From 561f16fe7430eefce5b668afccde7c20790dda0f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 15 Sep 2021 17:46:29 +0200 Subject: [PATCH] update: MALT build version bump (#699) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Bump versions Co-authored-by: Harshil Patel --- modules/malt/build/main.nf | 8 +++----- tests/modules/malt/build_test/test.yml | 8 ++++---- 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/modules/malt/build/main.nf b/modules/malt/build/main.nf index efadf9cf..a7e3751b 100644 --- a/modules/malt/build/main.nf +++ b/modules/malt/build/main.nf @@ -11,13 +11,11 @@ process MALT_BUILD { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } - // Do not **auto-bump** due to problem with change of version numbering between 0.4.1 and 0.5.2 - // (originally 0.4.1 was listed as 0.41, so is always selected as 'latest' even though it is not!) - conda (params.enable_conda ? "bioconda::malt=0.5.2" : null) + conda (params.enable_conda ? "bioconda::malt=0.53" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/malt:0.5.2--0" + container "https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0" } else { - container "quay.io/biocontainers/malt:0.5.2--0" + container "quay.io/biocontainers/malt:0.53--hdfd78af_0" } input: diff --git a/tests/modules/malt/build_test/test.yml b/tests/modules/malt/build_test/test.yml index 23ca4550..c3ed4b8f 100644 --- a/tests/modules/malt/build_test/test.yml +++ b/tests/modules/malt/build_test/test.yml @@ -17,9 +17,9 @@ - path: output/malt/malt_index/taxonomy.idx md5sum: bb335e7c378a5bd85761b6eeed16d984 - path: output/malt/malt_index/taxonomy.map - md5sum: ae2ea08b2119eba932a9cbcd9e634917 + md5sum: f6b05bbab2149e388cb769098e14d433 - path: output/malt/malt_index/taxonomy.tre - md5sum: 511ec8ff4fd8aaa20d59b5a91ed4e852 + md5sum: bde26a1fff5c63d3046d3863607a1e70 - name: malt build gff command: nextflow run ./tests/modules/malt/build_test -entry test_malt_build_gff -c tests/config/nextflow.config tags: @@ -43,6 +43,6 @@ - path: output/malt/malt_index/taxonomy.idx md5sum: bb335e7c378a5bd85761b6eeed16d984 - path: output/malt/malt_index/taxonomy.map - md5sum: ae2ea08b2119eba932a9cbcd9e634917 + md5sum: f6b05bbab2149e388cb769098e14d433 - path: output/malt/malt_index/taxonomy.tre - md5sum: 511ec8ff4fd8aaa20d59b5a91ed4e852 + md5sum: bde26a1fff5c63d3046d3863607a1e70