From 7abf6b53fec9cc582c87b948c37385bb62563600 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Thu, 28 Nov 2024 15:52:51 +0000 Subject: [PATCH] fix prettier --- conf/modules.config | 2 +- modules.json | 5 -- .../nf-core/magus/guidetree/environment.yml | 5 -- modules/nf-core/magus/guidetree/main.nf | 48 ------------------- modules/nf-core/magus/guidetree/meta.yml | 46 ------------------ .../magus/guidetree/tests/main.nf.test | 39 --------------- .../magus/guidetree/tests/main.nf.test.snap | 23 --------- .../nf-core/magus/guidetree/tests/tags.yml | 2 - 8 files changed, 1 insertion(+), 169 deletions(-) delete mode 100644 modules/nf-core/magus/guidetree/environment.yml delete mode 100644 modules/nf-core/magus/guidetree/main.nf delete mode 100644 modules/nf-core/magus/guidetree/meta.yml delete mode 100644 modules/nf-core/magus/guidetree/tests/main.nf.test delete mode 100644 modules/nf-core/magus/guidetree/tests/main.nf.test.snap delete mode 100644 modules/nf-core/magus/guidetree/tests/tags.yml diff --git a/conf/modules.config b/conf/modules.config index ad87b637..daf1df3d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -67,7 +67,7 @@ // Tree building // - withName: '*_GUIDETREE' { + withName: "CLUSTALO_GUIDETREE|FAMSA_GUIDETREE" { tag = { [ "${meta.id}", diff --git a/modules.json b/modules.json index ef4ef255..3b7e8f53 100644 --- a/modules.json +++ b/modules.json @@ -72,11 +72,6 @@ "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, - "magus/guidetree": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] - }, "mtmalign/align": { "branch": "master", "git_sha": "4eecd9a0c06fa508ae314c06ac952c161c019679", diff --git a/modules/nf-core/magus/guidetree/environment.yml b/modules/nf-core/magus/guidetree/environment.yml deleted file mode 100644 index 423a5985..00000000 --- a/modules/nf-core/magus/guidetree/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::magus-msa=0.2.0 diff --git a/modules/nf-core/magus/guidetree/main.nf b/modules/nf-core/magus/guidetree/main.nf deleted file mode 100644 index eb37fb9d..00000000 --- a/modules/nf-core/magus/guidetree/main.nf +++ /dev/null @@ -1,48 +0,0 @@ -process MAGUS_GUIDETREE { - tag "$meta.id" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/magus-msa:0.2.0--pyhdfd78af_0': - 'biocontainers/magus-msa:0.2.0--pyhdfd78af_0' }" - - input: - tuple val(meta), path(fasta) - - output: - tuple val(meta), path("*.tree"), emit: tree - 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}" - """ - magus \\ - -np $task.cpus \\ - -i $fasta \\ - -o ${prefix}.tree \\ - --onlyguidetree TRUE \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - MAGUS: \$(magus --version) - END_VERSIONS - """ - - stub: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.tree - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - MAGUS: \$(magus --version) - END_VERSIONS - """ -} diff --git a/modules/nf-core/magus/guidetree/meta.yml b/modules/nf-core/magus/guidetree/meta.yml deleted file mode 100644 index 2cc3020d..00000000 --- a/modules/nf-core/magus/guidetree/meta.yml +++ /dev/null @@ -1,46 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: "magus_guidetree" -description: Multiple Sequence Alignment using Graph Clustering -keywords: - - MSA - - guidetree - - genomics - - graph -tools: - - "magus": - description: "Multiple Sequence Alignment using Graph Clustering" - homepage: "https://github.com/vlasmirnov/MAGUS" - documentation: "https://github.com/vlasmirnov/MAGUS" - tool_dev_url: "https://github.com/vlasmirnov/MAGUS" - doi: "10.1093/bioinformatics/btaa992" - licence: ["MIT"] - identifier: biotools:magus - -input: - - - meta: - type: map - description: | - Groovy Map containing fasta meta information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Input sequences in FASTA format. - pattern: "*.{fa,fna,fasta}" -output: - - tree: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - "*.tree": - type: file - description: File containing the output guidetree, in newick format. - pattern: "*.tree" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@lrauschning" diff --git a/modules/nf-core/magus/guidetree/tests/main.nf.test b/modules/nf-core/magus/guidetree/tests/main.nf.test deleted file mode 100644 index 953e37e5..00000000 --- a/modules/nf-core/magus/guidetree/tests/main.nf.test +++ /dev/null @@ -1,39 +0,0 @@ -nextflow_process { - - name "Test Process MAGUS_GUIDETREE" - script "../main.nf" - process "MAGUS_GUIDETREE" - - tag "modules" - tag "modules_nfcore" - tag "magus" - tag "magus/guidetree" - - test("setoxin - fasta") { - - when { - process { - """ - input[0] = [ [ id:'test' ], // meta map - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - //{ assert snapshot(process.out.tree).match("tree")}, - // tests seem to be reproducible on a single machine, but not across different machines - // test the correct samples are in there - { assert path(process.out.tree[0][1]).getText().contains("1apf") }, - { assert path(process.out.tree[0][1]).getText().contains("1ahl") }, - { assert path(process.out.tree[0][1]).getText().contains("1atx") }, - { assert path(process.out.tree[0][1]).getText().contains("1sh1") }, - { assert path(process.out.tree[0][1]).getText().contains("1bds") }, - { assert snapshot(process.out.versions).match("versions") } - ) - } - } -} \ No newline at end of file diff --git a/modules/nf-core/magus/guidetree/tests/main.nf.test.snap b/modules/nf-core/magus/guidetree/tests/main.nf.test.snap deleted file mode 100644 index d564be3d..00000000 --- a/modules/nf-core/magus/guidetree/tests/main.nf.test.snap +++ /dev/null @@ -1,23 +0,0 @@ -{ - "versions": { - "content": [ - [ - "versions.yml:md5,5a2ad92c9ea945c4bf4890f02ca2562f" - ] - ], - "timestamp": "2024-03-28T18:25:41.292337485" - }, - "tree": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.tree:md5,c742636229d166322a2824d409595738" - ] - ] - ], - "timestamp": "2024-03-28T18:25:41.226027114" - } -} \ No newline at end of file diff --git a/modules/nf-core/magus/guidetree/tests/tags.yml b/modules/nf-core/magus/guidetree/tests/tags.yml deleted file mode 100644 index 12b89af8..00000000 --- a/modules/nf-core/magus/guidetree/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -magus/guidetree: - - "modules/nf-core/magus/guidetree/**"