From 82839e65535424f9aa54657ae31004149ba8a2bb Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 1 Nov 2023 15:58:12 +0000 Subject: [PATCH] chore(deps): update biocontainers/checkm-genome docker tag to v1.2.2 (#4213) * chore(deps): update biocontainers/checkm-genome docker tag to v1.2.2 * Fix meta.yml and update singularity container --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Mahesh Binzer-Panchal --- modules/nf-core/checkm/lineagewf/main.nf | 4 ++-- modules/nf-core/checkm/lineagewf/meta.yml | 2 +- modules/nf-core/checkm/qa/main.nf | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/checkm/lineagewf/main.nf b/modules/nf-core/checkm/lineagewf/main.nf index f754d78bcdbf..dbaab0b619e8 100644 --- a/modules/nf-core/checkm/lineagewf/main.nf +++ b/modules/nf-core/checkm/lineagewf/main.nf @@ -4,8 +4,8 @@ process CHECKM_LINEAGEWF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : - 'biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.2--pyhdfd78af_0' : + 'biocontainers/checkm-genome:1.2.2--pyhdfd78af_0' }" input: tuple val(meta), path(fasta, stageAs: "input_bins/*") diff --git a/modules/nf-core/checkm/lineagewf/meta.yml b/modules/nf-core/checkm/lineagewf/meta.yml index b1deed0d0183..239b8d2eba23 100644 --- a/modules/nf-core/checkm/lineagewf/meta.yml +++ b/modules/nf-core/checkm/lineagewf/meta.yml @@ -31,7 +31,7 @@ input: description: One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value pattern: "*.{$fasta_ext}" - fasta_ext: - type: value + type: string description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas) - db: type: directory diff --git a/modules/nf-core/checkm/qa/main.nf b/modules/nf-core/checkm/qa/main.nf index df4f9ba7268c..a4c475cc632d 100644 --- a/modules/nf-core/checkm/qa/main.nf +++ b/modules/nf-core/checkm/qa/main.nf @@ -5,7 +5,7 @@ process CHECKM_QA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' : - 'biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }" + 'biocontainers/checkm-genome:1.2.2--pyhdfd78af_0' }" input: tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file)