Merge branch 'update-busco' of github.com:dialvarezs/nf-core-modules …

…into update-busco

modules/nf-core/clustalo/align/main.nf

@@ -31,7 +31,7 @@ process CLUSTALO_ALIGN {
     def fhmm_batch   = hmm_batch ? "--hmm-batch=${hmm_batch}" : ""
     def fprofile1    = profile1  ? "--profile1=${profile1}"   : ""
     def fprofile2    = profile2  ? "--profile2=${profile2}"   : ""
-    def write_output = compress ? "--force -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "> ${prefix}.aln"
+    def write_output = compress ? "--force -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "-o ${prefix}.aln"
     // using >() is necessary to preserve the return value,
     // so nextflow knows to display an error when it failed
     // the --force -o is necessary, as clustalo expands the commandline input,

modules/nf-core/limma/differential/main.nf

@@ -5,7 +5,7 @@ process LIMMA_DIFFERENTIAL {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/af/afd9579a0ff62890ff451d82b360d85e82a0d61a3da40736ee0eee4e45926269/data' :
-        'community.wave.seqera.io/library/bioconductor-limma_bioconductor-edger:54dd09078d5db3b3' }"
+        'community.wave.seqera.io/library/bioconductor-edger_bioconductor-limma:176c202c82450990' }"
 
     input:
     tuple val(meta), val(contrast_variable), val(reference), val(target)

modules/nf-core/propr/grea/environment.yml

@@ -1,5 +1,7 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - conda-forge::r-propr=5.0.4
+  - bioconda::bioconductor-limma=3.58.1
+  - conda-forge::r-propr=5.1.5

modules/nf-core/propr/grea/main.nf

@@ -1,20 +1,20 @@
 process PROPR_GREA {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-propr:5.0.4':
-        'biocontainers/r-propr:5.0.4' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b6/b65f7192866fbd9a947df15b104808abb720e7a224bbe3ca8f7f8f680f52c97a/data' :
+        'community.wave.seqera.io/library/bioconductor-limma_r-propr:f52f1d4fea746393' }"
 
     input:
-    tuple val(meta), path(adj)
+    tuple val(meta), path(adjacency)
     tuple val(meta2), path(gmt)
 
     output:
-    tuple val(meta), path("*.go.tsv"),  emit: enrichedGO
-    path "versions.yml",                emit: versions
-    path "*.R_sessionInfo.log",         emit: session_info
+    tuple val(meta), path("*.grea.tsv"), emit: results
+    path "versions.yml",                 emit: versions
+    path "*.R_sessionInfo.log",          emit: session_info
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/propr/grea/meta.yml

@@ -2,12 +2,12 @@
 name: "propr_grea"
 description: Perform Gene Ratio Enrichment Analysis
 keywords:
-  - logratio
-  - differential
   - propr
   - grea
-  - enrichment
-  - expression
+  - logratio
+  - differential expression
+  - functional enrichment
+  - functional analysis
 tools:
   - "grea":
       description: "Gene Ratio Enrichment Analysis"
@@ -21,34 +21,42 @@ input:
   - - meta:
         type: map
         description: |
-          Groovy Map containing sample information.
+          Groovy Map containing data information.
           This can be used at the workflow level to pass optional parameters to the module.
           [id: 'test', ...]
-    - adj:
+    - adjacency:
         type: file
-        description: adjacency matrix for gene ratio proportionality/differential proportionality
+        description: |
+          Adjacency matrix representing the graph connections (ie. 1 for edges, 0 otherwise).
+          This can be the adjacency matrix output from gene ratio approaches like propr/propd.
         pattern: "*.{csv,tsv}"
   - - meta2:
         type: map
         description: |
-          Groovy map containing study-wide metadata related to the knowledge database
+          Groovy Map containing data information.
+          This can be used at the workflow level to pass optional parameters to the module.
+          [id: 'test', ...]
     - gmt:
         type: file
-        description: relational database containing genes and GO terms (generated by
-          mygene module)
+        description: |
+          A tab delimited file format that describes gene sets. The first column is the
+          concept id (eg. GO term, pathway, etc), the second column is the concept description, and the
+          rest are nodes (eg. genes) that is associated to the given concept.
         pattern: "*.{gmt}"
 output:
-  - enrichedGO:
+  - results:
       - meta:
-          type: map
+          type: file
           description: |
             Groovy Map containing sample information.
             This can be used at the workflow level to pass optional parameters to the module.
             [id: 'test', ...]
-      - "*.go.tsv":
+      - "*.grea.tsv":
           type: file
-          description: File containing GO terms and their enrichment values
-          pattern: "*.{csv}"
+          description: |
+            Output file containing the information about the tested concepts (ie. gene sets)
+            and enrichment statistics.
+          pattern: "*.grea.tsv"
   - versions:
       - versions.yml:
           type: file
@@ -57,9 +65,11 @@ output:
   - session_info:
       - "*.R_sessionInfo.log":
           type: file
-          description: R session log
+          description: dump of R SessionInfo
           pattern: "*.R_sessionInfo.log"
 authors:
   - "@caraiz2001"
+  - "@suzannejin"
 maintainers:
   - "@caraiz2001"
+  - "@suzannejin"