diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf index 72314eee..a0928333 100644 --- a/modules/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/antismash/antismashlitedownloaddatabases/main.nf @@ -27,9 +27,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { output: path("antismash_db") , emit: database - path("css"), emit: css_dir - path("detection"), emit: detection_dir - path("modules"), emit: modules_dir + path("antismash_dir"), emit: antismash_dir path "versions.yml", emit: versions when: @@ -37,11 +35,19 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { script: def args = task.ext.args ?: '' + conda = params.enable_conda """ download-antismash-databases \\ --database-dir antismash_db \\ $args + if [[ $conda = false ]]; \ + then \ + cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir; \ + else \ + cp -r \$(python -c 'import antismash;print(antismash.__file__.split("/__")[0])') antismash_dir; \ + fi + cat <<-END_VERSIONS > versions.yml "${task.process}": antismash-lite: \$(antismash --version | sed 's/antiSMASH //') diff --git a/modules/antismash/antismashlitedownloaddatabases/meta.yml b/modules/antismash/antismashlitedownloaddatabases/meta.yml index 619dc8c2..f7ddf3b0 100644 --- a/modules/antismash/antismashlitedownloaddatabases/meta.yml +++ b/modules/antismash/antismashlitedownloaddatabases/meta.yml @@ -50,21 +50,11 @@ output: type: directory description: Download directory for antiSMASH databases pattern: "antismash_db" - - css_dir: + - antismash_dir: type: directory description: | - antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. - pattern: "css" - - detection_dir: - type: directory - description: | - antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. - pattern: "detection" - - modules_dir: - type: directory - description: | - antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. - pattern: "modules" + antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines. + pattern: "antismash_dir" authors: - "@jasmezz" diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml index 1079363c..b4a964a0 100644 --- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml +++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml @@ -1,8 +1,8 @@ - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config tags: - - antismash - antismash/antismashlitedownloaddatabases + - antismash files: - path: output/antismash/versions.yml md5sum: 24859c67023abab99de295d3675a24b6 @@ -12,6 +12,5 @@ - path: output/antismash/antismash_db/pfam - path: output/antismash/antismash_db/resfam - path: output/antismash/antismash_db/tigrfam - - path: output/antismash/css - - path: output/antismash/detection - - path: output/antismash/modules + - path: output/antismash/antismash_dir + - path: output/antismash/antismash_dir/detection/hmm_detection/data/bgc_seeds.hmm