Merge pull request #720 from d4straub/update-modules

Update nf-core modules, DADA2, and Phyloseq
nf-core · Mar 26, 2024 · 43378b5 · 43378b5
2 parents 0c24ff3 + 717aa49
commit 43378b5
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
+- [#720](https://github.com/nf-core/ampliseq/pull/720) - Updated nf-core modules, DADA2, and Phyloseq
+
+| software | previously | now    |
+| -------- | ---------- | ------ |
+| cutadapt | 3.4        | 4.6    |
+| DADA2    | 1.28.0     | 1.30.0 |
+| Phyloseq | 1.44.0     | 1.46.0 |
+
 ### `Removed`
 
 - [#710](https://github.com/nf-core/ampliseq/pull/710) - Removed Phyloref from DADA2 reference option because it's part of PR2 5.0.0

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "cutadapt": {
                         "branch": "master",
-                        "git_sha": "0efbaeb95c58da5a1096c99b5e919bc0c99cc952",
+                        "git_sha": "6618151ed69274863dc6fe6d2920afa90abaca1f",
                         "installed_by": ["modules"]
                     },
                     "epang/place": {
@@ -62,7 +62,7 @@
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "653218e79ffa76fde20319e9062f8b8da5cf7555",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff"
                     },
@@ -84,22 +84,22 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["modules"]
                     },
                     "vsearch/cluster": {
                         "branch": "master",
-                        "git_sha": "89945ea085b94d3413013b6c82e2633b5184f24d",
+                        "git_sha": "d97b335eb448073c1b680710303c02a55f40c77c",
                         "installed_by": ["modules"]
                     },
                     "vsearch/sintax": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "vsearch/usearchglobal": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/cutadapt_summary_merge.nf b/modules/local/cutadapt_summary_merge.nf
@@ -2,10 +2,10 @@ process CUTADAPT_SUMMARY_MERGE {
     tag "${files}"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     val(action)

diff --git a/modules/local/dada2_addspecies.nf b/modules/local/dada2_addspecies.nf
@@ -3,10 +3,10 @@ process DADA2_ADDSPECIES {
     label 'process_high'
     label 'single_cpu'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     path(taxtable)

diff --git a/modules/local/dada2_denoising.nf b/modules/local/dada2_denoising.nf
@@ -3,10 +3,10 @@ process DADA2_DENOISING {
     label 'process_medium'
     label 'process_long'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path("filtered/*"), path(errormodel)

diff --git a/modules/local/dada2_err.nf b/modules/local/dada2_err.nf
@@ -2,10 +2,10 @@ process DADA2_ERR {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/dada2_filtntrim.nf b/modules/local/dada2_filtntrim.nf
@@ -2,10 +2,10 @@ process DADA2_FILTNTRIM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(reads), val(trunclenf), val(trunclenr)

diff --git a/modules/local/dada2_quality.nf b/modules/local/dada2_quality.nf
@@ -2,10 +2,10 @@ process DADA2_QUALITY {
     tag "$meta"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/dada2_rmchimera.nf b/modules/local/dada2_rmchimera.nf
@@ -2,10 +2,10 @@ process DADA2_RMCHIMERA {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(seqtab)

diff --git a/modules/local/dada2_stats.nf b/modules/local/dada2_stats.nf
@@ -2,10 +2,10 @@ process DADA2_STATS {
     tag "$meta.run"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path("filter_and_trim_files/*"), path(denoised), path(mergers), path(seqtab_nochim)

diff --git a/modules/local/dada2_taxonomy.nf b/modules/local/dada2_taxonomy.nf
@@ -2,10 +2,10 @@ process DADA2_TAXONOMY {
     tag "${fasta},${database}"
     label 'process_high'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     path(fasta)

diff --git a/modules/local/format_pplacetax.nf b/modules/local/format_pplacetax.nf
@@ -2,10 +2,10 @@ process FORMAT_PPLACETAX {
     tag "${tax.baseName}"
     label 'process_high'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(tax)

diff --git a/modules/local/merge_stats.nf b/modules/local/merge_stats.nf
@@ -1,10 +1,10 @@
 process MERGE_STATS {
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     path('file1.tsv')

diff --git a/modules/local/metadata_all.nf b/modules/local/metadata_all.nf
@@ -2,10 +2,10 @@ process METADATA_ALL {
     tag "$metadata"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     path(metadata)

diff --git a/modules/local/metadata_pairwise.nf b/modules/local/metadata_pairwise.nf
@@ -2,10 +2,10 @@ process METADATA_PAIRWISE {
     tag "$metadata"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     path(metadata)

diff --git a/modules/local/novaseq_err.nf b/modules/local/novaseq_err.nf
@@ -2,10 +2,10 @@ process NOVASEQ_ERR {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.28.0"
+    conda "bioconda::bioconductor-dada2=1.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
-        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(errormodel)

diff --git a/modules/local/phyloseq.nf b/modules/local/phyloseq.nf
@@ -2,10 +2,10 @@ process PHYLOSEQ {
     tag "$prefix"
     label 'process_low'
 
-    conda "bioconda::bioconductor-phyloseq=1.44.0"
+    conda "bioconda::bioconductor-phyloseq=1.46.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-phyloseq:1.44.0--r43hdfd78af_0' :
-        'biocontainers/bioconductor-phyloseq:1.44.0--r43hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-phyloseq:1.46.0--r43hdfd78af_0' :
+        'biocontainers/bioconductor-phyloseq:1.46.0--r43hdfd78af_0' }"
 
     input:
     tuple val(prefix), path(tax_tsv), path(otu_tsv)

diff --git a/modules/nf-core/cutadapt/environment.yml b/modules/nf-core/cutadapt/environment.yml
diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf
diff --git a/modules/nf-core/cutadapt/meta.yml b/modules/nf-core/cutadapt/meta.yml
diff --git a/modules/nf-core/cutadapt/tests/main.nf.test b/modules/nf-core/cutadapt/tests/main.nf.test