[LINT] fix linting issues

conf/modules.config

@@ -163,7 +163,7 @@ process {
             mode: 'copy',
             enabled: params.hicpro_maps
         ]
-	ext.prefix = { "${meta.id}.${resolution}" }
+        ext.prefix = { "${meta.id}.${resolution}" }
     }
 
     withName: 'ICE_NORMALIZATION' {
@@ -194,7 +194,7 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             mode: 'copy'
         ]
-	ext.prefix={ "cooler_bins_${cool_bin}" }
+        ext.prefix={ "cooler_bins_${cool_bin}" }
     }
 
     withName: 'COOLER_CLOAD' {
@@ -204,7 +204,7 @@ process {
             mode: 'copy',
             enabled : params.save_raw_maps
         ]
-	ext.prefix = { "${meta.id}.${cool_bin}" }
+        ext.prefix = { "${meta.id}.${cool_bin}" }
         ext.args = "pairs -c1 2 -p1 3 -c2 4 -p2 5"
     }
 
@@ -215,7 +215,7 @@ process {
             mode: 'copy'
         ]
         ext.args = '--force'
-	ext.prefix = { "${cool.baseName}_balanced" }
+        ext.prefix = { "${cool.baseName}_balanced" }
     }
 
     withName: 'COOLER_DUMP' {
@@ -261,7 +261,7 @@ process {
             mode: 'copy'
         ]
         ext.args = '--bigwig'
-	ext.prefix = { "${meta.id}.${resolution}" }
+        ext.prefix = { "${meta.id}.${resolution}" }
     }
 
     //********************************
@@ -274,7 +274,7 @@ process {
             mode: 'copy'
         ]
         ext.args = '15 25 50 --window-pixels'
-	ext.prefix = { "${cool.baseName}" }
+        ext.prefix = { "${cool.baseName}" }
     }
 
     withName: 'HIC_FIND_TADS' {
@@ -284,6 +284,6 @@ process {
             mode: 'copy'
         ]
         ext.args = '--correctForMultipleTesting fdr'
-	ext.prefix = { "${cool.baseName}" }
+        ext.prefix = { "${cool.baseName}" }
     }
 }

modules.json

@@ -8,72 +8,52 @@
                     "bowtie2/align": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cooler/balance": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cooler/cload": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cooler/dump": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cooler/makebins": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cooler/zoomify": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/getchromsizes": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -82,4 +62,4 @@
             }
         }
     }
-}
\ No newline at end of file
+}

modules/local/multiqc.nf

@@ -2,7 +2,7 @@ process MULTIQC {
     label 'process_medium'
 
     conda "bioconda::multiqc=1.13"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 

modules/local/split_cooler_dump.nf

@@ -4,9 +4,9 @@ process SPLIT_COOLER_DUMP {
 
     conda "conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-      'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-      'ubuntu:20.04' }"
-   
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
+
     input:
     tuple val(meta), path(bedpe)