cut -d ' ' -f 2) - Stimulus-py: ${STIMULUS_VER} + Stimulus-py: \$( pip show stimulus-py | grep Version | sed 's/Version: //') END_VERSIONS """ From f67edf55bdf39777945009d20f27f4ce56a0e7c2 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Wed, 30 Oct 2024 11:34:36 +0000 Subject: [PATCH 13/13] remove memory --- modules/nf-core/stimulus/transform/main.nf | 2 +- modules/nf-core/stimulus/transform/tests/main.nf.test | 4 +--- modules/nf-core/stimulus/transform/tests/memory.config | 3 --- 3 files changed, 2 insertions(+), 7 deletions(-) delete mode 100644 modules/nf-core/stimulus/transform/tests/memory.config diff --git a/modules/nf-core/stimulus/transform/main.nf b/modules/nf-core/stimulus/transform/main.nf index 98e4499d821..83ec09acb5a 100644 --- a/modules/nf-core/stimulus/transform/main.nf +++ b/modules/nf-core/stimulus/transform/main.nf @@ -1,7 +1,7 @@ process STIMULUS_TRANSFORM { tag "$meta.id" label 'process_medium' - container "docker.io/mathysgrapotte/stimulus-py:latest" + container "docker.io/luisas/stimulus-py:0.0.10" input: tuple val(meta), path(transform_json) diff --git a/modules/nf-core/stimulus/transform/tests/main.nf.test b/modules/nf-core/stimulus/transform/tests/main.nf.test index 521f90a607e..7372507e5f0 100644 --- a/modules/nf-core/stimulus/transform/tests/main.nf.test +++ b/modules/nf-core/stimulus/transform/tests/main.nf.test @@ -11,8 +11,6 @@ nextflow_process { test("test") { - config "./memory.config" - when { process { """ @@ -35,7 +33,7 @@ nextflow_process { } test("test - stub") { - config "./memory.config" + options "-stub" when { diff --git a/modules/nf-core/stimulus/transform/tests/memory.config b/modules/nf-core/stimulus/transform/tests/memory.config deleted file mode 100644 index d21ca74ea32..00000000000 --- a/modules/nf-core/stimulus/transform/tests/memory.config +++ /dev/null @@ -1,3 +0,0 @@ -process{ - memory = "12.GB" -}