Update nf-core odgi modules to version 0.9.0

modules.json

@@ -17,47 +17,47 @@
                     },
                     "odgi/build": {
                         "branch": "master",
-                        "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47",
+                        "git_sha": "759d9b3002b7019129c83be00e986ec58da38b09",
                         "installed_by": ["modules"]
                     },
                     "odgi/draw": {
                         "branch": "master",
-                        "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47",
+                        "git_sha": "759d9b3002b7019129c83be00e986ec58da38b09",
                         "installed_by": ["modules"]
                     },
                     "odgi/layout": {
                         "branch": "master",
-                        "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47",
+                        "git_sha": "759d9b3002b7019129c83be00e986ec58da38b09",
                         "installed_by": ["modules"]
                     },
                     "odgi/sort": {
                         "branch": "master",
-                        "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47",
+                        "git_sha": "759d9b3002b7019129c83be00e986ec58da38b09",
                         "installed_by": ["modules"]
                     },
                     "odgi/squeeze": {
                         "branch": "master",
-                        "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47",
+                        "git_sha": "759d9b3002b7019129c83be00e986ec58da38b09",
                         "installed_by": ["modules"]
                     },
                     "odgi/stats": {
                         "branch": "master",
-                        "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47",
+                        "git_sha": "759d9b3002b7019129c83be00e986ec58da38b09",
                         "installed_by": ["modules"]
                     },
                     "odgi/unchop": {
                         "branch": "master",
-                        "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47",
+                        "git_sha": "759d9b3002b7019129c83be00e986ec58da38b09",
                         "installed_by": ["modules"]
                     },
                     "odgi/view": {
                         "branch": "master",
-                        "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47",
+                        "git_sha": "759d9b3002b7019129c83be00e986ec58da38b09",
                         "installed_by": ["modules"]
                     },
                     "odgi/viz": {
                         "branch": "master",
-                        "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47",
+                        "git_sha": "759d9b3002b7019129c83be00e986ec58da38b09",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {

modules/local/multiqc_community/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::multiqc=1.25.1

modules/local/multiqc_community/main.nf

@@ -2,16 +2,18 @@ process MULTIQC_COMMUNITY {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::multiqc=1.15"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(multiqc_files, stageAs: "?/*")
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
 
     output:
     path "*/*multiqc_report.html", emit: report
@@ -24,14 +26,22 @@ process MULTIQC_COMMUNITY {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
     def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
+        $prefix \\
         $extra_config \\
+        $logo \\
+        $replace \\
+        $samples \\
         .
 
     cat <<-END_VERSIONS > versions.yml
@@ -42,8 +52,8 @@ process MULTIQC_COMMUNITY {
 
     stub:
     """
-    touch multiqc_data
-    touch multiqc_plots
+    mkdir multiqc_data
+    mkdir multiqc_plots
     touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml

modules/local/multiqc_community/meta.yml

@@ -1,5 +1,6 @@
-name: MultiQC
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+name: multiqc
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,50 +13,66 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
-
+      identifier: biotools:multiqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
-      pattern: "*.{yml,yaml}"
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
-
+  - - multiqc_files:
+        type: file
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+  - - extra_multiqc_config:
+        type: file
+        description: Second optional config yml for MultiQC. Will override common sections
+          in multiqc_config.
+        pattern: "*.{yml,yaml}"
+  - - multiqc_logo:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
 output:
   - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
   - data:
-      type: dir
-      description: MultiQC data dir
-      pattern: "multiqc_data"
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
   - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@bunop"
   - "@drpatelh"
   - "@jfy133"
-  - "@subwaystation"
+maintainers:
+  - "@abhi18av"
+  - "@bunop"
+  - "@drpatelh"
+  - "@jfy133"