From 1712c0a9df4c9b971d0dd5c170af27472d467e2f Mon Sep 17 00:00:00 2001 From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Date: Wed, 11 Oct 2023 16:08:26 +0200 Subject: [PATCH 01/19] bump version --- CHANGELOG.md | 10 ++++++++++ assets/multiqc_config.yml | 4 ++-- docs/images/taxprofiler_logo.svg | 2 +- 3 files changed, 13 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 453515a3..7ae9f442 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.1.2dev - Augmented Akita Patch [2023-10-11] + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## v1.1.1 - Augmented Akita Patch [2023-10-11] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index a6335053..d06e86d6 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/taxprofiler + This report has been generated by the nf-core/taxprofiler analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-taxprofiler-methods-description": diff --git a/docs/images/taxprofiler_logo.svg b/docs/images/taxprofiler_logo.svg index 0cb901d9..c9aefbd2 100644 --- a/docs/images/taxprofiler_logo.svg +++ b/docs/images/taxprofiler_logo.svg @@ -7,7 +7,7 @@ viewBox="0 0 210 297" version="1.1" id="svg5" - inkscape:version="1.1.1 (c3084ef, 2021-09-22)" + inkscape:version="1.1.2dev (c3084ef, 2021-09-22)" sodipodi:docname="taxprofiler_logo.svg" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" From 785b8f02eb4c7d1770dcf587dba7f336038156a5 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 12 Oct 2023 11:12:33 +0200 Subject: [PATCH 02/19] Update nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 3ac23306..a23d9caf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -368,7 +368,7 @@ manifest { description = """Taxonomic classification and profiling of shotgun short- and long-read metagenomic data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.1' + version = '1.1.2dev' doi = '10.5281/zenodo.7728364' } From ca73d4db188542a993b56c75915fb9f3d9f22a86 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 12 Oct 2023 11:12:56 +0200 Subject: [PATCH 03/19] Apply suggestions from code review --- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7ae9f442..2c5fa4a9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.1.2dev - Augmented Akita Patch [2023-10-11] +## dev - [unreleased] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d06e86d6..fa6c4e17 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/taxprofiler + This report has been generated by the nf-core/taxprofiler analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-taxprofiler-methods-description": From 936528a20675397cfeb4317a6de43fc2302ffe7d Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 19 Oct 2023 14:18:05 +0200 Subject: [PATCH 04/19] Fix KAIJU2KRONA input tool/db mismatch --- CHANGELOG.md | 2 ++ subworkflows/local/visualization_krona.nf | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0693863f..374c8388 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#405] Fix database to tool mismatching in the KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) + ### `Dependencies` ### `Deprecated` diff --git a/subworkflows/local/visualization_krona.nf b/subworkflows/local/visualization_krona.nf index 7d8e4f01..7c3d6604 100644 --- a/subworkflows/local/visualization_krona.nf +++ b/subworkflows/local/visualization_krona.nf @@ -50,8 +50,8 @@ workflow VISUALIZATION_KRONA { Combine Kaiju profiles with their databases */ ch_input_for_kaiju2krona = ch_input_classifications.kaiju - .map{ [it[0]['db_name'], it[0], it[1]] } - .combine( databases.map{ [it[0]['db_name'], it[1]] }, by: 0 ) + .map{ meta, profiles -> [[meta['tool'], meta['db_name']], meta, profiles] } + .combine( databases.map{ meta, db -> [[meta['tool'], meta['db_name']], db] }, by: 0 ) .multiMap{ it -> profiles: [it[1], it[2]] From 82459809dac8b13bdec24beabe92e5fe6e585341 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 19 Oct 2023 14:19:05 +0200 Subject: [PATCH 05/19] Tweak changelgo --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 374c8388..36a21226 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#405] Fix database to tool mismatching in the KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#405] Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) ### `Dependencies` From 25a80a2170dbccd44eff9869562dc689a80b095b Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sun, 22 Oct 2023 06:25:11 +0200 Subject: [PATCH 06/19] Disambiguate same-db name but bracken step kraken from profile merging steps --- conf/modules.config | 2 +- subworkflows/local/profiling.nf | 10 +++++--- .../local/standardisation_profiles.nf | 25 ++++++++++++++----- subworkflows/local/visualization_krona.nf | 9 +++++-- 4 files changed, 34 insertions(+), 12 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 36209f3a..90ca6919 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -485,7 +485,7 @@ process { } withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN { - ext.prefix = { "kraken2_${meta.id}_combined_reports" } + ext.prefix = { "kraken2_${meta.db_name}_combined_reports" } publishDir = [ path: { "${params.outdir}/kraken2/" }, mode: params.publish_dir_mode, diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index bfe3398e..c02f7755 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -172,9 +172,13 @@ workflow PROFILING { ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment ) ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report - // Set the tool to be strictly 'kraken2' instead of potentially 'bracken' for downstream use. - // Will remain distinct from 'pure' Kraken2 results due to distinct database names in file names. - .map { meta, report -> [meta + [tool: 'kraken2'], report]} + // Rename tool in the meta for the for-bracken files to disambiguate from only-kraken2 results in downstream steps. + // Note may need to rename back to to just bracken in those downstream steps depending on context. + .map { + meta, report -> + def new_tool = meta['tool'] == 'bracken' ? 'kraken2-bracken' : meta['tool'] + [meta + [tool: new_tool], report] + } ) } diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf index c4e36009..d8688d75 100644 --- a/subworkflows/local/standardisation_profiles.nf +++ b/subworkflows/local/standardisation_profiles.nf @@ -52,12 +52,19 @@ workflow STANDARDISATION_PROFILES { .map { meta, profile -> def meta_new = [:] - meta_new.id = meta.db_name meta_new.tool = meta.tool == 'malt' ? 'megan6' : meta.tool + meta_new.db_name = meta.db_name [meta_new, profile] } .groupTuple () - .map { [ it[0], it[1].flatten() ] } + .map { + meta, profiles -> + meta = meta + [ + tool: meta.tool == 'kraken2-bracken' ? 'kraken2' : meta.tool, // replace to get the right output-format description + id: meta.tool == 'kraken2-bracken' ? "${meta.db_name}-bracken" : "${meta.db_name}" // append so to disambiguate when we have same databases for kraken2 step of bracken, with normal bracken + ] + [ meta, profiles.flatten() ] + } ch_taxpasta_tax_dir = params.taxpasta_taxonomy_dir ? Channel.fromPath(params.taxpasta_taxonomy_dir, checkIfExists: true).collect() : [] @@ -85,7 +92,7 @@ workflow STANDARDISATION_PROFILES { centrifuge: it[0]['tool'] == 'centrifuge' ganon: it[0]['tool'] == 'ganon' kmcp: it [0]['tool'] == 'kmcp' - kraken2: it[0]['tool'] == 'kraken2' + kraken2: it[0]['tool'] == 'kraken2' || it[0]['tool'] == 'kraken2-bracken' metaphlan: it[0]['tool'] == 'metaphlan' motus: it[0]['tool'] == 'motus' unknown: true @@ -158,11 +165,17 @@ workflow STANDARDISATION_PROFILES { // Have to sort by size to ensure first file actually has hits otherwise // the script fails ch_profiles_for_kraken2 = ch_input_profiles.kraken2 - .map { [it[0]['db_name'], it[1]] } - .groupTuple(sort: {-it.size()} ) .map { - [[id:it[0]], it[1]] + meta, profiles -> + def new_meta = [:] + new_meta.tool = meta.tool == 'kraken2-bracken' ? 'kraken2' : meta.tool // replace to get the right output-format description + new_meta.id = meta.tool // append so to disambiguate when we have same databases for kraken2 step of bracken, with normal bracken + new_meta.db_name = meta.tool == 'kraken2-bracken' ? "${meta.db_name}-bracken" : "${meta.db_name}" // append so to disambiguate when we have same databases for kraken2 step of bracken, with normal bracken + [ new_meta, profiles ] } + .dump(tag: 'b4group') + .groupTuple(sort: {-it.size()}) + .dump(tag: 'whatsgoingon') KRAKENTOOLS_COMBINEKREPORTS_KRAKEN ( ch_profiles_for_kraken2 ) ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.txt ) diff --git a/subworkflows/local/visualization_krona.nf b/subworkflows/local/visualization_krona.nf index 7d8e4f01..4cbaaf1a 100644 --- a/subworkflows/local/visualization_krona.nf +++ b/subworkflows/local/visualization_krona.nf @@ -27,7 +27,7 @@ workflow VISUALIZATION_KRONA { ch_input_profiles = profiles .branch { centrifuge: it[0]['tool'] == 'centrifuge' - kraken2: it[0]['tool'] == 'kraken2' + kraken2: it[0]['tool'] == 'kraken2' || it[0]['tool'] == 'kraken2-bracken' unknown: true } ch_input_classifications = classifications @@ -41,7 +41,12 @@ workflow VISUALIZATION_KRONA { Convert Kraken2 formatted reports into Krona text files */ ch_kraken_reports = ch_input_profiles.kraken2 - .mix( ch_input_profiles.centrifuge ) + .map { + meta, report -> + def new_tool = meta['tool'] == 'kraken2-bracken' ? 'bracken' : meta['tool'] + [meta + [tool: new_tool], report] + } + .mix( ch_input_profiles.centrifuge ) KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports ) ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt ) ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() ) From f87ed97e393f7d0741b8f1875284d681f197114c Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Mon, 23 Oct 2023 13:43:49 +0200 Subject: [PATCH 07/19] Add final docs --- docs/output.