Merge branch 'master' into master

adamrtalbot · Oct 16, 2023 · ce2478a · ce2478a
2 parents 27291c6 + a444cf4
commit ce2478a
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Showing 14 changed files with 594 additions and 23 deletions.
diff --git a/.github/modules.yml b/.github/modules.yml
@@ -22,5 +22,8 @@ fastq_download_prefetch_fasterqdump_sratools:
 nextflowpipelineutils:
   - subworkflows/nf-core/nextflowpipelineutils/**
 
+nfcorepipelineutils:
+  - subworkflows/nf-core/nfcore_pipeline_utils/**
+
 nfvalidationpluginutils:
   - subworkflows/nf-core/nfvalidationpluginutils/**
diff --git a/.github/renovate.json5 b/.github/renovate.json5
@@ -6,7 +6,6 @@
     dependencyDashboardTitle: "Renovate Dashboard 🤖",
     suppressNotifications: ["prIgnoreNotification"],
     rebaseWhen: "conflicted",
-    schedule: ["every sunday"],
     reviewers: ["team:maintainers"],
     regexManagers: [
         {

diff --git a/modules/nf-core/sourmash/compare/main.nf b/modules/nf-core/sourmash/compare/main.nf
@@ -1,11 +1,11 @@
 process SOURMASH_COMPARE {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_low'
 
-    conda "bioconda::sourmash=4.6.1"
+    conda "bioconda::sourmash=4.8.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
-        'biocontainers/sourmash:4.6.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sourmash:4.8.4--hdfd78af_0':
+        'biocontainers/sourmash:4.8.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(signatures)
@@ -33,7 +33,7 @@ process SOURMASH_COMPARE {
     """
     sourmash compare \\
         $args \\
-        --processes $task.cpus \\
+        --processes ${task.cpus} \\
         ${comp} \\
         ${csv} \\
         ${ffile} \\

diff --git a/modules/nf-core/sourmash/gather/main.nf b/modules/nf-core/sourmash/gather/main.nf
@@ -1,11 +1,11 @@
 process SOURMASH_GATHER {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
-    conda "bioconda::sourmash=4.6.1"
+    conda "bioconda::sourmash=4.8.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
-        'biocontainers/sourmash:4.6.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sourmash:4.8.4--hdfd78af_0':
+        'biocontainers/sourmash:4.8.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(signature)

diff --git a/modules/nf-core/sourmash/index/main.nf b/modules/nf-core/sourmash/index/main.nf
@@ -2,10 +2,10 @@ process SOURMASH_INDEX {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::sourmash=4.6.1"
+    conda "bioconda::sourmash=4.8.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
-        'biocontainers/sourmash:4.6.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sourmash:4.8.4--hdfd78af_0':
+        'biocontainers/sourmash:4.8.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(signatures)

diff --git a/modules/nf-core/sourmash/sketch/main.nf b/modules/nf-core/sourmash/sketch/main.nf
@@ -1,11 +1,11 @@
 process SOURMASH_SKETCH {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
-    conda "bioconda::sourmash=4.6.1"
+    conda "bioconda::sourmash=4.8.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
-        'biocontainers/sourmash:4.6.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sourmash:4.8.4--hdfd78af_0':
+        'biocontainers/sourmash:4.8.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(sequence)

diff --git a/modules/nf-core/sourmash/taxannotate/main.nf b/modules/nf-core/sourmash/taxannotate/main.nf
@@ -2,10 +2,10 @@ process SOURMASH_TAXANNOTATE {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::sourmash=4.6.1"
+    conda "bioconda::sourmash=4.8.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
-        'biocontainers/sourmash:4.6.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sourmash:4.8.4--hdfd78af_0':
+        'biocontainers/sourmash:4.8.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gather_results)

diff --git a/modules/nf-core/tcoffee/align/main.nf b/modules/nf-core/tcoffee/align/main.nf
@@ -2,10 +2,10 @@ process TCOFFEE_ALIGN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::t-coffee=13.45.0.4846264"
+    conda "bioconda::t-coffee=13.46.0.919e8c6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/t-coffee:13.45.0.4846264--hc57179f_5':
-        'biocontainers/t-coffee:13.45.0.4846264--hc57179f_5' }"
+        'https://depot.galaxyproject.org/singularity/t-coffee:13.46.0.919e8c6b--hfc96bf3_0':
+        'biocontainers/t-coffee:13.46.0.919e8c6b--hfc96bf3_0' }"
 
     input:
     tuple val(meta) ,  path(fasta)
@@ -25,6 +25,7 @@ process TCOFFEE_ALIGN {
     def tree_args = tree ? "-usetree $tree" : ""
     def template_args = template ? "-template_file $template" : ""
     """
+    export TEMP='./'
     t_coffee -seq ${fasta} \
         $tree_args \
         $template_args \