Nextflow Language Server Compliance for Freec Modules

modules/nf-core/controlfreec/assesssignificance/main.nf

@@ -1,46 +1,47 @@
 process CONTROLFREEC_ASSESSSIGNIFICANCE {
-    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/control-freec:11.6b--hdbdd923_0' :
-        'biocontainers/control-freec:11.6b--hdbdd923_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0'
+        : 'biocontainers/control-freec:11.6b--hdbdd923_0'}"
 
     input:
     tuple val(meta), path(cnvs), path(ratio)
 
     output:
     tuple val(meta), path("*.p.value.txt"), emit: p_value_txt
-    path "versions.yml"                   , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b'
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     cat \$(which assess_significance.R) | R --slave --args ${cnvs} ${ratio}
 
     mv *.p.value.txt ${prefix}.p.value.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: $VERSION
+        controlfreec: ${VERSION}
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b'
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.p.value.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: $VERSION
+        controlfreec: ${VERSION}
     END_VERSIONS
     """
 }

modules/nf-core/controlfreec/assesssignificance/tests/nextflow.config

@@ -1,23 +1,24 @@
 process {
-    withName:CONTROLFREEC_FREEC{
-        ext.args = { [
-                    "sample":[
-                        inputformat: 'pileup',
-                        mateorientation: 'FR'
-                    ],
-                    "general" :[
-                        bedgraphoutput: "TRUE",
-                        noisydata: "TRUE",
-                        minexpectedgc: "0",
-                        readcountthreshold: "1",
-                        sex: meta.sex,
-                        window: "10",
-                        ],
-                    "control":[
-                        inputformat: "pileup",
-                        mateorientation: "FR"
-                    ]
-                    ]
+    withName: CONTROLFREEC_FREEC {
+        ext.args = {
+            [
+                "sample": [
+                    inputformat: 'pileup',
+                    mateorientation: 'FR',
+                ],
+                "general": [
+                    bedgraphoutput: "TRUE",
+                    noisydata: "TRUE",
+                    minexpectedgc: "0",
+                    readcountthreshold: "1",
+                    sex: meta.sex,
+                    window: "10",
+                ],
+                "control": [
+                    inputformat: "pileup",
+                    mateorientation: "FR",
+                ],
+            ]
         }
     }
 }

modules/nf-core/controlfreec/freec/tests/nextflow.config

@@ -1,23 +1,24 @@
 process {
-    withName:CONTROLFREEC_FREEC{
-        ext.args = { [
-                    "sample":[
-                        inputformat: 'pileup',
-                        mateorientation: 'FR'
-                    ],
-                    "general" :[
-                        bedgraphoutput: "TRUE",
-                        noisydata: "TRUE",
-                        minexpectedgc: "0",
-                        readcountthreshold: "1",
-                        sex: meta.sex,
-                        window: "10",
-                        ],
-                    "control":[
-                        inputformat: "pileup",
-                        mateorientation: "FR"
-                    ]
-                    ]
+    withName: CONTROLFREEC_FREEC {
+        ext.args = {
+            [
+                "sample": [
+                    inputformat: 'pileup',
+                    mateorientation: 'FR',
+                ],
+                "general": [
+                    bedgraphoutput: "TRUE",
+                    noisydata: "TRUE",
+                    minexpectedgc: "0",
+                    readcountthreshold: "1",
+                    sex: meta.sex,
+                    window: "10",
+                ],
+                "control": [
+                    inputformat: "pileup",
+                    mateorientation: "FR",
+                ],
+            ]
         }
     }
 }

modules/nf-core/controlfreec/freec2bed/main.nf

@@ -1,44 +1,46 @@
 process CONTROLFREEC_FREEC2BED {
-    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/control-freec:11.6b--hdbdd923_0' :
-        'biocontainers/control-freec:11.6b--hdbdd923_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0'
+        : 'biocontainers/control-freec:11.6b--hdbdd923_0'}"
 
     input:
     tuple val(meta), path(ratio)
 
     output:
     tuple val(meta), path("*.bed"), emit: bed
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b'
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     freec2bed.pl -f ${ratio} ${args} > ${prefix}.bed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: $VERSION
+        controlfreec: ${VERSION}
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b'
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.bed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: $VERSION
+        controlfreec: ${VERSION}
     END_VERSIONS
     """
 }

modules/nf-core/controlfreec/freec2bed/tests/nextflow.config

@@ -1,23 +1,24 @@
 process {
-    withName:CONTROLFREEC_FREEC{
-        ext.args = { [
-                    "sample":[
-                        inputformat: 'pileup',
-                        mateorientation: 'FR'
-                    ],
-                    "general" :[
-                        bedgraphoutput: "TRUE",
-                        noisydata: "TRUE",
-                        minexpectedgc: "0",
-                        readcountthreshold: "1",
-                        sex: meta.sex,
-                        window: "10",
-                        ],
-                    "control":[
-                        inputformat: "pileup",
-                        mateorientation: "FR"
-                    ]
-                    ]
+    withName: CONTROLFREEC_FREEC {
+        ext.args = {
+            [
+                "sample": [
+                    inputformat: 'pileup',
+                    mateorientation: 'FR',
+                ],
+                "general": [
+                    bedgraphoutput: "TRUE",
+                    noisydata: "TRUE",
+                    minexpectedgc: "0",
+                    readcountthreshold: "1",
+                    sex: meta.sex,
+                    window: "10",
+                ],
+                "control": [
+                    inputformat: "pileup",
+                    mateorientation: "FR",
+                ],
+            ]
         }
     }
 }

modules/nf-core/controlfreec/freec2circos/main.nf

@@ -1,44 +1,46 @@
 process CONTROLFREEC_FREEC2CIRCOS {
-    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/control-freec:11.6b--hdbdd923_0' :
-        'biocontainers/control-freec:11.6b--hdbdd923_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0'
+        : 'biocontainers/control-freec:11.6b--hdbdd923_0'}"
 
     input:
     tuple val(meta), path(ratio)
 
     output:
     tuple val(meta), path("*.circos.txt"), emit: circos
-    path "versions.yml"                  , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b'
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     freec2circos.pl -f ${ratio} ${args} > ${prefix}.circos.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: $VERSION
+        controlfreec: ${VERSION}
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b'
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.circos.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: $VERSION
+        controlfreec: ${VERSION}
     END_VERSIONS
     """
 }

modules/nf-core/controlfreec/freec2circos/tests/nextflow.config

@@ -1,23 +1,24 @@
 process {
-    withName:CONTROLFREEC_FREEC{
-        ext.args = { [
-                    "sample":[
-                        inputformat: 'pileup',
-                        mateorientation: 'FR'
-                    ],
-                    "general" :[
-                        bedgraphoutput: "TRUE",
-                        noisydata: "TRUE",
-                        minexpectedgc: "0",
-                        readcountthreshold: "1",
-                        sex: meta.sex,
-                        window: "10",
-                        ],
-                    "control":[
-                        inputformat: "pileup",
-                        mateorientation: "FR"
-                    ]
-                    ]
+    withName: CONTROLFREEC_FREEC {
+        ext.args = {
+            [
+                "sample": [
+                    inputformat: 'pileup',
+                    mateorientation: 'FR',
+                ],
+                "general": [
+                    bedgraphoutput: "TRUE",
+                    noisydata: "TRUE",
+                    minexpectedgc: "0",
+                    readcountthreshold: "1",
+                    sex: meta.sex,
+                    window: "10",
+                ],
+                "control": [
+                    inputformat: "pileup",
+                    mateorientation: "FR",
+                ],
+            ]
         }
     }
 }