Fix more style problems

modules/local/combine_tables/main.nf

@@ -6,15 +6,15 @@ process COMBINE_TABLES {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0':
         'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }"
-    
+
     input:
     tuple val(meta), path(files)
     val(method)
-    
+
     output:
     tuple val(meta), path("${prefix}.${extension}"), emit: combined
     path "versions.yml"                            , emit: versions
-    
+
     script:
     prefix = task.ext.prefix ?: "${meta.id}"
     extension = task.ext.extension ?: "tsv"
@@ -28,4 +28,4 @@ process COMBINE_TABLES {
         numpy: \$(python -c "import numpy; print(numpy.__version__)")
     END_VERSIONS
     """
-}
+}

modules/local/counts/calculate_tpm.nf

@@ -27,4 +27,4 @@ process CALCULATE_TPM {
         numpy: \$(python -c "import numpy; print(numpy.__version__)")
     END_VERSIONS
     """
-}
+}

modules/local/counts/combine.nf

@@ -27,4 +27,4 @@ process COMBINE_COUNTS {
         pandas: \$(python -c "import pandas; print(pandas.__version__)")
     END_VERSIONS
     """
-}
+}

modules/local/counts/filter_genes.nf

@@ -36,4 +36,4 @@ process FILTER_GENES {
         pandas: \$(python -c "import pandas; print(pandas.__version__)")
     END_VERSIONS
     """
-}
+}

modules/local/counts/prepare_design.nf

@@ -24,4 +24,4 @@ process PREPARE_DESIGN {
         pandas: \$(python -c "import pandas; print(pandas.__version__)")
     END_VERSIONS
     """
-}
+}

modules/local/dynamite/dynamite.nf

@@ -12,10 +12,10 @@ process DYNAMITE {
     val(ifolds)
     val(alpha)
     val(randomize)
-    
+
     output:
     tuple val(meta), path("${meta.id}_dynamite/Regression_Coefficients_Entire_Data_Set_classification.txt")
-    
+
     script:
     """
     DYNAMITE.R \\
@@ -29,4 +29,4 @@ process DYNAMITE {
         --randomise=$randomize \\
         --cores=$task.cpus
     """
-}
+}

modules/local/dynamite/preprocess.nf

@@ -28,4 +28,4 @@ process PREPROCESS {
         pandas: \$(python -c "import pandas; print(pandas.__version__)")
     END_VERSIONS
     """
-}
+}

modules/local/gtftools/length/main.nf

@@ -33,7 +33,7 @@ process GTFTOOLS_LENGTH {
 
     stub:
     def args = task.ext.args ?: ''
-    
+
     // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
     //               Have a look at the following examples:
     //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63

modules/local/ranking/combine_rankings.nf

@@ -26,4 +26,4 @@ process COMBINE_RANKINGS {
         numpy: \$(python -c "import numpy; print(numpy.__version__)")
     END_VERSIONS
     """
-}
+}

modules/local/ranking/ranking.nf

@@ -27,4 +27,4 @@ process RANKING {
         numpy: \$(python -c "import numpy; print(numpy.__version__)")
     END_VERSIONS
     """
-}
+}

modules/local/ranking/tf_tg_score.nf

@@ -18,15 +18,15 @@ process TF_TG_SCORE {
     script:
     """
     tf_tg_score.py \\
-     --differential ${differential} \\
-     --affinities ${affinities} \\
-     --regression_coefficients ${regression_coefficients} \\
-     --output ${meta.id}.score.tsv
+        --differential ${differential} \\
+        --affinities ${affinities} \\
+        --regression_coefficients ${regression_coefficients} \\
+        --output ${meta.id}.score.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version | sed 's/Python //g')
         pandas: \$(python -c "import pandas; print(pandas.__version__)")
     END_VERSIONS
     """
-}
+}

modules/local/stare/main.nf

@@ -4,7 +4,7 @@ process STARE {
 
     conda "bioconda::stare-abc"
     container "biocontainers/stare-abc:1.0.4--haf6292c_1"
-    
+
     input:
     tuple val(meta), path(candidate_regions)
     path(fasta)
@@ -28,4 +28,4 @@ process STARE {
         STARE: \$( STARE.sh --version )
     END_VERSIONS
     """
-}
+}

subworkflows/local/counts.nf

@@ -45,7 +45,7 @@ workflow COUNTS {
 
     DESEQ2_DIFFERENTIAL(
         Channel.value(["condition"]).combine(contrasts)
-            .map{ variable, reference, target -> 
+            .map{ variable, reference, target ->
                 [[id: reference + ":" + target,
                     contrast: reference + ":" + target,
                     condition1: reference,

subworkflows/local/dynamite.nf

@@ -15,13 +15,13 @@ workflow DYNAMITE {
 
     ch_versions = Channel.empty()
 
