Merge branch 'master' into vembrane_filter

Author: dhtt

modules/nf-core/picard/crosscheckfingerprints/main.nf

@@ -22,8 +22,8 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def input1_cmd = input1.collect{"--INPUT $it"}.join(' ')
-    def input2_cmd = input2.collect{"--SECOND_INPUT $it"}.join(' ')
+    def input1_cmd = input1.collect{ f1 -> "--INPUT $f1"}.join(' ')
+    def input2_cmd = input2.collect{ f2 -> "--SECOND_INPUT $f2"}.join(' ')
     def reference_cmd = fasta ? "--REFERENCE_SEQUENCE $fasta" : ""
 
     def avail_mem = 3072

modules/nf-core/picard/extractfingerprint/main.nf

@@ -27,7 +27,6 @@ process PICARD_EXTRACTFINGERPRINT {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
-    def bam_name = bam.simpleName
 
     def avail_mem = 3072
     if (!task.memory) {

modules/nf-core/picard/fixmateinformation/main.nf

@@ -36,7 +36,8 @@ process PICARD_FIXMATEINFORMATION {
         -Xmx${avail_mem}M \\
         --INPUT ${bam} \\
         --OUTPUT ${prefix}.bam \\
-        --VALIDATION_STRINGENCY ${STRINGENCY}
+        --VALIDATION_STRINGENCY ${STRINGENCY} \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/picard/positionbaseddownsamplesam/main.nf

@@ -13,7 +13,7 @@ process PICARD_POSITIONBASEDDOWNSAMPLESAM {
     output:
     tuple val(meta), path("*.ds*.bam")        , emit: bam
     tuple val(meta), path("*.ds*.bai")        , emit: bai, optional:true
-    tuple val(meta), env(ACTUAL_NUM_READS)    , emit: num_reads, optional:true
+    tuple val(meta), env("ACTUAL_NUM_READS")  , emit: num_reads, optional:true
     path  "versions.yml"                      , emit: versions
 
     when:

modules/nf-core/picard/renamesampleinvcf/main.nf

@@ -44,7 +44,6 @@ process PICARD_RENAMESAMPLEINVCF {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "" | gzip > ${prefix}_renam.vcf.gz

modules/nf-core/picard/setnmmdanduqtags/main.nf

@@ -47,7 +47,6 @@ process PICARD_SETNMMDANDUQTAGS {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam

modules/nf-core/picard/sortsam/main.nf

@@ -36,7 +36,8 @@ process PICARD_SORTSAM {
         -Xmx${avail_mem}M \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.bam \\
-        --SORT_ORDER $sort_order
+        --SORT_ORDER $sort_order \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/picard/splitsambynumberofreads/main.nf

@@ -63,15 +63,13 @@ process PICARD_SPLITSAMBYNUMBEROFREADS {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     if (!split_to_N_reads) {
         split_arg = "--SPLIT_TO_N_FILES ${split_to_N_files}"
     }
     else {
         split_arg = "--SPLIT_TO_N_READS ${split_to_N_reads}"
     }
-    def avail_mem = 3072
     def ext = input.name.tokenize('.')[-1]
     if ( !['bam', 'cram', 'sam'].contains(ext) )
         ext = 'bam'