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nf-core · Mar 26, 2024 · 1e9652d · 1e9652d
1 parent ea0dd41
commit 1e9652d
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Showing 5 changed files with 14 additions and 15 deletions.
diff --git a/bin/rose.py b/bin/rose.py
@@ -75,7 +75,7 @@ def region_stitching(input_gff, stitch_window, tss_window, annot_file, remove_ts
         return fixed_collection
     else:
         return stitched_collection
-    
+
 
 # ==================================================================
 # ==========================I/O FUNCTIONS===========================
@@ -630,7 +630,7 @@ def main():
     options, args = parser.parse_args()
 
     input_gff_file = options.input
-    
+
     stitch_window = int(options.stitch)
 
     tss_window = int(options.tss)
@@ -663,4 +663,4 @@ def main():
 
 
 if __name__ == '__main__':
-    main()
+    main()
diff --git a/modules/local/chromhmm/binarize_bams/main.nf b/modules/local/chromhmm/binarize_bams/main.nf
@@ -7,7 +7,7 @@ process BINARIZE_BAMS {
 
     input:
     tuple val(meta), path(bams, stageAs: "input/*")
-	tuple val(meta2), path(table)
+    tuple val(meta2), path(table)
     tuple val(meta3), path(chromsizes)
 
     output:
@@ -16,9 +16,9 @@ process BINARIZE_BAMS {
     script:
     """
     java -jar $moduleDir/ChromHMM.jar BinarizeBam \\
-       $chromsizes \\
-       input \\
-       $table \\
-       output
+        $chromsizes \\
+        input \\
+        $table \\
+        output
     """
-}
+}
diff --git a/modules/local/chromhmm/get_results/main.nf b/modules/local/chromhmm/get_results/main.nf
@@ -21,4 +21,4 @@ process GET_RESULTS {
         --bed $bed \\
         --output $output_file
     """
-}
+}
diff --git a/modules/local/rose/main.nf b/modules/local/rose/main.nf
@@ -28,4 +28,4 @@ process ROSE {
     """
     touch "${gff.baseName}_STITCHED.gff"
     """
-}
+}
diff --git a/subworkflows/local/chromhmm.nf b/subworkflows/local/chromhmm.nf
@@ -4,7 +4,7 @@ include { SAMTOOLS_REHEADER as REHEADER_CONTROL } from '../../modules/nf-core/sa
 include { BINARIZE_BAMS                         } from '../../modules/local/chromhmm/binarize_bams'
 include { LEARN_MODEL                           } from '../../modules/local/chromhmm/learn_model'
 include { GET_RESULTS                           } from '../../modules/local/chromhmm/get_results'
- 
+
 workflow CHROMHMM {
 
     take:
@@ -19,7 +19,7 @@ workflow CHROMHMM {
     ch_bams = ch_samplesheet_bam.map{meta, signal, control -> [meta, ["signal", "control"], [signal, control]]}
                                 .transpose()
                                 .map{meta, type, bam -> [meta + [type: type], bam]}
-                                .branch   {meta, bam -> 
+                                .branch   {meta, bam ->
                                     control: meta.type == "control"
                                     signal:  meta.type == "signal"
                                 }
@@ -57,7 +57,7 @@ workflow CHROMHMM {
                                 .map{meta, emmisions, bed ->
                                     [meta + [id: bed.simpleName.split("_")[0]],
                                     emmisions, bed]})
-    
+
     ch_enhancers = GET_RESULTS.out.map{meta, bed -> [[condition: meta.id, assay: "chromHMM_enhancers"], bed]}
                                     .map{meta, bed -> [meta + [id: meta.condition + "_" + meta.assay], bed]}
 
@@ -66,4 +66,3 @@ workflow CHROMHMM {
 
     versions = ch_versions
 }
-