Extract reads for viral taxids

.nf-core.yml

@@ -16,3 +16,8 @@ lint:
     - docs/README.md
     - pyproject.toml
 repository_type: pipeline
+template:
+  author: LilyAnderssonLee
+  description: nf-core/taxprofiler post processing
+  name: metaval
+  prefix: genomic-medicine-sweden

CHANGELOG.md

@@ -1,4 +1,4 @@
-# nf-core/metaval: Changelog
+# genomic-medicine-sweden/meta-val: Changelog
 
 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).

CITATIONS.md

@@ -18,6 +18,9 @@
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [KrakenTools](https://www.nature.com/articles/s41596-022-00738-y)
+  > Lu J, Rincon N, Wood DE, et al. Metagenome analysis using the Kraken software suite. Nat Protoc. 2022;17(12). doi:10.1038/s41596-022-00738-y
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

README.md

@@ -5,8 +5,8 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/genomic-medicine-sweden/tomte/workflows/nf-core%20CI/badge.svg)](https://github.com/genomic-medicine-sweden/meta-val/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/tomte/workflows/nf-core%20linting/badge.svg)](https://github.com/genomic-medicine-sweden/meta-val/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/metaval/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions CI Status](https://github.com/genomic-medicine-sweden/meta-val/workflows/nf-core%20CI/badge.svg)](https://github.com/genomic-medicine-sweden/meta-val/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/meta-val/workflows/nf-core%20linting/badge.svg)](https://github.com/genomic-medicine-sweden/meta-val/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/metaval/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -16,9 +16,9 @@
 
 ## Introduction
 
-**genomic-medicine-sweden/metaval** is a bioinformatics pipeline constructed using the `nf-core` [template](https://nf-co.re/tools#creating-a-new-pipeline). The pipeline verifies the organisms predicted by the `nf-core/taxprofiler pipeline using metagenomic data, including both Illumina short-gun sequencing and Nanopore sequencing data.
+**genomic-medicine-sweden/meta-val** is a bioinformatics pipeline for post-processing of [nf-core/taxprofiler](https://github.com/nf-core/taxprofiler) results. It verifies the organisms predicted by the nf-core/taxprofiler pipeline using metagenomic data, which includes both Illumina shortgun sequencing and Nanopore sequencing data. At moment, `genomic-medicine-sweden/meta-val` only verifies the classification results from three classifiers `Kraken2`, `Centrifuge` and `diamond`.
 
-At moment, `metaval` only checks the classification results from three classifiers `Kraken2`, `Centrifuge` and `diamond`.
+The pipeline, constructed using the `nf-core` [template](https://nf-co.re/tools#creating-a-new-pipeline), utilizing Docker/Singularity containers for easy installation and reproducible results. The implementation follows [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl1.html), employing one container per process for simplified maintenance and dependency management. Processes are sourced from [nf-core/modules](https://github.com/nf-core/modules) for broader accessibility within the Nextflow community.
 
 ## Pipeline summary
 
@@ -42,17 +42,17 @@ First, prepare a samplesheet with your input data that looks as follows:
 `samplesheet.csv`:
 
 ```csv
-sample,run_accession,instrument_platform,fastq_1,fastq_2,kraken2_report,kraken2_result,centrifuge_report,centrifuge_result,diamond
-sample1,run1,ILLUMINA,sample1.unmapped_1.fastq.gz,sample1.unmapped_2.fastq.gz,sample1.kraken2.kraken2.report.txt,sample1.kraken2.kraken2.classifiedreads.txt,sample1.centrifuge.txt,sample1.centrifuge.results.txt,sample1.diamond.tsv
-sample2,run1,ILLUMINA,sample2.unmapped_1.fastq.gz,sample2.unmapped_2.fastq.gz,sample2.kraken2.kraken2.report.txt,sample2.kraken2.kraken2.classifiedreads.txt,sample2.centrifuge.txt,sample2.centrifuge.results.txt,sample2.diamond.tsv
+sample,run_accession,instrument_platform,fastq_1,fastq_2,kraken2_report,kraken2_result,kraken2_taxpasta,centrifuge_report,centrifuge_result,centrifuge_taxpasta,diamond,diamond_taxpasta
+sample1,run1,ILLUMINA,sample1.unmapped_1.fastq.gz,sample1.unmapped_2.fastq.gz,sample1.kraken2.kraken2.report.txt,sample1.kraken2.kraken2.classifiedreads.txt,kraken2_kraken2-db.tsv,sample1.centrifuge.txt,sample1.centrifuge.results.txt,centrifuge_centrifuge-db.tsv,sample1.diamond.tsv,diamond_diamond-db.tsv
+sample2,run1,ILLUMINA,sample2.unmapped_1.fastq.gz,sample2.unmapped_2.fastq.gz,sample2.kraken2.kraken2.report.txt,sample2.kraken2.kraken2.classifiedreads.txt,kraken2_kraken2-db.tsv,sample2.centrifuge.txt,sample2.centrifuge.results.txt,centrifuge_centrifuge-db.tsv,sample2.diamond.tsv,diamond_diamond-db.tsv
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
 
 Now, you can run the pipeline using:
 