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/output.md b/docs/output.md index 493eed21..11b07fe5 100644 --- a/docs/output.md +++ b/docs/output.md @@ -360,6 +360,7 @@ The main taxonomic profiling file from Bracken is the `*.tsv` file. This provide - `kraken2/` - `_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by `krakentools`) + - If you have also run Bracken, the original Kraken report (i.e., _before_ read re-assignment) will also be included in this directory with `-bracken` suffixed to your Bracken database name. For example: `kraken2--bracken.tsv`. However in most cases you want to use the actual Bracken file (i.e., `bracken_.tsv`). - `/` - `_.classified.fastq.gz`: FASTQ file containing all reads that had a hit against a reference in the database for a given sample - `_.unclassified.fastq.gz`: FASTQ file containing all reads that did not have a hit in the database for a given sample @@ -582,6 +583,7 @@ The resulting HTML files can be loaded into your web browser for exploration. Ea - `_*.{tsv,csv,arrow,parquet,biom}`: Standardised taxon table containing multiple samples. The standard format is the `tsv`. - The first column describes the taxonomy ID and the rest of the columns describe the read counts for each sample. - Note that the file naming scheme will apply regardless of whether `TAXPASTA_MERGE` (multiple sample run) or `TAXPASTA_STANDARDISE` (single sample run) are executed. + - If you have also run Bracken, the initial Kraken report (i.e., _before_ read re-assignment) will also be included in this directory with `-bracken` suffixed to your Bracken database name. For example: `kraken2--bracken.tsv`. However in most cases you want to use the actual Bracken file (i.e., `bracken_.tsv`). From 51cf6be7165faa14d61c442ec1deb2ded2dc9528 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Mon, 23 Oct 2023 13:48:06 +0200 Subject: [PATCH 08/19] Update changelgo --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0693863f..3f392df1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#406] Fixed overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133) + ### `Dependencies` ### `Deprecated` From c5582aae9d8d40f498eb0a6742d5036b94bea044 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 24 Oct 2023 10:20:57 +0200 Subject: [PATCH 09/19] Add preprint citation info --- README.md | 8 +++++++- nextflow.config | 2 +- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 2e6a5705..46e822a6 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,8 @@ [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Cite Preprint](https://img.shields.io/badge/Cite%20Us!-Cite%20Preprint-orange)](https://doi.org/10.1101/2023.10.20.563221) + ## Introduction **nf-core/taxprofiler** is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, and produces standardised output tables for facilitating results comparison between different tools and databases. @@ -142,7 +144,11 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If you use nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.5281/zenodo.7728364](https://doi.org/10.5281/zenodo.7728364) +If you use nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.1101/2023.10.20.563221](https://doi.org/10.1101/2023.10.20.563221). + +> Stamouli, S., Beber, M. E., Normark, T., Christensen, T. A., Andersson-Li, L., Borry, M., Jamy, M., nf-core community, & Fellows Yates, J. A. (2023). nf-core/taxprofiler: Highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. In bioRxiv (p. 2023.10.20.563221). https://doi.org/10.1101/2023.10.20.563221 + +For the latest version of the code, cite the Zenodo doi: [10.5281/zenodo.7728364](https://doi.org/10.5281/zenodo.7728364) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/nextflow.config b/nextflow.config index a23d9caf..e2b69297 100644 --- a/nextflow.config +++ b/nextflow.config @@ -369,7 +369,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '1.1.2dev' - doi = '10.5281/zenodo.7728364' + doi = '10.1101/2023.10.20.563221' } // Load modules.config for DSL2 module specific options From 16b81575169acaa43721584cf6e12e18f20dd6cf Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 24 Oct 2023 10:39:24 +0200 Subject: [PATCH 10/19] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 46e822a6..5be8affe 100644 --- a/README.md +++ b/README.md @@ -146,7 +146,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# If you use nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.1101/2023.10.20.563221](https://doi.org/10.1101/2023.10.20.563221). -> Stamouli, S., Beber, M. E., Normark, T., Christensen, T. A., Andersson-Li, L., Borry, M., Jamy, M., nf-core community, & Fellows Yates, J. A. (2023). nf-core/taxprofiler: Highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. In