Editorconfig

modules/local/motifs/convert_motifs/main.nf

@@ -10,12 +10,12 @@ process CONVERT_MOTIFS {
     input:
     tuple val(meta), path(in_file), val(in_type)
     val(out_type)
-    
+
     output:
     tuple val(meta), path("${out_file}"), emit: converted
     path "versions.yml"                 , emit: versions
-    
+
     script:
     out_file = "${meta.id}.converted.${out_type}"
     template "convert.R"
-}
+}

modules/local/motifs/convert_motifs/templates/convert.R

@@ -8,32 +8,32 @@ in_type <- "$in_type"
 allowed_in_types <- c("cisbp", "homer", "jaspar", "meme", "transfac", "uniprobe", "universal")
 
 if (!(in_type %in% allowed_in_types)) {
-  stop("Input type '", in_type, "' not supported. Supported types are: ", paste(allowed_in_types, collapse=", "))
+    stop("Input type '", in_type, "' not supported. Supported types are: ", paste(allowed_in_types, collapse=", "))
 }
 
 out_type <- "$out_type"
 allowed_out_types <- c("homer", "jaspar", "meme", "transfac", "universal")
 
 if (!(out_type %in% allowed_out_types)) {
-  stop("Output type '", out_type, "' not supported. Supported types are: ", paste(allowed_out_types, collapse=", "))
+    stop("Output type '", out_type, "' not supported. Supported types are: ", paste(allowed_out_types, collapse=", "))
 }
 
 u.motif <- switch(in_type,
-  cisbp = read_cisbp,
-  homer = read_homer,
-  jaspar = read_jaspar,
-  meme = read_meme,
-  transfac = read_transfac,
-  uniprobe = read_uniprobe,
-  universal = readRDS
+    cisbp = read_cisbp,
+    homer = read_homer,
+    jaspar = read_jaspar,
+    meme = read_meme,
+    transfac = read_transfac,
+    uniprobe = read_uniprobe,
+    universal = readRDS
 )(in_file)
 
 switch(out_type,
-  homer = write_homer,
-  jaspar = write_jaspar,
-  meme = write_meme,
-  transfac = write_transfac,
-  universal = saveRDS
+    homer = write_homer,
+    jaspar = write_jaspar,
+    meme = write_meme,
+    transfac = write_transfac,
+    universal = saveRDS
 )(u.motif, "$out_file")
 
 writeLines(

modules/local/motifs/fetch_jaspar/main.nf

@@ -16,4 +16,4 @@ process FETCH_JASPAR {
 
     script:
     template "fetch_jaspar.py"
-}
+}

modules/local/motifs/filter_motifs/main.nf

@@ -10,12 +10,12 @@ process FILTER_MOTIFS {
     input:
     tuple val(meta), path(in_file)
     tuple val(meta2), path(tfs)
-    
+
     output:
     tuple val(meta), path("${out_file}"), emit: filtered
     path "versions.yml"                 , emit: versions
-    
+
     script:
     out_file = "${meta.id}.filtered.RDS"
     template "filter_motifs.R"
-}
+}

modules/local/motifs/transfac_to_psem/main.nf

@@ -9,11 +9,11 @@ process TRANSFAC_TO_PSEM {
 
     input:
     tuple val(meta), path(transfac)
-    
+
     output:
     tuple val(meta), path("*.psem"), emit: psem
     path "versions.yml"            , emit: versions
-    
+
     script:
     template "convert.py"
-}
+}

modules/local/motifs/transfac_to_psem/templates/convert.py

@@ -46,10 +46,10 @@ def write_pwm(f, matrix, name, ma_id):
 
     pwm = np.zeros_like(matrix)
 
-    for i, active, active_content, other, other_content in zip([A, C, G, T], 
-                                            [maxAT, maxGC, maxGC, maxAT], 
+    for i, active, active_content, other, other_content in zip([A, C, G, T],
+                                            [maxAT, maxGC, maxGC, maxAT],
                                             [at_content, gc_content, gc_content, at_content],
-                                            [maxGC, maxAT, maxAT, maxGC], 
+                                            [maxGC, maxAT, maxAT, maxGC],
                                             [gc_content, at_content, at_content, gc_content]):
         pwm[:, i] = np.where(active<other,
                     np.log((other / other_content) * (active_content / matrix[:, i])) / lamda,

subworkflows/local/motifs.nf

@@ -10,7 +10,7 @@ workflow MOTIFS {
     ch_input_motifs
     ch_tfs
     ch_taxon_id
-    
+
     main:
     ch_versions = Channel.empty()
 
@@ -43,4 +43,4 @@ workflow MOTIFS {
     psem = TRANSFAC_TO_PSEM.out.psem
 
     versions = ch_versions
-}
+}