update changelog & remove nextclade_dataset_reference param

nf-core · Nov 5, 2024 · b88cdcf · b88cdcf
1 parent 5f6e0c7
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,22 +29,24 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #438](https://github.com/nf-core/viralrecon/pull/438)] - Update fastp container to 0.23.4
 - [[PR #439](https://github.com/nf-core/viralrecon/pull/439)] - Fix cardinality issue when using `--bowtie2_index`
 - [[PR #435](https://github.com/nf-core/viralrecon/pull/435)] - Changed to a patched cutadapt from nf-core modules, added `skip_noninternal_primers` param to allow users to process primers inside the pipeline, and added `threeprime_adapters` to determine whether primers are 3' or 5' adapters.
+- [[PR #446](https://github.com/nf-core/viralrecon/pull/446)] - Update nextclade & pangolin modules
 
 ### Parameters
 
-| Old parameter | New parameter                |
-| ------------- | ---------------------------- |
-|               | `--skip_freyja`              |
-|               | `--freyja_repeats`           |
-|               | `--freyja_db_name`           |
-|               | `--freyja_barcodes`          |
-|               | `--freyja_lineages`          |
-|               | `--skip_freyja_boot`         |
-|               | `--additional_annotation`    |
-|               | `--min_contig_length`        |
-|               | `--min_perc_contig_aligned`  |
-|               | `--skip_noninternal_primers` |
-|               | `--threeprime_adapters`      |
+| Old parameter                   | New parameter                |
+| ------------------------------- | ---------------------------- |
+|                                 | `--skip_freyja`              |
+|                                 | `--freyja_repeats`           |
+|                                 | `--freyja_db_name`           |
+|                                 | `--freyja_barcodes`          |
+|                                 | `--freyja_lineages`          |
+|                                 | `--skip_freyja_boot`         |
+|                                 | `--additional_annotation`    |
+|                                 | `--min_contig_length`        |
+|                                 | `--min_perc_contig_aligned`  |
+|                                 | `--skip_noninternal_primers` |
+|                                 | `--threeprime_adapters`      |
+| `--nextclade_dataset_reference` |                              |
 
 > **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.
@@ -54,12 +56,14 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
 
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
-| `cutadapt` |             | 4.6         |
-| `fastp`    | 0.23.2      | 0.23.4      |
-| `freyja`   |             | 1.5.0       |
-| `multiqc`  | 1.14        | 1.19        |
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `cutadapt`  |             | 4.6         |
+| `fastp`     | 0.23.2      | 0.23.4      |
+| `freyja`    |             | 1.5.0       |
+| `multiqc`   | 1.14        | 1.19        |
+| `nextclade` | 2.12.0      | 3.8.2       |
+| `pangolin`  | 4.2         | 4.3         |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >

diff --git a/main.nf b/main.nf
@@ -33,7 +33,6 @@ params.primer_bed    = getGenomeAttribute('primer_bed', primer_set, primer_set_v
 
 params.nextclade_dataset           = getGenomeAttribute('nextclade_dataset')
 params.nextclade_dataset_name      = getGenomeAttribute('nextclade_dataset_name')
-params.nextclade_dataset_reference = getGenomeAttribute('nextclade_dataset_reference')
 params.nextclade_dataset_tag       = getGenomeAttribute('nextclade_dataset_tag')
 
 
@@ -86,7 +85,6 @@ workflow NFCORE_VIRALRECON {
             params.bowtie2_index,
             params.nextclade_dataset,
             params.nextclade_dataset_name,
-            params.nextclade_dataset_reference,
             params.nextclade_dataset_tag
         )
 
@@ -102,7 +100,6 @@ workflow NFCORE_VIRALRECON {
             params.bowtie2_index,
             params.nextclade_dataset,
             params.nextclade_dataset_name,
-            params.nextclade_dataset_reference,
             params.nextclade_dataset_tag
         )
 

diff --git a/modules.json b/modules.json
@@ -182,17 +182,17 @@
                     },
                     "nextclade/datasetget": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "nextclade/run": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "pangolin": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "9530ba667bb6c809d998fb9bd567bb9514cb23e5",
                         "installed_by": ["modules"]
                     },
                     "picard/collectmultiplemetrics": {

diff --git a/modules/nf-core/nextclade/datasetget/environment.yml b/modules/nf-core/nextclade/datasetget/environment.yml
diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf
diff --git a/modules/nf-core/nextclade/datasetget/meta.yml b/modules/nf-core/nextclade/datasetget/meta.yml
diff --git a/modules/nf-core/nextclade/datasetget/tests/main.nf.test b/modules/nf-core/nextclade/datasetget/tests/main.nf.test
diff --git a/modules/nf-core/nextclade/datasetget/tests/main.nf.test.snap b/modules/nf-core/nextclade/datasetget/tests/main.nf.test.snap
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -243,11 +243,6 @@
                     "description": "Name of Nextclade dataset to retrieve. A list of available datasets can be obtained using the 'nextclade dataset list' command.",
                     "fa_icon": "fas fa-project-diagram"
                 },
-                "nextclade_dataset_reference": {
-                    "type": "string",
-                    "description": "Accession id to download dataset based on a particular reference sequence. A list of available datasets can be obtained using the 'nextclade dataset list' command.",
-                    "fa_icon": "fas fa-project-diagram"
-                },
                 "nextclade_dataset_tag": {
                     "type": "string",
                     "description": "Version tag of the dataset to download. A list of available datasets can be obtained using the 'nextclade dataset list' command.",

diff --git a/subworkflows/local/prepare_genome_illumina.nf b/subworkflows/local/prepare_genome_illumina.nf
@@ -28,7 +28,6 @@ workflow PREPARE_GENOME {
     bowtie2_index
     nextclade_dataset
     nextclade_dataset_name
-    nextclade_dataset_reference
     nextclade_dataset_tag
 
 
@@ -192,7 +191,6 @@ workflow PREPARE_GENOME {
         } else if (nextclade_dataset_name) {
             NEXTCLADE_DATASETGET (
                 nextclade_dataset_name,
-                nextclade_dataset_reference,
                 nextclade_dataset_tag
             )
             ch_nextclade_db = NEXTCLADE_DATASETGET.out.dataset

diff --git a/subworkflows/local/prepare_genome_nanopore.nf b/subworkflows/local/prepare_genome_nanopore.nf
@@ -20,7 +20,6 @@ workflow PREPARE_GENOME {
     bowtie2_index
     nextclade_dataset
     nextclade_dataset_name
-    nextclade_dataset_reference
     nextclade_dataset_tag
 
     main:
@@ -114,7 +113,6 @@ workflow PREPARE_GENOME {
         } else if (nextclade_dataset_name) {
             NEXTCLADE_DATASETGET (
                 nextclade_dataset_name,
-                nextclade_dataset_reference,
                 nextclade_dataset_tag
             )
             ch_nextclade_db = NEXTCLADE_DATASETGET.out.dataset

diff --git a/workflows/illumina.nf b/workflows/illumina.nf
@@ -130,7 +130,6 @@ workflow ILLUMINA {
     ch_bowtie2_index
     ch_nextclade_dataset
     ch_nextclade_dataset_name
-    ch_nextclade_dataset_reference
     ch_nextclade_dataset_tag
 
     main:
@@ -148,7 +147,6 @@ workflow ILLUMINA {
         ch_bowtie2_index,
         ch_nextclade_dataset,
         ch_nextclade_dataset_name,
-        ch_nextclade_dataset_reference,
         ch_nextclade_dataset_tag
     )
     ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)