Fix alignments

Author: prototaxites

modules/nf-core/gtdbtk/classifywf/main.nf

@@ -30,11 +30,10 @@ process GTDBTK_CLASSIFYWF {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args            = task.ext.args ?: ''
+    prefix              = task.ext.prefix ?: "${meta.id}"
     def pplacer_scratch = use_pplacer_scratch_dir ? "--scratch_dir pplacer_tmp" : ""
-    def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen"
-    prefix = task.ext.prefix ?: "${meta.id}"
-
+    def mash_mode       = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen"
     """
     export GTDBTK_DATA_PATH="\$(find -L ${db} -name 'metadata' -type d -exec dirname {} \\;)"
 

modules/nf-core/gtdbtk/gtdbtoncbimajorityvote/main.nf

@@ -23,10 +23,10 @@ process GTDBTK_GTDBTONCBIMAJORITYVOTE {
     if(!bac120_metadata && !ar53_metadata) {
         log.error("ERROR: Neither the ar53 or bac120 metadata files were provided to gtdbtk/gtdbtoncbimajorityvote!")
     }
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix        = task.ext.prefix ?: "${meta.id}"
+    bac120            = bac120_metadata ? "--bac120_metadata_file ${bac120_metadata}" : ""
+    ar53              = ar53_metadata   ? "--ar53_metadata_file ${ar53_metadata}"     : ""
     def gtdbtk_prefix = gtdbtk_output.find { it.name =~ /summary\.tsv/}.getName() - ~/\.(bac120|ar53)\.summary\.tsv/
-    bac120 = bac120_metadata ? "--bac120_metadata_file ${bac120_metadata}" : ""
-    ar53 = ar53_metadata     ? "--ar53_metadata_file ${ar53_metadata}"     : ""
     """
     gtdb_to_ncbi_majority_vote.py \\
         --gtdbtk_output_dir . \\