Merge pull request nf-core#426 from nf-core/417-allow-skipping-freyja…

…-boot 417 allow skipping freyja boot
BU-ISCIII · May 10, 2024 · c032f88 · c032f88
2 parents 6dee7cb + 6160aab
commit c032f88
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,17 +23,19 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #405](https://github.com/nf-core/viralrecon/pull/412)] - Including parameter `depthcutoff` to freyja demix and boot
 - [[PR #413](https://github.com/nf-core/viralrecon/pull/413)] - Update multiqc module & include freyja in report
 - [[PR #401](https://github.com/nf-core/viralrecon/pull/401)] - Added option to add a custom annotation
+- [[PR #417](https://github.com/nf-core/viralrecon/pull/417)] - Allow skipping of Freyja bootstrapping module & freyja module update
 
 ### Parameters
 
-| Old parameter       | New parameter             |
-| ------------------- | ------------------------- |
-| `--skip_freyja`     |                           |
-| `--freyja_repeats`  |                           |
-| `--freyja_db_name`  |                           |
-| `--freyja_barcodes` |                           |
-| `--freyja_lineages` |                           |
-|                     | `--additional_annotation` |
+| Old parameter | New parameter             |
+| ------------- | ------------------------- |
+|               | `--skip_freyja`           |
+|               | `--freyja_repeats`        |
+|               | `--freyja_db_name`        |
+|               | `--freyja_barcodes`       |
+|               | `--freyja_lineages`       |
+|               | `--skip_freyja_boot`      |
+|               | `--additional_annotation` |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.
@@ -45,7 +47,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
-| `freyja`   |             | 1.3.12      |
+| `freyja`   |             | 1.5.0       |
 | `multiqc`  | 1.14        | 1.19        |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.

diff --git a/docs/usage.md b/docs/usage.md
@@ -317,7 +317,7 @@ To learn how to provide additional arguments to a particular tool of the pipelin
 
 #### Freyja
 
-[Freyja](https://github.com/andersen-lab/Freyja) relies on a dataset of barcodes that use lineage defining mutations (see [UShER](https://usher-wiki.readthedocs.io/en/latest/#)). By default the most recent barcodes will be downloaded and used. However, if analyses need to be compared across multiple datasets, it might be of interest to re-use the same barcodes, or to rerun all Freyja analyses with the most recent dataset. To do this, specify the barcodes and lineages using the `--freyja_barcodes`, `--freyja_lineages` parameters, respectivly.
+[Freyja](https://github.com/andersen-lab/Freyja) relies on a dataset of barcodes that use lineage defining mutations (see [UShER](https://usher-wiki.readthedocs.io/en/latest/#)). By default the most recent barcodes will be downloaded and used. However, if analyses need to be compared across multiple datasets, it might be of interest to re-use the same barcodes, or to rerun all Freyja analyses with the most recent dataset. To do this, specify the barcodes and lineages using the `--freyja_barcodes`, `--freyja_lineages` parameters, respectivly. The boostrapping of Freyja can be skipped by specifying `--skip_freyja_boot`.
 
 ### nf-core/configs
 

diff --git a/modules.json b/modules.json
@@ -117,22 +117,22 @@
                     },
                     "freyja/boot": {
                         "branch": "master",
-                        "git_sha": "7e33bdd8b4faf45be1be6a6f49979f0f0820d243",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["bam_variant_demix_boot_freyja"]
                     },
                     "freyja/demix": {
                         "branch": "master",
-                        "git_sha": "7e33bdd8b4faf45be1be6a6f49979f0f0820d243",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["bam_variant_demix_boot_freyja"]
                     },
                     "freyja/update": {
                         "branch": "master",
-                        "git_sha": "7e33bdd8b4faf45be1be6a6f49979f0f0820d243",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["bam_variant_demix_boot_freyja"]
                     },
                     "freyja/variants": {
                         "branch": "master",
-                        "git_sha": "7e33bdd8b4faf45be1be6a6f49979f0f0820d243",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["bam_variant_demix_boot_freyja"]
                     },
                     "gunzip": {
@@ -296,7 +296,7 @@
                     },
                     "bam_variant_demix_boot_freyja": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_bowtie2": {
@@ -311,7 +311,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {

diff --git a/modules/nf-core/freyja/boot/environment.yml b/modules/nf-core/freyja/boot/environment.yml
diff --git a/modules/nf-core/freyja/boot/main.nf b/modules/nf-core/freyja/boot/main.nf
diff --git a/modules/nf-core/freyja/boot/tests/main.nf.test b/modules/nf-core/freyja/boot/tests/main.nf.test
diff --git a/modules/nf-core/freyja/boot/tests/main.nf.test.snap b/modules/nf-core/freyja/boot/tests/main.nf.test.snap
diff --git a/modules/nf-core/freyja/demix/environment.yml b/modules/nf-core/freyja/demix/environment.yml
diff --git a/modules/nf-core/freyja/demix/main.nf b/modules/nf-core/freyja/demix/main.nf
diff --git a/modules/nf-core/freyja/demix/tests/main.nf.test b/modules/nf-core/freyja/demix/tests/main.nf.test
diff --git a/modules/nf-core/freyja/demix/tests/main.nf.test.snap b/modules/nf-core/freyja/demix/tests/main.nf.test.snap
diff --git a/modules/nf-core/freyja/update/environment.yml b/modules/nf-core/freyja/update/environment.yml
diff --git a/modules/nf-core/freyja/update/main.nf b/modules/nf-core/freyja/update/main.nf
diff --git a/modules/nf-core/freyja/update/tests/main.nf.test.snap b/modules/nf-core/freyja/update/tests/main.nf.test.snap
diff --git a/modules/nf-core/freyja/variants/environment.yml b/modules/nf-core/freyja/variants/environment.yml
diff --git a/modules/nf-core/freyja/variants/main.nf b/modules/nf-core/freyja/variants/main.nf
diff --git a/modules/nf-core/freyja/variants/tests/main.nf.test.snap b/modules/nf-core/freyja/variants/tests/main.nf.test.snap
diff --git a/nextflow.config b/nextflow.config
@@ -43,6 +43,7 @@ params {
     multiqc_config             = null
     max_multiqc_email_size     = '25.MB'
     skip_freyja                = false
+    skip_freyja_boot           = false
     freyja_repeats             = 100
     freyja_depthcutoff         = null
     freyja_db_name             = 'freyja_db'

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -265,6 +265,11 @@
                     "fa_icon": "fas fa-forward",
                     "description": "Skip freyja deep SARS-CoV-2 variant analysis using a depth weighted approach."
                 },
+                "skip_freyja_boot": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-forward",
+                    "description": "Skip the bootstrapping  module of Freyja"
+                },
                 "freyja_db_name": {
                     "type": "string",
                     "default": "freyja_db",
@@ -281,7 +286,8 @@
                     "type": "integer",
                     "default": 100,
                     "fa_icon": "fas fa-hand-paper",
-                    "description": "Specify the number of bootstrap repeats to do."
+                    "description": "Specify the number of bootstrap repeats to do.",
+                    "minimum": 1
                 },
                 "freyja_barcodes": {
                     "type": "string",

diff --git a/subworkflows/nf-core/bam_variant_demix_boot_freyja/main.nf b/subworkflows/nf-core/bam_variant_demix_boot_freyja/main.nf