test(gcta/remlldms): generate LDMS inputs in setup

Author: lyh970817

modules/nf-core/gcta/remlldms/tests/helpers/makegrm/main.nf

@@ -0,0 +1,36 @@
+process GCTA_MAKEGRM_HELPER {
+    tag "${meta.id}"
+    label "process_medium"
+    conda "${projectDir}/modules/nf-core/gcta/remlldms/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'docker://community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9' :
+        'community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9'}"
+
+    input:
+    tuple val(meta), path(bed), path(bim), path(fam)
+    tuple val(meta2), path(extract_file)
+
+    output:
+    tuple val(meta), path("${meta.id}.grm.id"), path("${meta.id}.grm.bin"), path("${meta.id}.grm.N.bin"), emit: grm_files
+
+    script:
+    def extract_param = extract_file ? "--extract ${extract_file}" : ""
+    def bfile_prefix = bed.baseName
+    """
+    set -euo pipefail
+
+    gcta \\
+        --bfile "${bfile_prefix}" \\
+        ${extract_param} \\
+        --make-grm \\
+        --out "${meta.id}" \\
+        --thread-num ${task.cpus}
+    """
+
+    stub:
+    """
+    touch "${meta.id}.grm.id"
+    touch "${meta.id}.grm.bin"
+    touch "${meta.id}.grm.N.bin"
+    """
+}