 ```bash
-nextflow run main.nf \
+nextflow run genomic-medicine-sweden/meta-val \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir <OUTDIR>
@@ -63,7 +63,7 @@ nextflow run main.nf \
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
 > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
-For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/metaval/usage) and the [parameter documentation](https://nf-co.re/metaval/parameters).
+For more details and further functionality, please refer to the [usage documentation](https://github.com/genomic-medicine-sweden/meta-val/blob/dev/docs/usage.md).
 
 ## Test data
 
@@ -123,13 +123,12 @@ SRR13439790.7	0	0
 
 ## Pipeline output
 
-To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/metaval/results) tab on the nf-core website pipeline page.
 For more details about the output files and reports, please refer to the
-[output documentation](https://nf-co.re/metaval/output).
+[output documentation](https://github.com/genomic-medicine-sweden/meta-val/blob/dev/docs/output.md).
 
 ## Credits
 
-nf-core/metaval was originally written by LilyAnderssonLee.
+genomic-medicine-sweden/meta-val was originally written by [LilyAnderssonLee](https://github.com/LilyAnderssonLee). Additional contributors were [sofstam](https://github.com/sofstam), [lokeshbio](https://github.com/lokeshbio)
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
@@ -139,17 +138,21 @@ We thank the following people for their extensive assistance in the development
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-For further information or help, don't hesitate to get in touch on the [Slack `#metaval` channel](https://nfcore.slack.com/channels/metaval) (you can join with [this invite](https://nf-co.re/join/slack)).
+For further information or help, don't hesitate to get in touch by opening an [issue](https://github.com/genomic-medicine-sweden/meta-val/issues).
 
 ## Citations
 
+If you use genomic-medicine-sweden/meta-val for your analysis, pelase cite it using the following doi:xxxxx
+
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use nf-core/metaval for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
 <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
+
 You can cite the `nf-core` publication as follows:
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**

assets/data/taxprofiler_test_data/centrifuge_db3.tsv

@@ -0,0 +1,52 @@
+taxonomy_id	lineage	ERR3201952_se_db3.centrifuge	2613_se_db3.centrifuge	2612_se_db3.centrifuge
+0		4773	434053	1801191
+1		0	0	0
+131567		0	0	0
+2759	Eukaryota	0	0	0
+33090	Eukaryota;Viridiplantae	0	0	0
+35493	Eukaryota;Viridiplantae;Streptophyta	0	0	0
+131221	Eukaryota;Viridiplantae;Streptophyta;Streptophytina	0	0	0
+3193	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta	0	0	0
+58023	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta	0	0	0
+78536	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta	0	0	0
+58024	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta	0	0	0
+3398	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Magnoliopsida	0	0	0
+1437183	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta	0	0	0
+71240	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta	0	0	0
+91827	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta	0	0	0
+1437201	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta	0	0	0
+71274	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta	0	0	0
+91888	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta	0	0	0
+91889	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta;Garryales	0	0	0
+4390	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta;Garryales;Eucommiaceae	0	0	0
+4391	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta;Garryales;Eucommiaceae;Eucommia	0	0	0
+4392	Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Magnoliopsida;Embryophyta;Garryales;Eucommiaceae;Eucommia;Eucommia ulmoides	164	364	8972
+33154	Eukaryota;Opisthokonta	0	0	0
+33208	Eukaryota;Opisthokonta;Metazoa	0	0	0
+6072	Eukaryota;Metazoa;Opisthokonta	0	0	0
+33213	Eukaryota;Metazoa;Opisthokonta	0	0	0
+33511	Eukaryota;Metazoa;Opisthokonta	0	0	0
+7711	Eukaryota;Metazoa;Opisthokonta;Chordata	0	0	0
+89593	Eukaryota;Metazoa;Opisthokonta;Chordata;Craniata	0	0	0
+7742	Eukaryota;Metazoa;Chordata;Craniata;Opisthokonta	0	0	0
+7776	Eukaryota;Metazoa;Chordata;Craniata;Opisthokonta	0	0	0
+117570	Eukaryota;Metazoa;Chordata;Craniata;Opisthokonta	0	0	0
+117571	Eukaryota;Metazoa;Chordata;Craniata;Opisthokonta	0	0	0
+8287	Eukaryota;Metazoa;Chordata;Craniata;Opisthokonta;Sarcopterygii	0	0	0
+1338369	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Opisthokonta	0	0	0
+32523	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Opisthokonta	0	0	0
+32524	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Opisthokonta	0	0	0
+40674	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Opisthokonta;Mammalia	0	0	0
+32525	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta	0	0	0
+9347	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta	0	0	0
+1437010	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta	0	0	0
+314146	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires	0	0	0
+9443	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates	0	0	0
+376913	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini	0	0	0
+314293	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes	0	0	0
+9526	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini	0	0	0
+314295	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea	0	0	0
+9604	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae	0	0	0
+207598	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae	0	0	0
+9605	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo	0	0	0
+9606	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens	0	76	341

