From d24f9a622b741e6c929a6e04b94db51335fc5a3a Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 3 Nov 2023 10:10:53 +0100 Subject: [PATCH] Fix metaBAT2 bin publishing --- CHANGELOG.md | 3 ++- conf/modules.config | 4 ++-- docs/output.md | 2 ++ 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bdea0e5b..ebe2edb8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#489](https://github.com/nf-core/mag/pull/489) Fix file name collision clashes for CHECKM, CAT, GTDBTK, and QUAST (by @maxibor) +- [#489](https://github.com/nf-core/mag/pull/489) Fix file name collision clashes for CHECKM, CAT, GTDBTK, and QUAST (reported by @tillenglert and @maxibor, fix by @maxibor) +- [#527](https://github.com/nf-core/mag/pull/489) Fix glob pattern for publishing MetaBAT2 bins in results (reported by @patriciatran, fix by @jfy133) ### `Dependencies` diff --git a/conf/modules.config b/conf/modules.config index d2ebe7b2..cbfa51fb 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -570,9 +570,9 @@ process { withName: METABAT2_METABAT2 { publishDir = [ [ - path: { "${params.outdir}/GenomeBinning/MetaBAT2/" }, + path: { "${params.outdir}/GenomeBinning/MetaBAT2/bins/" }, mode: params.publish_dir_mode, - pattern: 'bins/*.fa.gz' + pattern: '*[!lowDepth|tooShort|unbinned].fa.gz' ], [ path: { "${params.outdir}/GenomeBinning/MetaBAT2/discarded" }, diff --git a/docs/output.md b/docs/output.md index c8eeee14..615c1f65 100644 --- a/docs/output.md +++ b/docs/output.md @@ -333,6 +333,8 @@ These depth files are used for downstream binning steps. All the files and contigs in these folders will be assessed by QUAST and BUSCO. +All other files that were discarded by the tool, or from the low-quality unbinned contigs , can be found here. +
Output files