Refine gcta/calculateldscores module contract

Author: lyh970817

modules/nf-core/gcta/calculateldscores/main.nf

@@ -2,9 +2,9 @@ process GCTA_CALCULATELDSCORES {
     tag "${meta.id}"
     label 'process_medium'
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://community.wave.seqera.io/library/gcta_r-base:31127c93877b38de' :
-        'community.wave.seqera.io/library/gcta_r-base:31127c93877b38de' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/ed2d6a4b4f43f3230014aa67bb40feb0acbd7cc41ef0b0a895002f1befc6502c/data'
+        : 'community.wave.seqera.io/library/gcta_r-base:31127c93877b38de'}"
 
     input:
     tuple val(meta), path(bed), path(bim), path(fam)
@@ -13,19 +13,20 @@ process GCTA_CALCULATELDSCORES {
     output:
     tuple val(meta), path("*_gcta_ld.score.ld"), emit: ld_scores
     tuple val(meta), path("*_snp_group1.txt"), path("*_snp_group2.txt"), path("*_snp_group3.txt"), path("*_snp_group4.txt"), emit: snp_group_files
-    tuple val("${task.process}"), val("gcta"), eval("gcta --version 2>&1 | grep 'version v' | tr -s ' ' | cut -d' ' -f3 | sed 's/^v//'"), emit: versions_gcta, topic: versions
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'"), emit: versions_gcta, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def extra_args = task.ext.args ?: ''
+    def bfile_prefix = bed.baseName
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
 
     gcta \\
-        --bfile ${meta.id} \\
+        --bfile ${bfile_prefix} \\
         --ld-score-region ${ld_score_region} \\
         --out ${prefix}_gcta_ld \\
         --thread-num ${task.cpus} ${extra_args}

modules/nf-core/gcta/calculateldscores/meta.yml

@@ -3,8 +3,11 @@ name: "gcta_calculateldscores"
 description: Calculate LD scores with GCTA and segment variants into LD-based SNP groups
 keywords:
   - gcta
+  - genome-wide complex trait analysis
   - ld score
+  - linkage disequilibrium score
   - ldms
+  - linkage disequilibrium and minor allele frequency stratification
   - genetics
 tools:
   - "gcta":
@@ -13,6 +16,7 @@ tools:
       documentation: "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf"
       tool_dev_url: "https://github.com/jianyangqt/gcta"
       licence: ["GPL-3.0-only"]
+      identifier: "biotools:gcta"
 input:
   - - meta:
         type: map
@@ -90,7 +94,7 @@ output:
       - "gcta":
           type: string
           description: The tool name
-      - "gcta --version 2>&1 | grep 'version v' | tr -s ' ' | cut -d' ' -f3 | sed 's/^v//'":
+      - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'":
           type: eval
           description: The command used to generate the version of the tool
 topics:
@@ -101,10 +105,10 @@ topics:
       - gcta:
           type: string
           description: The tool name
-      - gcta --version 2>&1 | grep 'version v' | tr -s ' ' | cut -d' ' -f3 | sed 's/^v//':
+      - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'":
           type: eval
           description: The command used to generate the version of the tool
 authors:
-  - "@andongni"
+  - "@lyh970817"
 maintainers:
-  - "@andongni"
+  - "@lyh970817"