Update fasta_build_add_kraken2_bracken subworkflow

CITATIONS.md

@@ -40,6 +40,10 @@
 
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
 
+- [Bracken](https://doi.org/10.7717/peerj-cs.104)
+
+  > Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ. Computer Science, 3(e104), e104. https://doi.org/10.7717/peerj-cs.104
+
 - [Centrifuge](https://doi.org/10.1101/gr.210641.116)
 
   > Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research, 26(12), 1721–1729. https://doi.org/10.1101/gr.210641.116

README.md

@@ -32,6 +32,7 @@
 
 1. Prepares input FASTA files for building
 2. Builds databases for:
+   - [Bracken](https://doi.org/10.7717/peerj-cs.104)
    - [Centrifuge](https://doi.org/10.1101/gr.210641.116)
    - [DIAMOND](https://doi.org/10.1038/nmeth.3176)
    - [Kaiju](https://doi.org/10.1038/ncomms11257)
@@ -84,7 +85,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/createtaxdb was originally written by James A. Fellows Yates and the nf-core community.
+nf-core/createtaxdb was originally written by James A. Fellows Yates, Joon Klaps, Alexander Ramos Díaz and the nf-core community.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 

conf/test.config

@@ -22,13 +22,16 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input         = params.pipelines_testdata_base_path + 'createtaxdb/samplesheets/test.csv'
+    input            = params.pipelines_testdata_base_path + 'createtaxdb/samplesheets/test.csv'
+
+    dbname           = "database"
 
     build_diamond    = true
     build_kaiju      = true
     build_malt       = true
     build_centrifuge = true
     build_kraken2    = true
+    build_bracken    = true
 
     accession2taxid  = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/nucl_gb.accession2taxid'
     nucl2taxid       = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/nucl2tax.map'

conf/test_full.config

@@ -18,4 +18,12 @@ params {
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+
+    build_diamond    = true
+    build_kaiju      = true
+    build_malt       = true
+    build_centrifuge = true
+    build_kraken2    = true
+    build_bracken    = true
+
 }

conf/test_nothing.config

@@ -30,5 +30,6 @@ params {
     build_malt       = false
     build_centrifuge = false
     build_kraken2    = false
+    build_bracken    = false
 
 }

docs/output.md

@@ -14,6 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+- [Bracken](#bracken) - Database files for Brakcen
 - [Centrifuge](#centrifuge) - Database files for Centrifuge
 - [DIAMOND](#diamond) - Database files for DIAMOND
 - [Kaiju](#kaiju) - Database files for Kaiju
@@ -51,6 +52,31 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 
 [Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
 
+### Bracken
+
+[Bracken](https://github.com/jenniferlu717/Bracken/)(Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `bracken/`
+  - `<db_name>/`
+    - `database100mers.kmer_distrib`: Bracken kmer distribution file
+    - `database100mers.kraken`: Bracken index file
+    - `database.kraken`: Bracken database file
+    - `hash.k2d`: Kraken2 hash database file
+    - `opts.k2d`: Kraken2 opts database file
+    - `taxo.k2d`: Kraken2 taxo database file
+    - `library/`: Intermediate Kraken2 directory containing FASTAs and related files of added genomes
+    - `taxonomy/`: Intermediate Kraken2 directory containing taxonomy files of added genomes
+    - `seqid2taxid.map`: Intermediate Kraken2 file containing taxonomy files of added genomes
+
+</details>
+
+Note that all intermediate files are required for Bracken2 database, even if Kraken2 itself only requires the `*.k2d` files.
+
+The resulting `<db_name>/` directory can be given to Bracken itself with `bracken -d <your_database_name>` etc.
+
 ### Centrifuge
 
 [Centrifuge](https://github.com/bbuchfink/diamond) is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples.
@@ -105,6 +131,9 @@ The `fmi` file can be given to Kaiju itself with `kaiju -f <your_database>.fmi`
     - `hash.k2d`: Kraken2 hash database file
     - `opts.k2d`: Kraken2 opts database file
     - `taxo.k2d`: Kraken2 taxo database file
+    - `library/`: Intermediate directory containing FASTAs and related files of added genomes (only present if `--build_bracken` or `--kraken2_keepintermediate` supplied)
+    - `taxonomy/`: Intermediate directory containing taxonomy files of added genomes (only present if `--build_bracken` or `--kraken2_keepintermediate` supplied)
+    - `seqid2taxid.map`: Intermediate file containing taxonomy files of added genomes (only present if `--build_bracken` or `--kraken2_keepintermediate` supplied)
 
 </details>
 

modules.json

@@ -5,6 +5,11 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "bracken/build": {
+                        "branch": "master",
+                        "git_sha": "dcbe6e77bc6cc0843ce93e6c7bd884d65c215984",
+                        "installed_by": ["fasta_build_add_kraken2_bracken"]
+                    },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
@@ -38,12 +43,12 @@
                     "kraken2/add": {
                         "branch": "master",
                         "git_sha": "ca87ad032a62f025f0c373facacef2df0c5411b2",
-                        "installed_by": ["fasta_build_add_kraken2"]
+                        "installed_by": ["fasta_build_add_kraken2_bracken"]
                     },
                     "kraken2/build": {
                         "branch": "master",
                         "git_sha": "ca87ad032a62f025f0c373facacef2df0c5411b2",
-                        "installed_by": ["fasta_build_add_kraken2"]
+                        "installed_by": ["fasta_build_add_kraken2_bracken"]
                     },
                     "malt/build": {
                         "branch": "master",
@@ -69,9 +74,9 @@
             },
             "subworkflows": {
                 "nf-core": {
-                    "fasta_build_add_kraken2": {
+                    "fasta_build_add_kraken2_bracken": {
                         "branch": "master",
-                        "git_sha": "a4d1e13a2da05307deb65a87d501aa6520162dcd",
+                        "git_sha": "9758e4dedd5788369e61b57e7d6f4751e682b17a",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {