Remove echo usage in topic evaluation (#12112)

* Update ataqv version

* Update leafcutter version

* Update authentict version

* Update links version

* Update arcashla

* Update bamcmp

* Update busco/phylogenomics

* Update vafe

* Update clusty

* Update hlala

* Update merquryfk

* Update arcashla

* Update mitohifi

* Update rapidnj

* Update slimfastq

* Update telseq

* Fix ataqv

* Fix errors

* Update links

* Update bamcmp

* Update hlala

* Update hlala

* Add registry

* Update .nf-core.yml

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* Add missing registry

---------

Co-authored-by: Louis Le Nezet <louis.le-nezet@inserm.fr>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Author: 3 people

.nf-core.yml

@@ -1,5 +1,10 @@
 repository_type: modules
 org_path: nf-core
+container-registry:
+  - ghcr.io/marcelauliano/
+  - ghcr.io/schapirolabor
+  - ghcr.io/nbisweden
+  - ghcr.io/scverse
 bump-versions:
   rseqc/junctionannotation: False
   rseqc/bamstat: False

modules/nf-core/arcashla/extract/main.nf

@@ -16,7 +16,8 @@ process ARCASHLA_EXTRACT {
     tuple val(meta), path("temp_files/**.sam")       , emit: intermediate_sam       , optional: true
     tuple val(meta), path("temp_files/**.bam")       , emit: intermediate_bam       , optional: true
     tuple val(meta), path("temp_files/**.sorted.bam"), emit: intermediate_sorted_bam, optional: true
-    tuple val("${task.process}"), val('arcashla'), eval('echo 0.5.0'), emit: versions_arcashla, topic: versions
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    tuple val("${task.process}"), val('arcashla'), val('0.5.0'), emit: versions_arcashla, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/arcashla/extract/meta.yml

@@ -1,6 +1,6 @@
 name: "arcashla_extract"
-description: Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome
-  6 alternates.
+description: Extracts reads mapped to chromosome 6 and any HLA decoys or
+  chromosome 6 alternates.
 keywords:
   - HLA
   - genotype
@@ -13,7 +13,8 @@ tools:
       documentation: "https://github.com/RabadanLab/arcasHLA"
       tool_dev_url: "https://github.com/RabadanLab/arcasHLA"
       doi: "10.1093/bioinformatics/btz474"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: ""
 input:
   - - meta:
@@ -23,8 +24,8 @@ input:
           e.g. [ id:'test', single_end:false ]
     - bam:
         type: file
-        description: BAM file. If the BAM file is not indexed, this tool will run samtools
-          index before extracting reads.
+        description: BAM file. If the BAM file is not indexed, this tool will run
+          samtools index before extracting reads.
         pattern: "*.bam"
         ontologies:
           - edam: "http://edamontology.org/format_2572" # BAM
@@ -37,7 +38,8 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.fq.gz":
           type: file
-          description: FASTQ file(s) containing chromosome 6 reads and related HLA sequences
+          description: FASTQ file(s) containing chromosome 6 reads and related HLA
+            sequences
           pattern: "*.fq.gz"
           ontologies:
             - edam: "http://edamontology.org/format_1930" # FASTQ
@@ -85,26 +87,28 @@ output:
           ontologies:
             - edam: "http://edamontology.org/format_2572" # BAM
   versions_arcashla:
-    - - "${task.process}":
+    - - ${task.process}:
           type: string
           description: The name of the process
-      - "arcashla":
+      - arcashla:
           type: string
           description: The name of the tool
-      - "echo 0.5.0":
-          type: eval
-          description: The expression to obtain the version of the tool
+      - 0.5.0:
+          type: string
+          description: The version of the tool
+
 topics:
   versions:
-    - - "${task.process}":
+    - - ${task.process}:
           type: string
           description: The name of the process
-      - "arcashla":
+      - arcashla:
           type: string
           description: The name of the tool
-      - "echo 0.5.0":
-          type: eval
-          description: The expression to obtain the version of the tool
+      - 0.5.0:
+          type: string
+          description: The version of the tool
+
 authors:
   - "@christopher-mohr"
 maintainers:

modules/nf-core/ataqv/ataqv/main.nf

@@ -18,7 +18,7 @@ process ATAQV_ATAQV {
     output:
     tuple val(meta), path("*.ataqv.json"), emit: json
     tuple val(meta), path("*.problems")  , emit: problems, optional: true
-    tuple val("${task.process}"), val('ataqv'), eval("echo \$(ataqv --version)"), emit: versions_ataqv, topic: versions
+    tuple val("${task.process}"), val('ataqv'), eval("ataqv --version 2>&1 || true"), emit: versions_ataqv, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/ataqv/ataqv/meta.yml