assets/data/taxprofiler_test_data/diamond_db1.tsv

@@ -0,0 +1,3 @@
+taxonomy_id	lineage	2611_se_db1.diamond	ERR3201952_se_db1.diamond	2613_se_db1.diamond	2612_se_db1.diamond
+0		787877	4937	434491	1810485
+8058	Eukaryota;Metazoa;Chordata;Craniata;Actinopterygii;Actinopteri;Neopterygii;Teleostei;Euteleosteomorpha;Opisthokonta;Gadiformes;Gadoidei;Gadidae;Merlangius;Merlangius merlangus	0	0	2	19

assets/data/taxprofiler_test_data/kraken2_db2.tsv

@@ -0,0 +1,45 @@
+taxonomy_id	lineage	2611_se_db2.kraken2.kraken2.report	ERR3201952_se_db2.kraken2.kraken2.report	2613_se_db2.kraken2.kraken2.report	2612_se_db2.kraken2.kraken2.report
+0		787758	4937	434423	1810182
+1		0	0	0	0
+131567		0	0	0	0
+2759	Eukaryota	0	0	0	0
+33154	Eukaryota;Opisthokonta	0	0	0	0
+4751	Eukaryota;Opisthokonta;Fungi	0	0	0	0
+451864	Eukaryota;Opisthokonta;Fungi;Dikarya	0	0	0	0
+4890	Eukaryota;Opisthokonta;Fungi;Dikarya;Ascomycota	0	0	0	0
+716545	Eukaryota;Fungi;Dikarya;Ascomycota;Opisthokonta	0	0	0	0
+147537	Eukaryota;Fungi;Dikarya;Ascomycota;Opisthokonta;Saccharomycotina	0	0	0	0
+4891	Eukaryota;Fungi;Dikarya;Ascomycota;Opisthokonta;Saccharomycotina;Saccharomycetes	0	0	0	0
+4892	Eukaryota;Fungi;Dikarya;Ascomycota;Opisthokonta;Saccharomycotina;Saccharomycetes;Saccharomycetales	0	0	0	0
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+4930	Eukaryota;Fungi;Dikarya;Ascomycota;Opisthokonta;Saccharomycotina;Saccharomycetes;Saccharomycetales;Saccharomycetaceae;Saccharomyces	0	0	0	0
+4932	Eukaryota;Fungi;Dikarya;Ascomycota;Opisthokonta;Saccharomycotina;Saccharomycetes;Saccharomycetales;Saccharomycetaceae;Saccharomyces;Saccharomyces cerevisiae	0	0	0	0
+559292	Eukaryota;Fungi;Dikarya;Ascomycota;Opisthokonta;Saccharomycotina;Saccharomycetes;Saccharomycetales;Saccharomycetaceae;Saccharomyces;Saccharomyces cerevisiae;Saccharomyces cerevisiae S288C	96	0	1	15
+33208	Eukaryota;Opisthokonta;Metazoa	0	0	0	0
+6072	Eukaryota;Metazoa;Opisthokonta	0	0	0	0
+33213	Eukaryota;Metazoa;Opisthokonta	0	0	0	0
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+8287	Eukaryota;Metazoa;Chordata;Craniata;Opisthokonta;Sarcopterygii	0	0	0	0
+1338369	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Opisthokonta	0	0	0	0
+32523	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Opisthokonta	0	0	0	0
+32524	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Opisthokonta	0	0	0	0
+40674	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Opisthokonta;Mammalia	0	0	0	0
+32525	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta	0	0	0	0
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+314293	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes	0	0	0	0
+9526	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini	0	0	0	0
+314295	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea	0	0	0	0
+9604	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae	0	0	0	0
+207598	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae	0	0	0	0
+9605	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo	0	0	0	0
+9606	Eukaryota;Metazoa;Chordata;Craniata;Sarcopterygii;Mammalia;Opisthokonta;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens	23	0	69	307