Standarize and alignment for all imputation and alignment modules

modules/nf-core/bcftools/index/main.nf

@@ -20,7 +20,6 @@ process BCFTOOLS_INDEX {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     bcftools \\
@@ -37,7 +36,6 @@ process BCFTOOLS_INDEX {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
     def extension = args.contains("--tbi") || args.contains("-t") ? "tbi" :
                     "csi"
     """

modules/nf-core/beagle5/beagle/main.nf

@@ -1,11 +1,11 @@
 process BEAGLE5_BEAGLE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/beagle:5.5_27Feb25.75f--hdfd78af_0':
-        'biocontainers/beagle:5.5_27Feb25.75f--hdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/beagle:5.5_27Feb25.75f--hdfd78af_0'
+        : 'biocontainers/beagle:5.5_27Feb25.75f--hdfd78af_0'}"
 
     input:
     // Including `val(region)` to prevent errors with multi-chromosome VCFs and single-chromosome reference panels.
@@ -21,26 +21,28 @@ process BEAGLE5_BEAGLE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}.bglout"
-    def ref_command = refpanel ? "ref=$refpanel" : ""
-    def map_command = genmap   ? "map=$genmap"   : ""
-    def region_cmd  = region   ? "chrom=$region" : ""
-    def excludesamples_command = exclsamples ? "excludesamples=$exclsamples" : ""
-    def excludemarkers_command = exclmarkers ? "excludemarkers=$exclmarkers" : ""
+
+    def ref_command = refpanel ? "ref=${refpanel}" : ""
+    def map_command = genmap   ? "map=${genmap}"   : ""
+    def region_cmd  = region   ? "chrom=${region}" : ""
+
+    def excludesamples_command = exclsamples ? "excludesamples=${exclsamples}" : ""
+    def excludemarkers_command = exclmarkers ? "excludemarkers=${exclmarkers}" : ""
 
     def avail_mem = 3072
     if (!task.memory) {
-        log.info '[beagle] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+        log.info('[beagle] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.')
     } else {
-        avail_mem = (task.memory.mega*0.8).intValue()
+        avail_mem = (task.memory.mega * 0.8).intValue()
     }
 
     """
     beagle -Xmx${avail_mem}M \\
         gt=${vcf} \\
         out=${prefix} \\
-        $args \\
+        ${args} \\
         ${ref_command} \\
         ${map_command} \\
         ${region_cmd} \\

modules/nf-core/glimpse/chunk/main.nf

@@ -1,32 +1,32 @@
 process GLIMPSE_CHUNK {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2':
-        'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2'
+        : 'biocontainers/glimpse-bio:1.1.1--hce55b13_1'}"
 
     input:
     tuple val(meta), path(input), path(input_index), val(region)
 
     output:
     tuple val(meta), path("*.txt"), emit: chunk_chr
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix  = task.ext.prefix ?: "${meta.id}"
-    def args    = task.ext.args   ?: ""
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args   = task.ext.args   ?: ""
 
     """
     GLIMPSE_chunk \\
-        $args \\
-        --input $input \\
-        --region $region \\
-        --thread $task.cpus \\
+        ${args} \\
+        --input ${input} \\
+        --region ${region} \\
+        --thread ${task.cpus} \\
         --output ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
@@ -36,7 +36,7 @@ process GLIMPSE_CHUNK {
     """
 
     stub:
-    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     touch ${prefix}.txt

modules/nf-core/glimpse/chunk/tests/nextflow.config

@@ -1,6 +1,6 @@
 process {
     withName: GLIMPSE_CHUNK {
-        ext.args = { "${params.glimpse_args}" }
+        ext.args   = { "${params.glimpse_args}" }
         ext.prefix = { "${meta.id}" }
     }
 }

modules/nf-core/glimpse/concordance/main.nf

@@ -1,17 +1,17 @@
 process GLIMPSE_CONCORDANCE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h0303221_3':
-        'biocontainers/glimpse-bio:1.1.1--h0303221_3' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h0303221_3'
+        : 'biocontainers/glimpse-bio:1.1.1--h0303221_3'}"
 
     input:
     tuple val(meta), path(estimate), path(estimate_index), path(freq), path(freq_index), path(truth), path(truth_index), val(region)
-    val(min_prob)
-    val(min_dp)
-    val(bins)
+    val min_prob
+    val min_dp
+    val bins
 
     output:
     tuple val(meta), path("*.error.cal.txt.gz")  , emit: errors_cal
@@ -20,6 +20,7 @@ process GLIMPSE_CONCORDANCE {
     tuple val(meta), path("*.rsquare.grp.txt.gz"), emit: rsquare_grp
     tuple val(meta), path("*.rsquare.spl.txt.gz"), emit: rsquare_spl
     path "versions.yml"                          , emit: versions
+
     when:
     task.ext.when == null || task.ext.when
 
@@ -30,15 +31,15 @@ process GLIMPSE_CONCORDANCE {
     def min_dp_cmd   = min_dp   ? "--minDP ${min_dp}"     : "--minDP 8"
     def bins_cmd     = bins     ? "--bins ${bins}"        : "--bins 0.00000 0.00100 0.00200 0.00500 0.01000 0.05000 0.10000 0.20000 0.50000"
     """
-    echo $region $freq $truth $estimate > input.txt
+    echo ${region} ${freq} ${truth} ${estimate} > input.txt
     GLIMPSE_concordance \\
-        $args \\
+        ${args} \\
         --input input.txt \\
-        --thread $task.cpus \\
+        --thread ${task.cpus} \\
         --output ${prefix} \\
-        $min_prob_cmd \\
-        $min_dp_cmd \\
-        $bins_cmd
+        ${min_prob_cmd} \\
+        ${min_dp_cmd} \\
+        ${bins_cmd}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -47,7 +48,7 @@ process GLIMPSE_CONCORDANCE {
     """
 
     stub:
-    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     echo "" | gzip > ${prefix}.error.cal.txt.gz

modules/nf-core/glimpse/ligate/main.nf

@@ -1,11 +1,11 @@
 process GLIMPSE_LIGATE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--hce55b13_1':
-        'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--hce55b13_1'
+        : 'biocontainers/glimpse-bio:1.1.1--hce55b13_1'}"
 
     input:
     tuple val(meta), path(input_list), path(input_index)
@@ -22,12 +22,12 @@ process GLIMPSE_LIGATE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ?: "vcf.gz"
     """
-    printf "%s\\n" $input_list | tr -d '[],' | sort -V > all_files.txt
+    printf "%s\\n" ${input_list} | tr -d '[],' | sort -V > all_files.txt
 