@@ -6,10 +6,10 @@ keywords:
   - ataqv
 tools:
   - ataqv:
-      description: ataqv is a toolkit for measuring and comparing ATAC-seq results.
-        It was written to help understand how well ATAC-seq assays have worked, and
-        to make it easier to spot differences that might be caused by library prep or
-        sequencing.
+      description: ataqv is a toolkit for measuring and comparing ATAC-seq
+        results. It was written to help understand how well ATAC-seq assays have
+        worked, and to make it easier to spot differences that might be caused by
+        library prep or sequencing.
       homepage: https://github.com/ParkerLab/ataqv/blob/master/README.rst
       documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst
       tool_dev_url: https://github.com/ParkerLab/ataqv
@@ -30,8 +30,8 @@ input:
         ontologies: []
     - bai:
         type: file
-        description: BAM index file with the same prefix as bam file. Required if tss_file
-          input is provided.
+        description: BAM index file with the same prefix as bam file. Required if
+          tss_file input is provided.
         pattern: "*.bam.bai"
         ontologies: []
     - peak_file:
@@ -41,30 +41,31 @@ input:
         ontologies: []
   - organism:
       type: string
-      description: The subject of the experiment, which determines the list of autosomes
-        (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv).
+      description: The subject of the experiment, which determines the list of
+        autosomes (see "Reference Genome Configuration" section at
+        https://github.com/ParkerLab/ataqv).
   - mito_name:
       type: string
       description: Name of the mitochondrial sequence.
   - tss_file:
       type: file
-      description: A BED file of transcription start sites for the experiment organism.
-        If supplied, a TSS enrichment score will be calculated according to the ENCODE
-        data standards. This calculation requires that the BAM file of alignments be
-        indexed.
+      description: A BED file of transcription start sites for the experiment
+        organism. If supplied, a TSS enrichment score will be calculated according
+        to the ENCODE data standards. This calculation requires that the BAM file
+        of alignments be indexed.
       pattern: "*.bed"
       ontologies: []
   - excl_regs_file:
       type: file
-      description: A BED file containing excluded regions. Peaks or TSS overlapping
-        these will be ignored.
+      description: A BED file containing excluded regions. Peaks or TSS
+        overlapping these will be ignored.
       pattern: "*.bed"
       ontologies: []
   - autosom_ref_file:
       type: file
-      description: A file containing autosomal reference names, one per line. The names
-        must match the reference names in the alignment file exactly, or the metrics
-        based on counts of autosomal alignments will be wrong.
+      description: A file containing autosomal reference names, one per line. The
+        names must match the reference names in the alignment file exactly, or the
+        metrics based on counts of autosomal alignments will be wrong.
       ontologies: []
 output:
   json:
@@ -85,10 +86,10 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.problems":
           type: file
-          description: If given, problematic reads will be logged to a file per read
-            group, with names derived from the read group IDs, with ".problems" appended.
-            If no read groups are found, the reads will be written to one file named
-            after the BAM file.
+          description: If given, problematic reads will be logged to a file per
+            read group, with names derived from the read group IDs, with
+            ".problems" appended. If no read groups are found, the reads will be
+            written to one file named after the BAM file.
           pattern: "*.problems"
           ontologies: []
   versions_ataqv:
@@ -98,9 +99,10 @@ output:
       - ataqv:
           type: string
           description: The name of the tool
-      - echo \$(ataqv --version):
+      - ataqv --version 2>&1 || true:
           type: eval
           description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
@@ -109,9 +111,10 @@ topics:
       - ataqv:
           type: string
           description: The name of the tool
-      - echo \$(ataqv --version):
+      - ataqv --version 2>&1 || true:
           type: eval
           description: The expression to obtain the version of the tool
+
 authors:
   - "@i-pletenev"
 maintainers:

