From 134272c7ee2de794554d51d1a55ea2a4a7e3f9a0 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Tue, 26 Apr 2022 17:04:57 +0200 Subject: [PATCH 01/10] Add missing container folders as output channels --- .../antismashlitedownloaddatabases/main.nf | 6 +++++- .../antismashlitedownloaddatabases/meta.yml | 21 ++++++++++++++++--- .../antismashlitedownloaddatabases/test.yml | 11 +++++++++- 3 files changed, 33 insertions(+), 5 deletions(-) diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf index 1853d80a..2154bafa 100644 --- a/modules/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/antismash/antismashlitedownloaddatabases/main.nf @@ -7,8 +7,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { 'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }" /* - These files are normally downloaded by download-antismash-databases itself, and must be retrieved for input 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. This is solely for use for CI tests of the nf-core/module version of antiSMASH. + These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input 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. This is solely for use for CI tests of the nf-core/module version of antiSMASH. Reason: Upon execution, the tool checks if certain database files are present within the container and if not, it tries to create them in /usr/local/bin, for which only root user has write permissions. Mounting those database files with this module prevents the tool from trying to create them. + These files are also emitted as output channels in this module to enable the antismash-lite module to use them as mount volumes to the docker/singularity containers. */ containerOptions { @@ -26,6 +27,9 @@ 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 "versions.yml", emit: versions when: diff --git a/modules/antismash/antismashlitedownloaddatabases/meta.yml b/modules/antismash/antismashlitedownloaddatabases/meta.yml index ad393bae..9e95957a 100644 --- a/modules/antismash/antismashlitedownloaddatabases/meta.yml +++ b/modules/antismash/antismashlitedownloaddatabases/meta.yml @@ -27,17 +27,17 @@ input: - database_css: 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 use 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. + 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 ther use 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" - database_detection: 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 use 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. + 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" - database_modules: 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 use 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. + 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" output: @@ -50,6 +50,21 @@ output: type: directory description: Download directory for antiSMASH databases pattern: "antismash_db" + - css_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" authors: - "@jasmezz" diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml index 3493bb4b..808e3b7e 100644 --- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml +++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml @@ -1,14 +1,23 @@ - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config tags: - - antismash/antismashlitedownloaddatabases - antismash + - antismash/antismashlitedownloaddatabases files: - path: output/antismash/versions.yml md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3 + - path: output/untar1/versions.yml + md5sum: b724089c7a3b22557626e3d6cf79884d + - path: output/untar2/versions.yml + md5sum: 7182a024e050e5fb6b8830930e551adc + - path: output/untar3/versions.yml + md5sum: d27a9b44dd969d74d237e52ac89bd8e5 - path: output/antismash/antismash_db - path: output/antismash/antismash_db/clusterblast - path: output/antismash/antismash_db/clustercompare - 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 From d79433dcac78aa231f21177a3d69fde3cceb1cec Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Wed, 27 Apr 2022 10:08:07 +0200 Subject: [PATCH 02/10] Apply suggestions from code review Co-authored-by: James A. Fellows Yates --- modules/antismash/antismashlitedownloaddatabases/meta.yml | 2 +- .../antismash/antismashlitedownloaddatabases/test.yml | 6 ------ 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/modules/antismash/antismashlitedownloaddatabases/meta.yml b/modules/antismash/antismashlitedownloaddatabases/meta.yml index 9e95957a..619dc8c2 100644 --- a/modules/antismash/antismashlitedownloaddatabases/meta.yml +++ b/modules/antismash/antismashlitedownloaddatabases/meta.yml @@ -27,7 +27,7 @@ input: - database_css: 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 ther use 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. + 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" - database_detection: type: directory diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml index 808e3b7e..ac38eee3 100644 --- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml +++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml @@ -6,12 +6,6 @@ files: - path: output/antismash/versions.yml md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3 - - path: output/untar1/versions.yml - md5sum: b724089c7a3b22557626e3d6cf79884d - - path: output/untar2/versions.yml - md5sum: 7182a024e050e5fb6b8830930e551adc - - path: output/untar3/versions.yml - md5sum: d27a9b44dd969d74d237e52ac89bd8e5 - path: output/antismash/antismash_db - path: output/antismash/antismash_db/clusterblast - path: output/antismash/antismash_db/clustercompare From 31547edc1e2491c16c00ffff4ed34de193f72b65 Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Wed, 27 Apr 2022 10:14:14 +0200 Subject: [PATCH 03/10] Update tool name --- modules/antismash/antismashlitedownloaddatabases/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf index 2154bafa..72314eee 100644 --- a/modules/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/antismash/antismashlitedownloaddatabases/main.nf @@ -44,7 +44,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { cat <<-END_VERSIONS > versions.yml "${task.process}": - antismash: \$(antismash --version | sed 's/antiSMASH //') + antismash-lite: \$(antismash --version | sed 's/antiSMASH //') END_VERSIONS """ } From 9108e2e2ec337978929cafc8d7cfedb656124786 Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Wed, 27 Apr 2022 12:22:05 +0200 Subject: [PATCH 04/10] Update test output checksum --- tests/modules/antismash/antismashlitedownloaddatabases/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml index ac38eee3..1079363c 100644 --- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml +++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml @@ -5,7 +5,7 @@ - antismash/antismashlitedownloaddatabases files: - path: output/antismash/versions.yml - md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3 + md5sum: 24859c67023abab99de295d3675a24b6 - path: output/antismash/antismash_db - path: output/antismash/antismash_db/clusterblast - path: output/antismash/antismash_db/clustercompare From c7408538746bd2c8d64418691c0e0440483c48da Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Thu, 28 Apr 2022 16:42:44 +0200 Subject: [PATCH 05/10] Antismash db output patch 1 (#3) * Update main.nf * Update meta.yml * Update test.yml --- .../antismashlitedownloaddatabases/main.nf | 6 +++--- .../antismashlitedownloaddatabases/meta.yml | 18 ++++-------------- .../antismashlitedownloaddatabases/test.yml | 9 ++++----- 3 files changed, 11 insertions(+), 22 deletions(-) diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf index 72314eee..5f9141f0 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: @@ -42,6 +40,8 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { --database-dir antismash_db \\ $args + cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir + cat <<-END_VERSIONS > versions.yml "${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..4b9644c4 100644 --- a/modules/antismash/antismashlitedownloaddatabases/meta.yml +++ b/modules/antismash/antismashlitedownloaddatabases/meta.yml @@ -27,7 +27,7 @@ input: - database_css: 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. + 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 ther use 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" - database_detection: type: directory @@ -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..f9143163 100644 --- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml +++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml @@ -1,17 +1,16 @@ - 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 + md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3 - path: output/antismash/antismash_db - path: output/antismash/antismash_db/clusterblast - path: output/antismash/antismash_db/clustercompare - 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 From 39258e53d7b6168fc576d1d46dbd78c286919ec1 Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Thu, 28 Apr 2022 17:09:40 +0200 Subject: [PATCH 06/10] Update checksum in test.yml --- tests/modules/antismash/antismashlitedownloaddatabases/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml index f9143163..b4a964a0 100644 --- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml +++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml @@ -5,7 +5,7 @@ - antismash files: - path: output/antismash/versions.yml - md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3 + md5sum: 24859c67023abab99de295d3675a24b6 - path: output/antismash/antismash_db - path: output/antismash/antismash_db/clusterblast - path: output/antismash/antismash_db/clustercompare From 5cd517e7596b8869d27c01505029ac1449067e95 Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Mon, 2 May 2022 14:31:40 +0200 Subject: [PATCH 07/10] Apply suggestions from code review Co-authored-by: James A. Fellows Yates --- modules/antismash/antismashlitedownloaddatabases/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/antismash/antismashlitedownloaddatabases/meta.yml b/modules/antismash/antismashlitedownloaddatabases/meta.yml index 4b9644c4..f7ddf3b0 100644 --- a/modules/antismash/antismashlitedownloaddatabases/meta.yml +++ b/modules/antismash/antismashlitedownloaddatabases/meta.yml @@ -27,7 +27,7 @@ input: - database_css: 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 ther use 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. + 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" - database_detection: type: directory From 0fc352188b8060331ee4268ee5492d9a54905b47 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 2 May 2022 14:40:35 +0200 Subject: [PATCH 08/10] Fix conda antismash path --- modules/antismash/antismashlitedownloaddatabases/main.nf | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf index 5f9141f0..da8a750d 100644 --- a/modules/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/antismash/antismashlitedownloaddatabases/main.nf @@ -35,12 +35,19 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { script: def args = task.ext.args ?: '' + conda = params.enable_conda """ download-antismash-databases \\ --database-dir antismash_db \\ $args - cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir + if [[ $conda = false ]]; \ + then \ + cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir; \ + else \ + antismash_path=\$(python -c 'import antismash;print(antismash.__file__.split("__")[0])') \ + cp -r \$antismash_path antismash_dir; \ + fi cat <<-END_VERSIONS > versions.yml "${task.process}": From 6a9f2077cf6f224c547e4c7ff0f703cedc69bda2 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 2 May 2022 16:41:59 +0200 Subject: [PATCH 09/10] Fix unbound variable crash --- modules/antismash/antismashlitedownloaddatabases/main.nf | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf index da8a750d..fbb92490 100644 --- a/modules/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/antismash/antismashlitedownloaddatabases/main.nf @@ -37,16 +37,15 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { def args = task.ext.args ?: '' conda = params.enable_conda """ - download-antismash-databases \\ - --database-dir antismash_db \\ - $args + #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 \ - antismash_path=\$(python -c 'import antismash;print(antismash.__file__.split("__")[0])') \ - cp -r \$antismash_path antismash_dir; \ + cp -r \$(python -c 'import antismash;print(antismash.__file__.split("/__")[0])') antismash_dir; \ fi cat <<-END_VERSIONS > versions.yml From 8db0b754c0422cb80d06f47986d660f8aaf02c89 Mon Sep 17 00:00:00 2001 From: Jasmin F <73216762+jasmezz@users.noreply.github.com> Date: Mon, 2 May 2022 16:56:39 +0200 Subject: [PATCH 10/10] Fix commented-out command --- modules/antismash/antismashlitedownloaddatabases/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf index fbb92490..a0928333 100644 --- a/modules/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/antismash/antismashlitedownloaddatabases/main.nf @@ -37,9 +37,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { def args = task.ext.args ?: '' conda = params.enable_conda """ - #download-antismash-databases \\ - # --database-dir antismash_db \\ - # $args + download-antismash-databases \\ + --database-dir antismash_db \\ + $args if [[ $conda = false ]]; \ then \