-    ch_combined = ch_differential.map{ meta, differential -> 
+    ch_combined = ch_differential.map{ meta, differential ->
             [meta.condition1, meta.condition2, meta, differential]}
-        .combine(ch_affinity_ratio.map{ meta, affinity_ratio -> 
+        .combine(ch_affinity_ratio.map{ meta, affinity_ratio ->
             [meta.condition1, meta.condition2, meta, affinity_ratio]}, by: [0,1])
         .map{ condition1, condition2, meta_differential, differential, meta_affinity, affinity_ratio ->
             [meta_affinity, differential, affinity_ratio]}
-    
+
     PREPROCESS(ch_combined)
 
     RUN_DYNAMITE(PREPROCESS.out.output, ofolds, ifolds, alpha, randomize)
@@ -39,4 +39,3 @@ workflow DYNAMITE {
 
     versions = ch_versions                     // channel: [ versions.yml ]
 }
-

subworkflows/local/footprinting.nf

@@ -10,17 +10,17 @@ workflow FOOTPRINTING {
 
     ch_versions = Channel.empty()
 
-    ch_footprint_split = ch_peaks.branch{ 
-        meta, peaks -> 
+    ch_footprint_split = ch_peaks.branch{
+        meta, peaks ->
             footprinting: meta.footprinting
             as_is: !meta.footprinting
     }
 
     BEDTOOLS_MERGE( ch_footprint_split.footprinting )
 
     ch_include_original_split = BEDTOOLS_MERGE.out.bed
-        .branch{ 
-            meta, bed -> 
+        .branch{
+            meta, bed ->
                 include: meta.include_original
                 subtract: !meta.include_original
         }
@@ -43,4 +43,3 @@ workflow FOOTPRINTING {
 
     versions = ch_versions                     // channel: [ versions.yml ]
 }
-

subworkflows/local/peaks.nf

@@ -67,8 +67,8 @@ workflow PEAKS {
             .map { meta, affinities -> [meta.condition, meta.assay, affinities] }
             .groupTuple(by: [0, 1])
             .map { condition, assay, affinities -> [[id: condition + "_" + assay,
-                                                     condition: condition,
-                                                     assay: assay], affinities] },
+                                                        condition: condition,
+                                                        assay: assay], affinities] },
             "mean"
         )
 
@@ -95,7 +95,7 @@ workflow PEAKS {
                     condition1: condition1, condition2: condition2,
                     assay: assay1],
                     [affinities1, affinities2]] }
-    
+
     AFFINITY_RATIO(ch_contrast_affinities, "ratio")
     AFFINITY_SUM(ch_contrast_affinities, "sum")
 

subworkflows/local/ranking.nf

@@ -14,7 +14,7 @@ workflow RANKING {
 
     ch_versions = Channel.empty()
 
-    ch_combined = ch_differential.map{meta, differential -> 
+    ch_combined = ch_differential.map{meta, differential ->
             [meta.condition1, meta.condition2, differential]}
         .combine(ch_affinities.map{meta, affinities ->
             [meta.condition1, meta.condition2, meta.assay, affinities]}, by: [0, 1])
@@ -33,8 +33,8 @@ workflow RANKING {
     )
 
     ch_versions = ch_versions.mix(TF_TG_SCORE.out.versions,
-                                  CREATE_RANKING.out.versions,
-                                  COMBINE_RANKINGS.out.versions
+                                    CREATE_RANKING.out.versions,
+                                    COMBINE_RANKINGS.out.versions
     )
 
 
@@ -45,4 +45,3 @@ workflow RANKING {
 
     versions = ch_versions                     // channel: [ versions.yml ]
 }
-

workflows/tfactivity.nf

@@ -57,7 +57,7 @@ workflow TFACTIVITY {
 
     ch_conditions = ch_samplesheet.map { meta, peak_file -> meta.condition }
                         .toSortedList().flatten().unique()
-    
+
     ch_contrasts = ch_conditions.combine(ch_conditions)
                                 .filter { condition1, condition2 -> condition1 < condition2 }