Harshil Alignment

Author: dwells-eit

modules/nf-core/autocycler/cluster/main.nf

@@ -11,20 +11,19 @@ process AUTOCYCLER_CLUSTER {
     tuple val(meta), path(gfa)
 
     output:
-    tuple val(meta), path("clustering/qc_pass/*/*.gfa"), emit: clusters
+    tuple val(meta), path("clustering/qc_pass/*/*.gfa"),  emit: clusters
     tuple val(meta), path("clustering/qc_pass/*/*.yaml"), emit: clusterstats
-    tuple val(meta), path("clustering/*.newick"), emit: newick
-    tuple val(meta), path("clustering/*.tsv"), emit: tsv
-    tuple val(meta), path("clustering/*.phylip"), emit: pairwisedistances
-    tuple val(meta), path("clustering/*.yaml"), emit: stats
-
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("clustering/*.newick"),         emit: newick
+    tuple val(meta), path("clustering/*.tsv"),            emit: tsv
+    tuple val(meta), path("clustering/*.phylip"),         emit: pairwisedistances
+    tuple val(meta), path("clustering/*.yaml"),           emit: stats
+    path "versions.yml",                                  emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     autocycler cluster \\
@@ -38,7 +37,7 @@ process AUTOCYCLER_CLUSTER {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir clustering/qc_pass/cluster_000 -p

modules/nf-core/autocycler/combine/main.nf

@@ -12,16 +12,16 @@ process AUTOCYCLER_COMBINE {
 
     output:
     tuple val(meta), path("$prefix/consensus_assembly.fasta"), emit: fasta
-    tuple val(meta), path("$prefix/consensus_assembly.gfa"), emit: gfa
-    tuple val(meta), path("$prefix/consensus_assembly.yaml"), emit: stats
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("$prefix/consensus_assembly.gfa"),   emit: gfa
+    tuple val(meta), path("$prefix/consensus_assembly.yaml"),  emit: stats
+    path "versions.yml",                                       emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
     """
     autocycler combine \\
         $args \\
@@ -35,8 +35,8 @@ process AUTOCYCLER_COMBINE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
     """
     mkdir $prefix
     touch $prefix/consensus_assembly.{fasta,gfa,yaml}

modules/nf-core/autocycler/compress/main.nf

@@ -12,17 +12,16 @@ process AUTOCYCLER_COMPRESS {
     tuple val(meta), path(assemblies)
 
     output:
-    tuple val(meta), path("$prefix/*.gfa"), emit: gfa
+    tuple val(meta), path("$prefix/*.gfa"),  emit: gfa
     tuple val(meta), path("$prefix/*.yaml"), emit: stats
-
-    path "versions.yml"           , emit: versions
+    path "versions.yml",                     emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
     """
     autocycler compress \\
         $args \\

modules/nf-core/autocycler/resolve/main.nf

@@ -12,15 +12,15 @@ process AUTOCYCLER_RESOLVE {
 
     output:
     tuple val(meta), path("3_bridged.gfa"), emit: bridged
-    tuple val(meta), path("4_merged.gfa"), emit: merged
-    tuple val(meta), path("5_final.gfa"), emit: resolved
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("4_merged.gfa"),  emit: merged
+    tuple val(meta), path("5_final.gfa"),   emit: resolved
+    path "versions.yml",                    emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     autocycler resolve \\
@@ -34,7 +34,7 @@ process AUTOCYCLER_RESOLVE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch 3_bridged.gfa

modules/nf-core/autocycler/subsample/main.nf

@@ -14,14 +14,14 @@ process AUTOCYCLER_SUBSAMPLE {
 
     output:
     tuple val(meta), path("$prefix/*.fastq.gz"), emit: subsampled_reads
-    path "versions.yml"           , emit: versions
+    path "versions.yml",                         emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
     """
     autocycler subsample \\
         $args \\
@@ -38,8 +38,8 @@ process AUTOCYCLER_SUBSAMPLE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
     """
 
     mkdir $prefix

modules/nf-core/autocycler/trim/main.nf

@@ -11,15 +11,15 @@ process AUTOCYCLER_TRIM {
     tuple val(meta), path(gfa)
 
     output:
-    tuple val(meta), path("*.gfa"), emit: gfa
+    tuple val(meta), path("*.gfa"),  emit: gfa
     tuple val(meta), path("*.yaml"), emit: stats
-    path "versions.yml"           , emit: versions
+    path "versions.yml",             emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     autocycler trim \\
@@ -34,7 +34,7 @@ process AUTOCYCLER_TRIM {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """