Merge branch 'nf-core:dev' into bug_fixes

nf-core · May 30, 2024 · 8a74a29 · 8a74a29
2 parents b398c5d + 6a40708
commit 8a74a29
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Showing 6 changed files with 21 additions and 10 deletions.
diff --git a/modules/local/fetch_eggnog_group_local.nf b/modules/local/fetch_eggnog_group_local.nf
@@ -3,7 +3,9 @@ process FETCH_EGGNOG_GROUP_LOCAL {
     label 'process_single'
 
     conda "conda-forge::python=3.12.3 conda-forge::ripgrep=14.1.0"
-    container "community.wave.seqera.io/library/python_ripgrep:324b372792aae9ce"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/python_ripgrep:6f07fd6cbda0142b' :
+        'community.wave.seqera.io/library/python_ripgrep:324b372792aae9ce' }"
 
     input:
     tuple val(meta), path(uniprot_id), path(taxid), path(exact)

diff --git a/modules/local/fetch_oma_group_local.nf b/modules/local/fetch_oma_group_local.nf
@@ -3,7 +3,9 @@ process FETCH_OMA_GROUP_LOCAL {
     label 'process_single'
 
     conda "conda-forge::python=3.12.3 conda-forge::ripgrep=14.1.0"
-    container "community.wave.seqera.io/library/python_ripgrep:324b372792aae9ce"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/python_ripgrep:6f07fd6cbda0142b' :
+        'community.wave.seqera.io/library/python_ripgrep:324b372792aae9ce' }"
 
     input:
     tuple val(meta), path(uniprot_id), path(taxid), path(exact)

diff --git a/modules/local/fetch_panther_group_local.nf b/modules/local/fetch_panther_group_local.nf
@@ -3,7 +3,9 @@ process FETCH_PANTHER_GROUP_LOCAL {
     label 'process_single'
 
     conda "conda-forge::python=3.12.3 conda-forge::ripgrep=14.1.0"
-    container "community.wave.seqera.io/library/python_ripgrep:324b372792aae9ce"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/python_ripgrep:6f07fd6cbda0142b' :
+        'community.wave.seqera.io/library/python_ripgrep:324b372792aae9ce' }"
 
     input:
     tuple val(meta), path(uniprot_id), path(taxid), path(exact)

diff --git a/modules/local/make_report.nf b/modules/local/make_report.nf
@@ -2,9 +2,12 @@ process MAKE_REPORT {
     tag "$meta.id"
     label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://itrujnara/orthologs-report:1.0.0' :
-        'itrujnara/orthologs-report:1.0.0' }"
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local MAKE_REPORT module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
+    container "itrujnara/orthologs-report:1.0.0"
 
     input:
     tuple val(meta), path(id), path(taxid), path(exact), path(score_table), path(filtered_hits), path(support_plot), path(venn_plot), path(jaccard_plot), path(orthostats), path(seq_hits), path(seq_misses), path(str_hits), path(str_misses), path(alignment), path(iqtree), path(fastme), path(params_file)

diff --git a/modules/local/plot_orthologs.nf b/modules/local/plot_orthologs.nf
@@ -2,9 +2,10 @@ process PLOT_ORTHOLOGS {
     tag "$meta.id"
     label 'process_single'
 
+    conda     "conda-forge::r-tidyverse=2.0.0 conda-forge::r-reshape2=1.4.4 conda-forge::r-ggvenndiagram=1.5.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://itrujnara/plot-orthologs:1.0.1' :
-        'itrujnara/plot-orthologs:1.0.1' }"
+        'oras://community.wave.seqera.io/library/r-ggvenndiagram_r-reshape2_r-tidyverse:3941632557872dac' :
+        'community.wave.seqera.io/library/r-ggvenndiagram_r-reshape2_r-tidyverse:6ab82708ae578c26' }"
 
     input:
     tuple val(meta), path(score_table)

diff --git a/modules/local/plot_tree.nf b/modules/local/plot_tree.nf
@@ -2,9 +2,10 @@ process PLOT_TREE {
     tag "$meta.id"
     label 'process_single'
 
+    conda "bioconda::bioconductor-treeio=1.26.0 bioconda::bioconductor-ggtree=3.10.0 conda-forge::r-ggplot2=3.5.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://itrujnara/plot-tree:1.0.0' :
-        'itrujnara/plot-tree:1.0.0' }"
+        'oras://community.wave.seqera.io/library/bioconductor-ggtree_bioconductor-treeio_r-ggplot2:89a30ee47c501fe4' :
+        'community.wave.seqera.io/library/bioconductor-ggtree_bioconductor-treeio_r-ggplot2:54fc04b8b0f7b6c7' }"
 
     input:
     tuple val(meta), path(tree)