From 51145aa4c3c721f65bf01849439b394eaa758b2b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20B=C3=A4uerle?= <45968370+famosab@users.noreply.github.com> Date: Tue, 10 Dec 2024 08:11:41 +0100 Subject: [PATCH 1/4] port parabricks/genotypegvcf to nf-test (#6980) * add test * remove pytest * remove pytest * change assertion * change assertion * add snap * update test yaml * rm test.yml * add to conda_skip * add tag gpu --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- .github/conda_skip.yml | 2 + .../nf-core/parabricks/genotypegvcf/main.nf | 4 +- .../genotypegvcf/tests/main.nf.test | 70 +++++++++++++++++++ .../genotypegvcf/tests/main.nf.test.snap | 50 +++++++++++++ tests/config/pytest_modules.yml | 3 - .../nf-core/parabricks/genotypegvcf/main.nf | 32 --------- .../parabricks/genotypegvcf/nextflow.config | 5 -- .../nf-core/parabricks/genotypegvcf/test.yml | 10 --- .../genotypegvcf/test_GPU_config.txt | 9 --- .../parabricks/genotypegvcf/test_GPU_yml.txt | 10 --- 10 files changed, 123 insertions(+), 72 deletions(-) create mode 100644 modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test create mode 100644 modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/parabricks/genotypegvcf/main.nf delete mode 100644 tests/modules/nf-core/parabricks/genotypegvcf/nextflow.config delete mode 100644 tests/modules/nf-core/parabricks/genotypegvcf/test.yml delete mode 100644 tests/modules/nf-core/parabricks/genotypegvcf/test_GPU_config.txt delete mode 100644 tests/modules/nf-core/parabricks/genotypegvcf/test_GPU_yml.txt diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml index 2ef7216da3e..14da877f04d 100644 --- a/.github/conda_skip.yml +++ b/.github/conda_skip.yml @@ -182,3 +182,5 @@ exclude: path: modules/nf-core/xeniumranger/resegment - profile: conda path: modules/nf-core/xeniumranger/import-segmentation + - profile: conda + path: modules/nf-core/parabricks/genotypegvcf diff --git a/modules/nf-core/parabricks/genotypegvcf/main.nf b/modules/nf-core/parabricks/genotypegvcf/main.nf index d94926bff8f..4ad7985cd6e 100644 --- a/modules/nf-core/parabricks/genotypegvcf/main.nf +++ b/modules/nf-core/parabricks/genotypegvcf/main.nf @@ -2,7 +2,7 @@ process PARABRICKS_GENOTYPEGVCF { tag "$meta.id" label 'process_high' - container "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1" + container "nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1" input: tuple val(meta), path(input) @@ -16,7 +16,6 @@ process PARABRICKS_GENOTYPEGVCF { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead." @@ -26,7 +25,6 @@ process PARABRICKS_GENOTYPEGVCF { def prefix = task.ext.prefix ?: "${meta.id}" def output_file = "${prefix}.vcf" """ - pbrun \\ genotypegvcf \\ --ref $fasta \\ diff --git a/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test b/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test new file mode 100644 index 00000000000..8d12071a215 --- /dev/null +++ b/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test @@ -0,0 +1,70 @@ +nextflow_process { + + name "Test Process PARABRICKS_GENOTYPEGVCF" + script "../main.nf" + process "PARABRICKS_GENOTYPEGVCF" + + tag "modules" + tag "modules_nfcore" + tag "parabricks" + tag "parabricks/genotypegvcf" + tag "gpu" + + test("human - gvcf") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true) + ] + input[1] = [ + [ id:'reference'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + process.out.versions + ).match() } + ) + } + + } + + test("human - gvf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true) + ] + input[1] = [ + [ id:'reference'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test.snap b/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test.snap new file mode 100644 index 00000000000..f53d217e3a8 --- /dev/null +++ b/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test.snap @@ -0,0 +1,50 @@ +{ + "human - gvcf": { + "content": [ + "da770258f27bf3837c38769e9dfb1df3", + [ + "versions.yml:md5,34667e15df7f35f16f97eaea3d257e7c" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-13T12:09:42.000067144" + }, + "human - gvf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,34667e15df7f35f16f97eaea3d257e7c" + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,34667e15df7f35f16f97eaea3d257e7c" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-13T11:09:01.981995733" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 019ad006b8c..01df2f69185 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -401,9 +401,6 @@ parabricks/dbsnp: parabricks/deepvariant: - modules/nf-core/parabricks/deepvariant/** - tests/modules/nf-core/parabricks/deepvariant/** -parabricks/genotypegvcf: - - modules/nf-core/parabricks/genotypegvcf/** - - tests/modules/nf-core/parabricks/genotypegvcf/** parabricks/haplotypecaller: - modules/nf-core/parabricks/haplotypecaller/** - tests/modules/nf-core/parabricks/haplotypecaller/** diff --git a/tests/modules/nf-core/parabricks/genotypegvcf/main.nf b/tests/modules/nf-core/parabricks/genotypegvcf/main.nf deleted file mode 100644 index 05788342dc0..00000000000 --- a/tests/modules/nf-core/parabricks/genotypegvcf/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PARABRICKS_GENOTYPEGVCF } from '../../../../../modules/nf-core/parabricks/genotypegvcf/main.nf' - -workflow test_parabricks_genotypegvcf { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) - ] - fasta = [ - [ id:'test'], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - - process stage { - input: - tuple val(meta), path(input) - - output: - tuple val(meta), path("*.g.vcf") - - script: - """ - mv $input test.genome.g.vcf - """ - } - - PARABRICKS_GENOTYPEGVCF ( stage( input ), fasta ) -} diff --git a/tests/modules/nf-core/parabricks/genotypegvcf/nextflow.config b/tests/modules/nf-core/parabricks/genotypegvcf/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/parabricks/genotypegvcf/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/parabricks/genotypegvcf/test.yml b/tests/modules/nf-core/parabricks/genotypegvcf/test.yml deleted file mode 100644 index 0943312b81c..00000000000 --- a/tests/modules/nf-core/parabricks/genotypegvcf/test.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: parabricks genotypegvcf test_parabricks_genotypegvcf - command: nextflow run ./tests/modules/nf-core/parabricks/genotypegvcf -entry test_parabricks_genotypegvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/genotypegvcf/nextflow.config -stub-run - tags: - - parabricks - - parabricks/genotypegvcf - files: - - path: output/parabricks/test.vcf - should_exist: true - - path: output/parabricks/versions.yml - should_exist: true diff --git a/tests/modules/nf-core/parabricks/genotypegvcf/test_GPU_config.txt b/tests/modules/nf-core/parabricks/genotypegvcf/test_GPU_config.txt deleted file mode 100644 index 2c916c20501..00000000000 --- a/tests/modules/nf-core/parabricks/genotypegvcf/test_GPU_config.txt +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - memory = "15.GB" - cpus = 4 - accelerator = 1 -} -docker.runOptions = "--gpus all" -singularity.runOptions = "--nv" \ No newline at end of file diff --git a/tests/modules/nf-core/parabricks/genotypegvcf/test_GPU_yml.txt b/tests/modules/nf-core/parabricks/genotypegvcf/test_GPU_yml.txt deleted file mode 100644 index 89e890b8136..00000000000 --- a/tests/modules/nf-core/parabricks/genotypegvcf/test_GPU_yml.txt +++ /dev/null @@ -1,10 +0,0 @@ -- name: parabricks genotypegvcf test_parabricks_genotypegvcf - command: nextflow run ./tests/modules/nf-core/parabricks/genotypegvcf -entry test_parabricks_genotypegvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/genotypegvcf/nextflow.config - tags: - - parabricks - - parabricks/genotypegvcf - files: - - path: output/parabricks/test.vcf - md5sum: e4ca0133b93c3c8e8469b817dcb34052 - - path: output/parabricks/versions.yml - should_exist: true From 8aef0e0ab044a6e756197302809b12ed2f77af26 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 07:19:27 +0000 Subject: [PATCH 2/4] Update GitHub Actions (#7126) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/lint.yml | 2 +- .github/workflows/pytest-workflow.yml | 2 +- .github/workflows/wave.yml | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 69963507b93..c617c10ccae 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -109,7 +109,7 @@ jobs: with: python-version: "3.11" - - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4 + - uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4 id: cache-pip with: path: ~/.cache/pip diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 49a73467b99..01fa7f39a98 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -247,7 +247,7 @@ jobs: with: python-version: "3.11" - - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4 + - uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4 id: cache-pip-pytest with: path: ~/.cache/pip diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml index 9d5901c7d95..b56ed4795d6 100644 --- a/.github/workflows/wave.yml +++ b/.github/workflows/wave.yml @@ -31,7 +31,7 @@ jobs: - name: Find conda differences id: conda-diff - uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45 + uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45 with: json: true escape_json: false @@ -40,7 +40,7 @@ jobs: - name: Find Dockerfile differences id: docker-diff - uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45 + uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45 with: json: true escape_json: false From 0270c0fbbbb09456d7823605e4285c4a2c5bbf40 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 10 Dec 2024 09:44:41 +0100 Subject: [PATCH 3/4] Add foldmason createdb (#7180) * add first version module * add test * add tests * add * ass * add * up * update containers * update version * update version easymsa * Update modules/nf-core/foldmason/createdb/main.nf Co-authored-by: Jose Espinosa-Carrasco * Update modules/nf-core/foldmason/createdb/meta.yml Co-authored-by: Jose Espinosa-Carrasco * Update modules/nf-core/foldmason/createdb/main.nf Co-authored-by: Jose Espinosa-Carrasco * Update modules/nf-core/foldmason/createdb/main.nf Co-authored-by: Jose Espinosa-Carrasco --------- Co-authored-by: Jose Espinosa-Carrasco --- .../foldmason/createdb/environment.yml | 5 + modules/nf-core/foldmason/createdb/main.nf | 47 +++++++ modules/nf-core/foldmason/createdb/meta.yml | 48 +++++++ .../foldmason/createdb/tests/main.nf.test | 66 +++++++++ .../createdb/tests/main.nf.test.snap | 128 ++++++++++++++++++ .../nf-core/foldmason/easymsa/environment.yml | 4 +- modules/nf-core/foldmason/easymsa/main.nf | 5 +- .../foldmason/easymsa/tests/main.nf.test.snap | 32 ++--- 8 files changed, 315 insertions(+), 20 deletions(-) create mode 100644 modules/nf-core/foldmason/createdb/environment.yml create mode 100644 modules/nf-core/foldmason/createdb/main.nf create mode 100644 modules/nf-core/foldmason/createdb/meta.yml create mode 100644 modules/nf-core/foldmason/createdb/tests/main.nf.test create mode 100644 modules/nf-core/foldmason/createdb/tests/main.nf.test.snap diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml new file mode 100644 index 00000000000..80d4dd371d9 --- /dev/null +++ b/modules/nf-core/foldmason/createdb/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::foldmason=2.7bd21ed diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf new file mode 100644 index 00000000000..c54b45f3f06 --- /dev/null +++ b/modules/nf-core/foldmason/createdb/main.nf @@ -0,0 +1,47 @@ +process FOLDMASON_CREATEDB { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a88d162c3f39a1518d48c3faec235e6fcde750586da868b62fc5f0a08a89aa9d/data' : + 'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }" + + input: + tuple val(meta) , path(structures) + + output: + tuple val(meta), path("${prefix}*"), emit: db + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + foldmason createdb \\ + ${structures} \\ + ${prefix} \\ + $args \\ + --threads $task.cpus + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}') + END_VERSIONS + """ +} diff --git a/modules/nf-core/foldmason/createdb/meta.yml b/modules/nf-core/foldmason/createdb/meta.yml new file mode 100644 index 00000000000..fd47efe2f90 --- /dev/null +++ b/modules/nf-core/foldmason/createdb/meta.yml @@ -0,0 +1,48 @@ +name: "foldmason_createdb" +description: Creates a database for Foldmason. +keywords: + - alignment + - MSA + - genomics + - structure +tools: + - "foldmason": + description: "Multiple Protein Structure Alignment at Scale with FoldMason" + homepage: "https://github.com/steineggerlab/foldmason" + documentation: "https://github.com/steineggerlab/foldmason" + tool_dev_url: "https://github.com/steineggerlab/foldmason" + doi: "10.1101/2024.08.01.606130" + licence: ["GPL v3"] + identifier: biotools:foldmason + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - structures: + type: file + description: Input protein structures in `PDB` or `mmCIF` format. + pattern: "*.