update DADA2

nf-core · Mar 26, 2024 · dc4067f · dc4067f
1 parent 8c0200c
commit dc4067f
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Showing 14 changed files with 42 additions and 42 deletions.
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)