bioRxiv (p. 2023.10.20.563221). https://doi.org/10.1101/2023.10.20.563221 +> Stamouli, S., Beber, M. E., Normark, T., Christensen II, T. A., Andersson-Li, L., Borry, M., Jamy, M., nf-core community, & Fellows Yates, J. A. (2023). nf-core/taxprofiler: Highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. In bioRxiv (p. 2023.10.20.563221). https://doi.org/10.1101/2023.10.20.563221 For the latest version of the code, cite the Zenodo doi: [10.5281/zenodo.7728364](https://doi.org/10.5281/zenodo.7728364) From 6282a694a2bf610827955041464975bac5f4dc0b Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 24 Oct 2023 11:14:18 +0200 Subject: [PATCH 11/19] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0693863f..097f650b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- [#408] Added preprint citation information to README and manifest (added by @jfy133) + ### `Fixed` ### `Dependencies` From da8bf5ae26d1d83a83d05ba017977e60969dba89 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 25 Oct 2023 15:08:14 +0200 Subject: [PATCH 12/19] Apply suggestions from code review Co-authored-by: Moritz E. Beber --- subworkflows/local/profiling.nf | 4 ++-- subworkflows/local/standardisation_profiles.nf | 2 -- subworkflows/local/visualization_krona.nf | 3 +-- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index c02f7755..b4c71efb 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -176,8 +176,8 @@ workflow PROFILING { // Note may need to rename back to to just bracken in those downstream steps depending on context. .map { meta, report -> - def new_tool = meta['tool'] == 'bracken' ? 'kraken2-bracken' : meta['tool'] - [meta + [tool: new_tool], report] + def new_tool = + [meta + [tool: meta.tool == 'bracken' ? 'kraken2-bracken' : meta.tool], report] } ) diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf index d8688d75..4592e9de 100644 --- a/subworkflows/local/standardisation_profiles.nf +++ b/subworkflows/local/standardisation_profiles.nf @@ -173,9 +173,7 @@ workflow STANDARDISATION_PROFILES { new_meta.db_name = meta.tool == 'kraken2-bracken' ? "${meta.db_name}-bracken" : "${meta.db_name}" // append so to disambiguate when we have same databases for kraken2 step of bracken, with normal bracken [ new_meta, profiles ] } - .dump(tag: 'b4group') .groupTuple(sort: {-it.size()}) - .dump(tag: 'whatsgoingon') KRAKENTOOLS_COMBINEKREPORTS_KRAKEN ( ch_profiles_for_kraken2 ) ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.txt ) diff --git a/subworkflows/local/visualization_krona.nf b/subworkflows/local/visualization_krona.nf index 44ac0b42..77e26a22 100644 --- a/subworkflows/local/visualization_krona.nf +++ b/subworkflows/local/visualization_krona.nf @@ -43,8 +43,7 @@ workflow VISUALIZATION_KRONA { ch_kraken_reports = ch_input_profiles.kraken2 .map { meta, report -> - def new_tool = meta['tool'] == 'kraken2-bracken' ? 'bracken' : meta['tool'] - [meta + [tool: new_tool], report] + [meta + [tool: meta.tool == 'bracken' ? 'kraken2-bracken' : meta.tool], report] } .mix( ch_input_profiles.centrifuge ) KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports ) From 527ca85c2ea9af64d2d7f64498f61a9360d72bab Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 26 Oct 2023 05:43:24 +0200 Subject: [PATCH 13/19] Update MEGAN --- modules/nf-core/megan/rma2info/environment.yml | 6 ++++++ modules/nf-core/megan/rma2info/main.nf | 6 +++--- modules/nf-core/megan/rma2info/meta.yml | 5 ++--- 3 files changed, 11 insertions(+), 6 deletions(-) create mode 100644 modules/nf-core/megan/rma2info/environment.yml diff --git a/modules/nf-core/megan/rma2info/environment.yml b/modules/nf-core/megan/rma2info/environment.yml new file mode 100644 index 00000000..471e5507 --- /dev/null +++ b/modules/nf-core/megan/rma2info/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::megan=6.21.7 diff --git a/modules/nf-core/megan/rma2info/main.nf b/modules/nf-core/megan/rma2info/main.nf index a1f2045a..e91af504 100644 --- a/modules/nf-core/megan/rma2info/main.nf +++ b/modules/nf-core/megan/rma2info/main.nf @@ -2,10 +2,10 @@ process MEGAN_RMA2INFO { tag "$meta.id" label 'process_single' - conda "bioconda::megan=6.21.7" + conda 'modules/nf-core/megan/rma2info/environment.yml' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0': - 'biocontainers/megan:6.21.7--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/megan:6.24.20--h9ee0642_0': + 'biocontainers/megan:6.24.20--h9ee0642_0' }" input: tuple val(meta), path(rma6) diff --git a/modules/nf-core/megan/rma2info/meta.yml b/modules/nf-core/megan/rma2info/meta.yml index 710d9346..af3dd96c 100644 --- a/modules/nf-core/megan/rma2info/meta.yml +++ b/modules/nf-core/megan/rma2info/meta.yml @@ -13,7 +13,6 @@ tools: tool_dev_url: "https://github.com/husonlab/megan-ce" doi: "10.1371/journal.pcbi.1004957" licence: "['GPL >=3']" - input: - meta: type: map @@ -27,7 +26,6 @@ input: - megan_summary: type: boolean description: Specify whether to generate an MEGAN summary file - output: - meta: type: map @@ -46,6 +44,7 @@ output: type: file description: Optionally generated MEGAN summary file pattern: "*.megan" - authors: - "@jfy133" +maintainers: + - "@jfy133" From 06d4360541eb92b14b85f7e5c293b6968b85ac8f Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 26 Oct 2023 05:45:56 +0200 Subject: [PATCH 14/19] Update CHANGELOG --- CHANGELOG.