{pdb,mmcif}" + +output: + - db: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "${prefix}*": + type: file + description: All database files created by Foldmason + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@luisas" +maintainers: + - "@luisas" diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test b/modules/nf-core/foldmason/createdb/tests/main.nf.test new file mode 100644 index 00000000000..9ac567a7504 --- /dev/null +++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test @@ -0,0 +1,66 @@ +nextflow_process { + + name "Test Process FOLDMASON_CREATEDB" + script "../main.nf" + process "FOLDMASON_CREATEDB" + + tag "modules" + tag "modules_nfcore" + tag "foldmason" + tag "foldmason/createdb" + tag "untar" + + setup { + + run("UNTAR") { + script "../../../../../modules/nf-core/untar/main.nf" + process { + """ + archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/af2_structures/seatoxin-ref.tar.gz", checkIfExists: true) + input[0] = Channel.of(tuple([id:'test'], archive)) + """ + } + } + } + + test("seatoxin") { + + when { + + process { + """ + input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("seatoxin - stub ") { + + when { + + process { + """ + input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap new file mode 100644 index 00000000000..dce5175dc90 --- /dev/null +++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap @@ -0,0 +1,128 @@ +{ + "seatoxin - stub ": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test:md5,941321067eae439b4a8ccf6425d84751", + "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015", + "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274", + "test.source:md5,7968a6cb6577ead230c31910380af948", + "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9", + "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3", + "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba", + "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16", + "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2", + "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4", + "test_ss:md5,75d329b63c0383c3e43090ba89238e14", + "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015" + ] + ] + ], + "1": [ + "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45" + ], + "db": [ + [ + { + "id": "test" + }, + [ + "test:md5,941321067eae439b4a8ccf6425d84751", + "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015", + "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274", + "test.source:md5,7968a6cb6577ead230c31910380af948", + "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9", + "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3", + "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba", + "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16", + "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2", + "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4", + "test_ss:md5,75d329b63c0383c3e43090ba89238e14", + "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015" + ] + ] + ], + "versions": [ + "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-09T15:11:27.426024133" + }, + "seatoxin": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test:md5,941321067eae439b4a8ccf6425d84751", + "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015", + "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274", + "test.source:md5,7968a6cb6577ead230c31910380af948", + "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9", + "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3", + "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba", + "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16", + "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2", + "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4", + "test_ss:md5,75d329b63c0383c3e43090ba89238e14", + "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015" + ] + ] + ], + "1": [ + "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45" + ], + "db": [ + [ + { + "id": "test" + }, + [ + "test:md5,941321067eae439b4a8ccf6425d84751", + "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015", + "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274", + "test.source:md5,7968a6cb6577ead230c31910380af948", + "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9", + "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3", + "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba", + "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16", + "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2", + "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4", + "test_ss:md5,75d329b63c0383c3e43090ba89238e14", + "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015" + ] + ] + ], + "versions": [ + "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-09T15:11:15.375341633" + } +} \ No newline at end of file diff --git a/modules/nf-core/foldmason/easymsa/environment.yml b/modules/nf-core/foldmason/easymsa/environment.yml index 64a5b3671d4..fa2909a9491 100644 --- a/modules/nf-core/foldmason/easymsa/environment.yml +++ b/modules/nf-core/foldmason/easymsa/environment.yml @@ -1,8 +1,6 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::foldmason=1.763a428 + - bioconda::foldmason=2.7bd21ed - conda-forge::pigz=2.8 diff --git a/modules/nf-core/foldmason/easymsa/main.nf b/modules/nf-core/foldmason/easymsa/main.nf index bb1737f05ef..b4870da0d10 100644 --- a/modules/nf-core/foldmason/easymsa/main.nf +++ b/modules/nf-core/foldmason/easymsa/main.nf @@ -3,7 +3,10 @@ process FOLDMASON_EASYMSA { label 'process_medium' conda "${moduleDir}/environment.yml" - container "community.wave.seqera.io/library/foldmason_pigz:54849036d93c89ed" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'oras://community.wave.seqera.io/library/foldmason_pigz:d8dfffbc768abe03': + 'community.wave.seqera.io/library/foldmason_pigz:88809eb5649534b0' }" + input: tuple val(meta) , path(pdbs) diff --git a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap index 384d2021284..4951f29bff3 100644 --- a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap +++ b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ], "msa_3di": [ [ @@ -38,7 +38,7 @@ ] ], "versions": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ] } ], @@ -46,7 +46,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-04T10:56:12.836231763" + "timestamp": "2024-12-09T15:22:29.135105042" }, "Test on seatoxin dataset - uncompressed": { "content": [ @@ -68,7 +68,7 @@ ] ], "2": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ], "msa_3di": [ [ @@ -87,7 +87,7 @@ ] ], "versions": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ] } ], @@ -95,7 +95,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-04T10:55:41.89060384" + "timestamp": "2024-12-09T15:21:46.797852094" }, "Test on seatoxin dataset - compressed": { "content": [ @@ -117,7 +117,7 @@ ] ], "2": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ], "msa_3di": [ [ @@ -136,7 +136,7 @@ ] ], "versions": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ] } ], @@ -144,7 +144,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-04T10:55:52.135344443" + "timestamp": "2024-12-09T15:21:58.958099076" }, "Test on seatoxin dataset - guide_tree": { "content": [ @@ -154,7 +154,7 @@ { "id": "test" }, - "test_3di.fa:md5,46fa911158bb736c054dfad0378832b4" + "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08" ] ], "1": [ @@ -162,18 +162,18 @@ { "id": "test" }, - "test_aa.fa:md5,7ada48f0152342787a46505b9e8a2fae" + "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731" ] ], "2": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ], "msa_3di": [ [ { "id": "test" }, - "test_3di.fa:md5,46fa911158bb736c054dfad0378832b4" + "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08" ] ], "msa_aa": [ @@ -181,11 +181,11 @@ { "id": "test" }, - "test_aa.fa:md5,7ada48f0152342787a46505b9e8a2fae" + "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731" ] ], "versions": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ] } ], @@ -193,6 +193,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-04T10:56:02.473496089" + "timestamp": "2024-12-09T15:22:11.0778334" } } \ No newline at end of file From d752b3edfab155e353c93ed868a24db2fc047ab0 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 10 Dec 2024 09:45:56 +0100 Subject: [PATCH 4/4] Update: deseq2/differential for upcoming improved standardisation of template modules (#7178) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Rename deseq_de.R to deseq2_differential.R for standaisation * Update main.nf --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --- modules/nf-core/deseq2/differential/main.nf | 2 +- .../templates/{deseq_de.R => deseq2_differential.R} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename modules/nf-core/deseq2/differential/templates/{deseq_de.R => deseq2_differential.R} (100%) diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf index 4d25602f7d6..c76187b50b5 100644 --- a/modules/nf-core/deseq2/differential/main.nf +++ b/modules/nf-core/deseq2/differential/main.nf @@ -29,7 +29,7 @@ process DESEQ2_DIFFERENTIAL { task.ext.when == null || task.ext.when script: - template 'deseq_de.R' + template 'deseq2_differential.R' stub: """ diff --git a/modules/nf-core/deseq2/differential/templates/deseq_de.R b/modules/nf-core/deseq2/differential/templates/deseq2_differential.R similarity index 100% rename from modules/nf-core/deseq2/differential/templates/deseq_de.R rename to modules/nf-core/deseq2/differential/templates/deseq2_differential.R