fixed prettier

nf-core · Nov 18, 2024 · 741a0e5 · 741a0e5
1 parent dafaa8f
commit 741a0e5
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Showing 3 changed files with 12 additions and 12 deletions.
diff --git a/subworkflows/local/faidx_cut_chr_size.nf b/subworkflows/local/faidx_cut_chr_size.nf
@@ -29,4 +29,4 @@ workflow FAIDX_SUBWORKFLOW {
 
     emit:
     path("sizes.genome"), from: CUT_SIZES_GENOME.out.ch_sizes_genome
-}
+}
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
@@ -16,8 +16,8 @@ workflow INPUT_CHECK {
         .set { reads }
 
     reads
-        
-        .map { meta, fastq -> 
+
+        .map { meta, fastq ->
             def expID = meta.expID  // Prendi l'expID da meta
             meta.remove('fraction') // Rimuovi il campo 'fraction'
 
@@ -27,7 +27,7 @@ workflow INPUT_CHECK {
         //.view()
         .map{ expID, meta , fastq ->
             meta = meta[0].clone()  // Prendi solo la prima mappa e crea una copia
-            meta.id = expID  // Sostituisci il valore nel campo id con expID 
+            meta.id = expID  // Sostituisci il valore nel campo id con expID
             [ [meta], fastq.flatten() ]
             }
         .set { reads_to_merge }

diff --git a/workflows/sammyseq.nf b/workflows/sammyseq.nf
@@ -238,7 +238,7 @@ workflow SAMMYSEQ {
     //a channel is created for the trimmed files and the id is renamed to meta, so that when passed to fastqc it does not overwrite the output files with non-trimmed ones
     ch_fastqc_trim=TRIMMOMATIC.out.trimmed_reads
     // ch_fastqc_trim=TRIMGALORE.out.reads
-                   .map{ meta, path ->
+                    .map{ meta, path ->
                         def id=meta.subMap('id')
                         newid=id.id + "_trim"
                         sng=meta.subMap('single_end').single_end
@@ -281,7 +281,7 @@ workflow SAMMYSEQ {
     // Index Fasta File for Markduplicates
     SAMTOOLS_FAIDX (
             ch_fasta_meta,
-             [[], []]
+            [[], []]
         )
 
     ch_fai_for_cut = SAMTOOLS_FAIDX.out.fai.collect()
@@ -328,7 +328,7 @@ workflow SAMMYSEQ {
 
     //ch_bam_bai_combined = BAM_MARKDUPLICATES_PICARD.out.bam.join(BAM_MARKDUPLICATES_PICARD.out.bai, by: [0])
 
-   ch_bam_bai_combined =  BAM_MARKDUPLICATES_PICARD.out.bam
+    ch_bam_bai_combined =  BAM_MARKDUPLICATES_PICARD.out.bam
         .join(BAM_MARKDUPLICATES_PICARD.out.bai, by: [0], remainder: true)
         .map {
             meta, bam, bai  ->
@@ -377,9 +377,9 @@ workflow SAMMYSEQ {
         Channel.fromPath(params.comparisonFile)
                 .splitCsv(header : true)
                 .map{ row ->
-                   // [ row.sample2 + "_T1", row.sample1 + "_T1",row.sample1 + "_T1_VS_" + row.sample2 + "_T1"]
-                   //[ row.sample2 + "_T1", row.sample1 + "_T1_VS_" + row.sample2 + "_T1"]
-                   [ row.sample2 , row.sample1 + "_VS_" + row.sample2 ]
+                    // [ row.sample2 + "_T1", row.sample1 + "_T1",row.sample1 + "_T1_VS_" + row.sample2 + "_T1"]
+                    //[ row.sample2 + "_T1", row.sample1 + "_T1_VS_" + row.sample2 + "_T1"]
+                    [ row.sample2 , row.sample1 + "_VS_" + row.sample2 ]
                 }
                 .set { comparisons_ch_s2 }
 
@@ -421,8 +421,8 @@ workflow SAMMYSEQ {
         //4.run rscript
 
         RTWOSAMPLESMLE (comparisons_merge_ch,
-                       CUT_SIZES_GENOME.out.ch_sizes_genome
-                       )
+                        CUT_SIZES_GENOME.out.ch_sizes_genome
+                        )
 
         if (params.stopAt == 'RTWOSAMPLESMLE') {
         return
-Original file line number
+Diff line change
@@ Expand Up / @@ -29,4 +29,4 @@ workflow FAIDX_SUBWORKFLOW { @@
         emit:
         path("sizes.genome"), from: CUT_SIZES_GENOME.out.ch_sizes_genome
-    }
+    }