Formatting

Author: dialvarezs

modules/local/samtools/unmapped/main.nf

@@ -1,18 +1,18 @@
 process SAMTOOLS_UNMAPPED {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "bioconda::samtools=1.21"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9edc2564215d5cd137a8b25ca8a311600987186d406b092022444adf3c4447f7/data' :
-        'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9edc2564215d5cd137a8b25ca8a311600987186d406b092022444adf3c4447f7/data'
+        : 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf'}"
 
     input:
     tuple val(meta), path(input), path(index)
 
     output:
     tuple val(meta), path("*hostremoved.fastq.gz"), emit: fastq
-    path  "versions.yml",                        emit: versions
+    path "versions.yml"                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,16 +26,16 @@ process SAMTOOLS_UNMAPPED {
     """
     samtools \\
         view \\
-        --threads ${task.cpus-1} \\
-        $args \\
-        $input \\
+        --threads ${task.cpus - 1} \\
+        ${args} \\
+        ${input} \\
         | \\
     samtools \\
         fastq \\
-        $args2 \\
-        --threads ${task.cpus-1} \\
+        ${args2} \\
+        --threads ${task.cpus - 1} \\
         -0 ${prefix}.fastq.gz \\
-        $mapped
+        ${mapped}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -44,7 +44,6 @@ process SAMTOOLS_UNMAPPED {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.fastq.gz

subworkflows/local/tiara/main.nf

@@ -118,8 +118,7 @@ workflow TIARA {
         .map { _meta, classification ->
             [ classification ]
         }
-        .collect()
-        .map { classifications ->
+        .collect { classifications ->
             [[:], classifications]
         }
 

subworkflows/local/utils_nfcore_mag_pipeline/main.nf

@@ -97,17 +97,15 @@ workflow PIPELINE_INITIALISATION {
         ch_samplesheet
             .map { meta, _sr1, _sr2, _lr -> meta.sr_platform }
             .unique()
-            .collect()
-            .map {
+            .collect {
                 if (it.size() > 1) {
                     error("[nf-core/mag] ERROR: Multiple short read sequencing platforms found in samplesheet. Use same platform for all samples when running with binning_map_mode 'all'.")
                 }
             }
         ch_samplesheet
             .map { meta, _sr1, _sr2, _lr -> meta.lr_platform }
             .unique()
-            .collect()
-            .map {
+            .collect {
                 if (it.size() > 1) {
                     error("[nf-core/mag] ERROR: Multiple long read sequencing platforms found in samplesheet. Use same platform for all samples when running with binning_map_mode 'all'.")
                 }
@@ -138,7 +136,7 @@ workflow PIPELINE_INITIALISATION {
     ch_raw_long_reads
         .map { meta, lr -> [ meta.id, lr ] }
         .join(ch_raw_long_reads.map {meta, sr1 -> [meta.id, sr1] }, by: 0, remainder: true)
-        .map { id, lr, sr1 ->
+        .map { _id, lr, sr1 ->
             if (lr && sr1) {
                 hybrid = true
             }