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3ffd9c45..7eac5e3b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,10 +12,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - [#405] Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) -- [#406] Fixed overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#406] Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#409] Fix a null pointer exception error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133) ### `Dependencies` +| Tool | Previous version | New version | +| -------------- | ---------------- | ----------- | +| megan/rma2info | 6.21.7 | 6.24.20 | + ### `Deprecated` ## v1.1.1 - Augmented Akita Patch [2023-10-11] From aa4e9162f2567b4a30a8fb19a1846d418bfbd80f Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 26 Oct 2023 05:46:48 +0200 Subject: [PATCH 15/19] Update Changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7eac5e3b..e1c13b4b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#405] Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) - [#406] Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133) -- [#409] Fix a null pointer exception error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#409] Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133) ### `Dependencies` From 19865202a0077f3b351d2ebc8953a25430a9ec69 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 26 Oct 2023 05:47:32 +0200 Subject: [PATCH 16/19] Add PR links in CHANGELOG --- CHANGELOG.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e1c13b4b..c8bc3b12 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,13 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -- [#408] Added preprint citation information to README and manifest (added by @jfy133) +- [#408](https://github.com/nf-core/taxprofiler/pull/408) Added preprint citation information to README and manifest (added by @jfy133) ### `Fixed` -- [#405] Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) -- [#406] Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133) -- [#409] Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#405](https://github.com/nf-core/taxprofiler/pull/405) Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#406](https://github.com/nf-core/taxprofiler/pull/406) Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133) +- [#409](https://github.com/nf-core/taxprofiler/pull/409) Fix a NullPointerException error occurring occasionally in older version of MEGAN's rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133) ### `Dependencies` From c22f719be45faa27c70cba324d74c1f915ef8149 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 26 Oct 2023 06:01:52 +0200 Subject: [PATCH 17/19] Add missing modules.json update --- modules.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules.json b/modules.json index 9dc77080..aa63d31d 100644 --- a/modules.json +++ b/modules.json @@ -163,7 +163,7 @@ }, "megan/rma2info": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "dbce8951ff9a39ad08d87e563636bbcc6ef34032", "installed_by": ["modules"] }, "metaphlan/mergemetaphlantables": { From e27ac826bfd04a250de6aea8f803d4f48a753d28 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 27 Oct 2023 05:15:58 +0200 Subject: [PATCH 18/19] Release version bump --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index fa6c4e17..90a87168 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/taxprofiler + This report has been generated by the nf-core/taxprofiler analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-taxprofiler-methods-description": diff --git a/nextflow.config b/nextflow.config index e2b69297..1b32246c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -368,7 +368,7 @@ manifest { description = """Taxonomic classification and profiling of shotgun short- and long-read metagenomic data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.2dev' + version = '1.1.2' doi = '10.1101/2023.10.20.563221' } From 32d0d6eac9fd9003ab01cb07737f28728660e307 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 27 Oct 2023 06:44:32 +0200 Subject: [PATCH 19/19] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c8bc3b12..d3fb99ba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## dev - [unreleased] +## v1.1.2 - Augmented Akita Patch [2023-10-27] ### `Added`