modules/nf-core/ataqv/mkarv/main.nf

@@ -11,7 +11,7 @@ process ATAQV_MKARV {
 
     output:
     path "html"        , emit: html
-    tuple val("${task.process}"), val('ataqv'), eval('echo \$(ataqv --version)'), emit: versions_ataqv, topic: versions
+    tuple val("${task.process}"), val('ataqv'), eval("ataqv --version 2>&1 || true"), emit: versions_ataqv, topic: versions
     // tuple val("${task.process}"), val('mkarv'), eval('mkarv --version'), emit: versions_mkarv, topic: versions //Use this when version string has been fixed
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/ataqv/mkarv/meta.yml

@@ -7,10 +7,10 @@ keywords:
   - mkarv
 tools:
   - "ataqv":
-      description: "ataqv is a toolkit for measuring and comparing ATAC-seq results.\
-        \ It was written to help understand how well ATAC-seq assays have worked, and\
-        \ to make it easier to spot differences that might be caused by library prep\
-        \ or sequencing."
+      description: "ataqv is a toolkit for measuring and comparing ATAC-seq results.
+        It was written to help understand how well ATAC-seq assays have worked, and
+        to make it easier to spot differences that might be caused by library prep or
+        sequencing."
       homepage: "https://github.com/ParkerLab/ataqv/blob/master/README.rst"
       documentation: "https://github.com/ParkerLab/ataqv/blob/master/README.rst"
       tool_dev_url: "https://github.com/ParkerLab/ataqv"
@@ -23,7 +23,7 @@ input:
       description: JSON files
       pattern: "*.json"
       ontologies:
-        - edam: http://edamontology.org/format_3464
+        - edam: http://edamontology.org/format_3464 # JSON
 output:
   html:
     - html:
@@ -37,9 +37,10 @@ output:
       - ataqv:
           type: string
           description: The name of the tool
-      - echo \$(ataqv --version):
+      - ataqv --version 2>&1 || true:
           type: eval
           description: The expression to obtain the version of the tool
+
   versions_mkarv:
     - - ${task.process}:
           type: string
@@ -58,9 +59,10 @@ topics:
       - ataqv:
           type: string
           description: The name of the tool
-      - echo \$(ataqv --version):
+      - ataqv --version 2>&1 || true:
           type: eval
           description: The expression to obtain the version of the tool
+
     - - ${task.process}:
           type: string
           description: The name of the process

modules/nf-core/authentict/deam2cont/main.nf

@@ -14,7 +14,7 @@ process AUTHENTICT_DEAM2CONT {
 
     output:
     tuple val(meta), path("*.txt"), emit: txt
-    tuple val("${task.process}"), val('authentict'), eval("echo \$(AuthentiCT --version 2>&1)"), emit: versions_authentict, topic: versions
+    tuple val("${task.process}"), val('authentict'), eval("AuthentiCT --version"), emit: versions_authentict, topic: versions
     tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //'"), emit: versions_samtools, topic: versions
 
     when:

modules/nf-core/authentict/deam2cont/meta.yml

@@ -71,9 +71,10 @@ output:
       - authentict:
           type: string
           description: The name of the tool
-      - echo \$(AuthentiCT --version 2>&1):
+      - AuthentiCT --version:
           type: eval
           description: The expression to obtain the version of the tool
+
   versions_samtools:
     - - ${task.process}:
           type: string
@@ -92,9 +93,10 @@ topics:
       - authentict:
           type: string
           description: The name of the tool
-      - echo \$(AuthentiCT --version 2>&1):
+      - AuthentiCT --version:
           type: eval
           description: The expression to obtain the version of the tool
+
     - - ${task.process}:
           type: string
           description: The name of the process

modules/nf-core/bamcmp/environment.yml

@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::bamcmp=2.2
-  - bioconda::samtools=1.23
+  - bioconda::samtools=1.23.1