Fix editorconfig

nf-core · Sep 25, 2024 · a90fd39 · a90fd39
1 parent 1e6b98d
commit a90fd39
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Showing 7 changed files with 12 additions and 12 deletions.
diff --git a/modules/local/ciriquant/de/main.nf b/modules/local/ciriquant/de/main.nf
@@ -32,4 +32,4 @@ process CIRIQUANT_DE {
         ciriquant: \$(echo \$(CIRIquant --version 2>&1) | sed 's/CIRIquant //g' )
     END_VERSIONS
     """
-}
+}
diff --git a/modules/local/ciriquant/prepde/main.nf b/modules/local/ciriquant/prepde/main.nf
@@ -39,4 +39,4 @@ process CIRIQUANT_PREPDE {
         ciriquant: \$(echo \$(CIRIquant --version 2>&1) | sed 's/CIRIquant //g' )
     END_VERSIONS
     """
-}
+}
diff --git a/modules/local/matrix/join_samples/templates/join.py b/modules/local/matrix/join_samples/templates/join.py
@@ -11,8 +11,8 @@
 
 dfs = {
     sample:
-    pl.scan_csv(matrix, 
-                separator="\\t", 
+    pl.scan_csv(matrix,
+                separator="\\t",
                 new_columns=metacols + [sample],
                 has_header="${has_header}" == "true")
         .group_by(metacols).agg(pl.sum(sample).alias(sample))

diff --git a/subworkflows/local/combine_transcriptomes.nf b/subworkflows/local/combine_transcriptomes.nf
@@ -7,10 +7,10 @@ workflow COMBINE_TRANSCRIPTOMES {
     ch_genome_fasta
     ch_genome_gtf
     ch_circ_gtf
-    
+
     main:
     ch_versions = Channel.empty()
-    
+
     COMBINE_TRANSCRIPTOME_GTFS(
         ch_genome_gtf.mix(ch_circ_gtf).map{meta, gtf -> gtf}.collect().map{[[id: "transcriptome"], it]},
     )
@@ -36,4 +36,4 @@ workflow COMBINE_TRANSCRIPTOMES {
     gtf   = EXCLUDE_OVERLONG_TRANSCRIPTS.out.output
 
     versions = ch_versions
-}
+}
diff --git a/subworkflows/local/quantification_tools/ciriquant.nf b/subworkflows/local/quantification_tools/ciriquant.nf
@@ -34,7 +34,7 @@ workflow CIRIQUANT {
         EXTRACT_CIRC.out.table.map{meta, table -> [[id: 'circ'], meta.id, table]}.groupTuple()
     )
     ch_versions = ch_versions.mix(JOIN_CIRC.out.versions)
-    
+
     emit:
     gene_tpm  = JOIN_GENE.out.joined
     circ_cpm  = JOIN_CIRC.out.joined

diff --git a/subworkflows/local/quantification_tools/psirc_quant.nf b/subworkflows/local/quantification_tools/psirc_quant.nf
@@ -114,4 +114,4 @@ workflow PSIRC_QUANT {
     circular_tx_tpm    = SPLIT_TYPES_TPM.out.circular
 
     versions           = ch_versions
-}
+}
diff --git a/subworkflows/local/statistical_tests.nf b/subworkflows/local/statistical_tests.nf
@@ -34,17 +34,17 @@ workflow STATISTICAL_TESTS {
         .join(ch_stringtie.map{ meta, gtf -> [meta.id, gtf] })
         .map{ sample, condition, ciriquant, stringtie -> [condition, [sample, ciriquant, stringtie]] }
         .groupTuple()
-        .map{ condition, samples -> 
+        .map{ condition, samples ->
             [condition, samples.sort({ a, b -> a[0] <=> b[0] }).transpose()]
         }
-        .map{ condition, samples -> 
+        .map{ condition, samples ->
             [condition, samples[0], samples[1], samples[2]]
         }
 
     ch_condition_pairs = ch_condition_samples
         .combine(ch_condition_samples)
         .filter{ c_control, s_control, f_ciri_control, f_stringtie_control, c_treatment, s_treatment, f_ciri_treatment, f_stringtie_treatment
-             -> c_control > c_treatment }
+            -> c_control > c_treatment }
         .map{ c_control, s_control, f_ciri_control, f_stringtie_control, c_treatment, s_treatment, f_ciri_treatment, f_stringtie_treatment ->
             [   [id: "${c_control}_${c_treatment}"],
                 s_control + s_treatment,
-Original file line number
+Diff line change
@@ Expand Up / @@ -32,4 +32,4 @@ process CIRIQUANT_DE { @@
             ciriquant: \$(echo \$(CIRIquant --version 2>&1) | sed 's/CIRIquant //g' )
         END_VERSIONS
         """
-    }
+    }