From ca8cf1c3058874d6c1e18bbf727d90ed390bd9e3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 12 Sep 2024 11:49:24 +0200 Subject: [PATCH] Additional minor fixes from @jfy133's review --- CHANGELOG.md | 4 +--- README.md | 2 +- subworkflows/local/profiling.nf | 18 +++++++++--------- 3 files changed, 11 insertions(+), 13 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d53cf0f6..be24fdfa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - [#417](https://github.com/nf-core/taxprofiler/pull/417) - Added reference-free metagenome complexity/coverage estimation with Nonpareil (added by @jfy133) -- [#466](https://github.com/nf-core/taxprofiler/pull/466) - Input database sheets now require a `db_type` column to distinguish between short- and long-read databases (added by @LilyAnderssonLee) +- [#466](https://github.com/nf-core/taxprofiler/pull/466) - Input database sheets can specify a `db_type` column to distinguish between short- and long-read databases (added by @LilyAnderssonLee) - [#505](https://github.com/nf-core/taxprofiler/pull/505) - Add small files to the file `tower.yml` (added by @LilyAnderssonLee) - [#508](https://github.com/nf-core/taxprofiler/pull/508) - Add `nanoq` as a filtering tool for nanopore reads (added by @LilyAnderssonLee) - [#511](https://github.com/nf-core/taxprofiler/pull/511) - Add `porechop_abi` as an alternative adapter removal tool for long reads nanopore data (added by @LilyAnderssonLee) @@ -26,7 +26,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | bbmap | 39.01 | 39.06 | | bowtie2 | 2.4.4 | 2.5.2 | | bracken | 2.7 | 2.9 | -| cat/fastq | 8.30 | | diamond | 2.0.15 | 2.1.8 | | ganon | 1.5.1 | 2.0.0 | | kraken2 | 2.1.2 | 2.1.3 | @@ -37,7 +36,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | motus/profile | 3.0.3 | 3.1.0 | | multiqc | 1.21 | 1.24.1 | | samtools | 1.17 | 1.20 | -| untar | 4.7 | 4.8 | ### `Deprecated` diff --git a/README.md b/README.md index a3edf867..5999cf12 100644 --- a/README.md +++ b/README.md @@ -73,7 +73,7 @@ Additionally, you will need a database sheet that looks as follows: `databases.csv`: -``` +```csv tool,db_name,db_params,db_path kraken2,db2,--quick,///kraken2/testdb-kraken2.tar.gz metaphlan,db1,,///metaphlan/metaphlan_database/ diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index 5e4570ce..dd9a39e8 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -90,16 +90,16 @@ workflow PROFILING { } .branch { meta, reads, db_meta, db -> centrifuge: db_meta.tool == 'centrifuge' - diamond: db_meta.tool == 'diamond' - kaiju: db_meta.tool == 'kaiju' - kraken2: db_meta.tool == 'kraken2' || db_meta.tool == 'bracken' // to reuse the kraken module to produce the input data for bracken + diamond: db_meta.tool == 'diamond' + kaiju: db_meta.tool == 'kaiju' + kraken2: db_meta.tool == 'kraken2' || db_meta.tool == 'bracken' // to reuse the kraken module to produce the input data for bracken krakenuniq: db_meta.tool == 'krakenuniq' - malt: db_meta.tool == 'malt' - metaphlan: db_meta.tool == 'metaphlan' - motus: db_meta.tool == 'motus' - kmcp: db_meta.tool == 'kmcp' - ganon: db_meta.tool == 'ganon' - unknown: true + malt: db_meta.tool == 'malt' + metaphlan: db_meta.tool == 'metaphlan' + motus: db_meta.tool == 'motus' + kmcp: db_meta.tool == 'kmcp' + ganon: db_meta.tool == 'ganon' + unknown: true } /*