feat: Add kraken2 taxonomy option (#29)

* feat: Add kraken2 taxonomy option Signed-off-by: jvfe <[email protected]> * docs: Update README Signed-off-by: jvfe <[email protected]> --------- Signed-off-by: jvfe <[email protected]>
dalmolingroup · Nov 7, 2023 · e4cb663 · e4cb663
1 parent e26b447
commit e4cb663
Show file tree

Hide file tree

Showing 17 changed files with 356 additions and 33 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,4 @@ results/
 testing/
 testing*
 *.pyc
+test_data/kraken_viral_db/
diff --git a/README.md b/README.md
@@ -36,7 +36,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 ### Taxonomic classification
 
 - Sequence classification ([`Kaiju`](https://github.com/bioinformatics-centre/kaiju/))
-- (**WIP**) Sequence classification ([`Kraken2`](https://github.com/DerrickWood/kraken2))
+- Sequence classification ([`Kraken2`](https://github.com/DerrickWood/kraken2))
 - Visualization ([`Krona`](https://github.com/marbl/Krona/wiki))
 
 ### Functional annotation

diff --git a/conf/modules.config b/conf/modules.config
@@ -59,6 +59,14 @@ process {
         ]
     }
 
+    withName: KRAKEN2_KRAKEN2 {
+        publishDir = [
+            path: { "${params.outdir}/taxonomy/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: KRONA_KTIMPORTTEXT {
         publishDir = [
             path: { "${params.outdir}/taxonomy/${meta.id}" },

diff --git a/docs/params.md b/docs/params.md
@@ -30,32 +30,36 @@ Choose to skip pipeline steps
 
 | Parameter | Description | Type | Default | Required | Hidden |
 |-----------|-----------|-----------|-----------|-----------|-----------|
-| `host_fasta` |  | `string` | None |  |  |
+| `host_fasta` | Host FASTA to use for decontamination | `string` |  |  |  |
+| `bowtie2_db` | Pre-built bowtie2 index. Directory where index is located. | `string` |  |  |  |
 
 ## Alignment
 
 
 
 | Parameter | Description | Type | Default | Required | Hidden |
 |-----------|-----------|-----------|-----------|-----------|-----------|
-| `reference_fasta` | Path to FASTA genome file. | `string` | None |  |  |
-| `diamond_db` | Path to pre-built DIAMOND db. | `string` | None |  |  |
+| `reference_fasta` | Path to FASTA genome file. | `string` |  |  |  |
+| `diamond_db` | Path to pre-built DIAMOND db. | `string` |  |  |  |
 
 ## Taxonomy
 
 
 
 | Parameter | Description | Type | Default | Required | Hidden |
 |-----------|-----------|-----------|-----------|-----------|-----------|
-| `kaiju_db` |  | `string` | None | True |  |
+| `kaiju_db` | Kaiju database | `string` |  | True |  |
+| `kraken2_db` | Kraken2 database | `string` |  |  |  |
+| `run_kaiju` | Run Kaiju classifier | `boolean` | True |  |  |
+| `run_kraken2` | Run Kraken2 classifier | `boolean` |  |  |  |
 
 ## Functional
 
 
 
 | Parameter | Description | Type | Default | Required | Hidden |
 |-----------|-----------|-----------|-----------|-----------|-----------|
-| `id_mapping` | Path to ID mapping file to be used for the Functional annotation | `string` | None | True |  |
+| `id_mapping` | Path to ID mapping file to be used for the Functional annotation | `string` |  | True |  |
 | `minimum_bitscore` | Minimum bitscore of a match to be used for annotation | `integer` | 50 |  |  |
 | `minimum_pident` | Minimum identity of a match to be used for annotation | `integer` | 80 |  |  |
 | `minimum_alen` | Minimum alignment length of a match to be used for annotation | `integer` | 50 |  |  |
@@ -78,7 +82,7 @@ Reference genome related files and options required for the workflow.
 | `genome` | Name of iGenomes reference. <details><summary>Help</summary><small>If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. <br><br>See the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.</small></details>| `string` |  |  |  |
 | `igenomes_base` | Directory / URL base for iGenomes references. | `string` | s3://ngi-igenomes/igenomes |  | True |
 | `igenomes_ignore` | Do not load the iGenomes reference config. <details><summary>Help</summary><small>Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.</small></details>| `boolean` |  |  | True |
-| `fasta` |  | `string` | None |  |  |
+| `fasta` |  | `string` |  |  |  |
 
 ## Max job request options
 
@@ -110,9 +114,4 @@ Less common options for the pipeline, typically set in a config file.
 | `tracedir` | Directory to keep pipeline Nextflow logs and reports. | `string` | ${params.outdir}/pipeline_info |  | True |
 | `validate_params` | Boolean whether to validate parameters against the schema at runtime | `boolean` | True |  | True |
 | `show_hidden_params` | Show all params when using `--help` <details><summary>Help</summary><small>By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters.</small></details>| `boolean` |  |  | True |
-
-## Other parameters
-
-| Parameter | Description | Type | Default | Required | Hidden |
-|-----------|-----------|-----------|-----------|-----------|-----------|
-| `schema_ignore_params` |  | `string` | genomes |  |  |
+| `schema_ignore_params` |  | `string` | genomes |  | True |
diff --git a/modules.json b/modules.json
@@ -68,6 +68,18 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/kaiju/kaiju2table/kaiju-kaiju2table.diff"
                     },
+                    "kraken2/kraken2": {
+                        "branch": "master",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff"
+                    },
+                    "krakentools/kreport2krona": {
+                        "branch": "master",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/krakentools/kreport2krona/krakentools-kreport2krona.diff"
+                    },
                     "krona/ktimporttext": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",

diff --git a/modules/nf-core/kraken2/kraken2/environment.yml b/modules/nf-core/kraken2/kraken2/environment.yml
diff --git a/modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff b/modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff
diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf
diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml
diff --git a/modules/nf-core/krakentools/kreport2krona/environment.yml b/modules/nf-core/krakentools/kreport2krona/environment.yml
diff --git a/modules/nf-core/krakentools/kreport2krona/krakentools-kreport2krona.diff b/modules/nf-core/krakentools/kreport2krona/krakentools-kreport2krona.diff
diff --git a/modules/nf-core/krakentools/kreport2krona/main.nf b/modules/nf-core/krakentools/kreport2krona/main.nf
diff --git a/modules/nf-core/krakentools/kreport2krona/meta.yml b/modules/nf-core/krakentools/kreport2krona/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -16,6 +16,7 @@ params {
 
     // References
     kaiju_db                   = null
+    kraken2_db                 = null
     diamond_db                 = null
     reference_fasta            = null
     genome                     = null
@@ -30,6 +31,10 @@ params {
     host_fasta                 = null
     bowtie2_db                 = null
 
+    // Taxonomy
+    run_kaiju                  = true
+    run_kraken2                = false
+
     // Functional
     id_mapping                 = null
     minimum_bitscore           = 50