Fix indenting

nf-core · Mar 14, 2024 · 37a4022 · 37a4022
1 parent 3196720
commit 37a4022
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Showing 5 changed files with 48 additions and 48 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -218,7 +218,7 @@ process {
                     def tokens = filename.split('[/]')
                     return "${meta.key}/orange/${tokens[-1]}"
                 }
-           }
+            }
         ]
     }
 

diff --git a/lib/Utils.groovy b/lib/Utils.groovy
@@ -359,9 +359,9 @@ class Utils {
 
     public static selectCurrentOrExisting(val, meta, key) {
         if (hasExistingInput(meta, key)) {
-          return getInput(meta, key)
+            return getInput(meta, key)
         } else {
-          return val
+            return val
         }
     }
 

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -161,9 +161,9 @@ class WorkflowMain {
 
         // NOTE(SW): this could be moved to the wgts.nf where we check that input files exist
         def null_check = [
-           'ref_data_genome_fasta',
-           'ref_data_genome_type',
-           'ref_data_genome_version',
+             'ref_data_genome_fasta',
+             'ref_data_genome_type',
+             'ref_data_genome_version',
         ]
         null_check.each { k ->
             if (!params[k]) {

diff --git a/modules/local/chord/main.nf b/modules/local/chord/main.nf
@@ -58,8 +58,8 @@ process CHORD {
 
     cat('[INFO] Performing chord HRD prediction\\n')
     prediction <- chordPredict(
-      signatures,
-      hrd.cutoff=0.5
+        signatures,
+        hrd.cutoff=0.5
     )
 
     cat('[INFO] Writing output file:', sigOutTxt,'\\n')

diff --git a/modules/local/orange/main.nf b/modules/local/orange/main.nf
@@ -67,7 +67,7 @@ process ORANGE {
         purple_dir_local=purple__prepared;
 
         if [[ -d \${purple_dir_local}/ ]]; then
-          rm -r \${purple_dir_local}/;
+            rm -r \${purple_dir_local}/;
         fi
 
         cp -rL ${purple_dir} \${purple_dir_local}/
@@ -105,45 +105,45 @@ process ORANGE {
         --add-opens java.base/java.time=ALL-UNNAMED \\
         -Xmx${Math.round(task.memory.bytes * 0.95)} \\
         -jar \${orange_jar} \\
-          \\
-          -experiment_date \$(date +%y%m%d) \\
-          -add_disclaimer \\
-          -pipeline_version_file pipeline_version.txt \\
-          \\
-          -tumor_sample_id ${meta.tumor_id} \\
-          -primary_tumor_doids 162 \\
-          -tumor_sample_wgs_metrics_file ${bam_metrics_somatic} \\
-          -tumor_sample_flagstat_file ${flagstat_somatic} \\
-          -sage_dir ${sage_somatic_dir} \\
-          -purple_dir \${purple_dir_local} \\
-          -purple_plot_dir \${purple_dir_local}/plot/ \\
-          -linx_dir ${linx_somatic_anno_dir} \\
-          -linx_plot_dir ${plot_dir}/ \\
-          -lilac_dir ${lilac_dir} \\
-          ${virus_dir_arg} \\
-          ${chord_dir_arg} \\
-          ${sigs_dir_arg} \\
-          ${cuppa_dir_arg} \\
-          \\
-          ${normal_id_arg} \\
-          ${normal_metrics_arg} \\
-          ${normal_flagstat_arg} \\
-          ${normal_sage_dir} \\
-          ${normal_linx_arg} \\
-          \\
-          ${rna_id_arg} \\
-          ${isofox_dir_arg} \\
-          \\
-          -ref_genome_version ${genome_ver} \\
-          -doid_json ${disease_ontology} \\
-          -cohort_mapping_tsv ${cohort_mapping} \\
-          -cohort_percentiles_tsv ${cohort_percentiles} \\
-          -known_fusion_file ${known_fusion_data} \\
-          -driver_gene_panel ${driver_gene_panel} \\
-          -ensembl_data_dir ${ensembl_data_resources} \\
-          ${isofox_gene_distribution_arg} \\
-          ${isofox_alt_sj_arg} \\
-          -output_dir output/
+            \\
+            -experiment_date \$(date +%y%m%d) \\
+            -add_disclaimer \\
+            -pipeline_version_file pipeline_version.txt \\
+            \\
+            -tumor_sample_id ${meta.tumor_id} \\
+            -primary_tumor_doids 162 \\
+            -tumor_sample_wgs_metrics_file ${bam_metrics_somatic} \\
+            -tumor_sample_flagstat_file ${flagstat_somatic} \\
+            -sage_dir ${sage_somatic_dir} \\
+            -purple_dir \${purple_dir_local} \\
+            -purple_plot_dir \${purple_dir_local}/plot/ \\
+            -linx_dir ${linx_somatic_anno_dir} \\
+            -linx_plot_dir ${plot_dir}/ \\
+            -lilac_dir ${lilac_dir} \\
+            ${virus_dir_arg} \\
+            ${chord_dir_arg} \\
+            ${sigs_dir_arg} \\
+            ${cuppa_dir_arg} \\
+            \\
+            ${normal_id_arg} \\
+            ${normal_metrics_arg} \\
+            ${normal_flagstat_arg} \\
+            ${normal_sage_dir} \\
+            ${normal_linx_arg} \\
+            \\
+            ${rna_id_arg} \\
+            ${isofox_dir_arg} \\
+            \\
+            -ref_genome_version ${genome_ver} \\
+            -doid_json ${disease_ontology} \\
+            -cohort_mapping_tsv ${cohort_mapping} \\
+            -cohort_percentiles_tsv ${cohort_percentiles} \\
+            -known_fusion_file ${known_fusion_data} \\
+            -driver_gene_panel ${driver_gene_panel} \\
+            -ensembl_data_dir ${ensembl_data_resources} \\
+            ${isofox_gene_distribution_arg} \\
+            ${isofox_alt_sj_arg} \\
+            -output_dir output/
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-Original file line number
+Diff line change
@@ Expand Up / @@ -218,7 +218,7 @@ process { @@
                         def tokens = filename.split('[/]')
                         return "${meta.key}/orange/${tokens[-1]}"
                     }
-               }
+                }
             ]
         }
@@ Expand Down @@