     GLIMPSE_ligate \\
-        $args \\
+        ${args} \\
         --input all_files.txt \\
-        --thread $task.cpus \\
+        --thread ${task.cpus} \\
         --output ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/glimpse/phase/main.nf

@@ -1,40 +1,40 @@
 process GLIMPSE_PHASE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--hce55b13_1':
-        'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--hce55b13_1'
+        : 'biocontainers/glimpse-bio:1.1.1--hce55b13_1'}"
 
     input:
-        tuple val(meta) , path(input), path(input_index), path(samples_file), val(input_region), val(output_region), path(reference), path(reference_index), path(map)
+    tuple val(meta), path(input), path(input_index), path(samples_file), val(input_region), val(output_region), path(reference), path(reference_index), path(map)
 
     output:
-        tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: phased_variants
-        path "versions.yml"                               , emit: versions
+    tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: phased_variants
+    path "versions.yml"                               , emit: versions
 
     when:
-        task.ext.when == null || task.ext.when
+    task.ext.when == null || task.ext.when
 
     script:
     def args   = task.ext.args   ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}_${input_region.replace(":","_")}"
+    def prefix = task.ext.prefix ?: "${meta.id}_${input_region.replace(":", "_")}"
     def suffix = task.ext.suffix ?: "vcf.gz"
 
-    def map_command           = map           ? "--map $map"                    :""
-    def samples_file_command  = samples_file  ? "--samples-file $samples_file"  :""
+    def map_command          = map          ? "--map ${map}"                   : ""
+    def samples_file_command = samples_file ? "--samples-file ${samples_file}" : ""
 
     """
     GLIMPSE_phase \\
-        $args \\
-        --input $input \\
-        --reference $reference \\
-        $map_command \\
-        $samples_file_command \\
-        --input-region $input_region \\
-        --output-region $output_region \\
-        --thread $task.cpus \\
+        ${args} \\
+        --input ${input} \\
+        --reference ${reference} \\
+        ${map_command} \\
+        ${samples_file_command} \\
+        --input-region ${input_region} \\
+        --output-region ${output_region} \\
+        --thread ${task.cpus} \\
         --output ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
@@ -44,7 +44,7 @@ process GLIMPSE_PHASE {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}_${input_region.replace(":","_")}"
+    def prefix = task.ext.prefix ?: "${meta.id}_${input_region.replace(":", "_")}"
     def suffix = task.ext.suffix ?: "vcf.gz"
 
     """

modules/nf-core/glimpse/sample/main.nf

@@ -1,11 +1,11 @@
 process GLIMPSE_SAMPLE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--hce55b13_1':
-        'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--hce55b13_1'
+        : 'biocontainers/glimpse-bio:1.1.1--hce55b13_1'}"
 
     input:
     tuple val(meta), path(input), path(index)
@@ -24,9 +24,9 @@ process GLIMPSE_SAMPLE {
 
     """
     GLIMPSE_sample \\
-        $args \\
-        --input $input \\
-        --thread $task.cpus \\
+        ${args} \\
+        --input ${input} \\
+        --thread ${task.cpus} \\
         --output ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/glimpse2/chunk/main.nf

@@ -1,8 +1,8 @@
 process GLIMPSE2_CHUNK {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
-    beforeScript  """
+    beforeScript """
         if cat /proc/cpuinfo | grep avx2 -q
         then
             echo "Feature AVX2 present on host"
@@ -12,13 +12,13 @@ process GLIMPSE2_CHUNK {
         fi
     """
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/glimpse-bio:2.0.1--h46b9e50_1':
-        'biocontainers/glimpse-bio:2.0.1--h46b9e50_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/glimpse-bio:2.0.1--h46b9e50_1'
+        : 'biocontainers/glimpse-bio:2.0.1--h46b9e50_1'}"
 
     input:
     tuple val(meta), path(input), path(input_index), val(region), path(map)
-    val(model)
+    val model
 
     output:
     tuple val(meta), path("*.txt"), emit: chunk_chr
@@ -28,18 +28,18 @@ process GLIMPSE2_CHUNK {
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix    = task.ext.prefix ?: "${meta.id}"
-    def args      = task.ext.args   ?: ""
-    def map_cmd   = map ? "--map ${map}":""
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def args    = task.ext.args   ?: ""
+    def map_cmd = map ? "--map ${map}" : ""
 
     """
     GLIMPSE2_chunk \\
-        $args \\
-        $map_cmd \\
+        ${args} \\
+        ${map_cmd} \\
         --${model} \\
-        --input $input \\
-        --region $region \\
-        --threads $task.cpus \\
+        --input ${input} \\
+        --region ${region} \\
+        --threads ${task.cpus} \\
         --output ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
@@ -49,7 +49,7 @@ process GLIMPSE2_CHUNK {
     """
 
     stub:
-    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     echo "${meta.id}\t${region}\t0\t0\t0\t0\t0\t0" > ${prefix}.txt