Refactor ext config as params

modules/local/aspera_cli/main.nf

@@ -10,14 +10,14 @@ process ASPERA_CLI {
     input:
     tuple val(meta), val(fastq)
     val user
+    val args
 
     output:
     tuple val(meta), path("*fastq.gz"), emit: fastq
     tuple val(meta), path("*md5")     , emit: md5
     path "versions.yml"               , emit: versions
 
     script:
-    def args = task.ext.args ?: ''
     def conda_prefix = ['singularity', 'apptainer'].contains(workflow.containerEngine) ? "export CONDA_PREFIX=/usr/local" : ""
     if (meta.single_end) {
         """

modules/local/aspera_cli/nextflow.config

@@ -1,6 +1,5 @@
 process {
     withName: 'ASPERA_CLI' {
-        ext.args = '-QT -l 300m -P33001'
         publishDir = [
             [
                 path: { "${params.outdir}/fastq" },

modules/local/sra_fastq_ftp/main.nf

@@ -11,14 +11,14 @@ process SRA_FASTQ_FTP {
 
     input:
     tuple val(meta), val(fastq)
+    val args
 
     output:
     tuple val(meta), path("*fastq.gz"), emit: fastq
     tuple val(meta), path("*md5")     , emit: md5
     path "versions.yml"               , emit: versions
 
     script:
-    def args = task.ext.args ?: ''
     if (meta.single_end) {
         """
         wget \\

modules/local/sra_fastq_ftp/nextflow.config

@@ -1,6 +1,5 @@
 process {
     withName: 'SRA_FASTQ_FTP' {
-        ext.args = '-t 5 -nv -c -T 60'
         publishDir = [
             [
                 path: { "${params.outdir}/fastq" },

nextflow.config

@@ -19,6 +19,11 @@ params {
     skip_fastq_download         = false
     dbgap_key                   = null
 
+    aspera_cli_args             = '-QT -l 300m -P33001'
+    sra_fastq_ftp_args          = '-t 5 -nv -c -T 60'
+    sratools_fasterqdump_args   = ''
+    sratools_pigz_args          = ''
+
     // Boilerplate options
     outdir                     = null
     publish_dir_mode           = 'copy'

workflows/sra/main.nf

@@ -93,7 +93,8 @@ workflow SRA {
         // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
         //
         SRA_FASTQ_FTP (
-            ch_sra_reads.ftp
+            ch_sra_reads.ftp,
+            params.sra_fastq_ftp_args ?: ''
         )
         ch_versions = ch_versions.mix(SRA_FASTQ_FTP.out.versions.first())
 
@@ -111,7 +112,8 @@ workflow SRA {
         //
         ASPERA_CLI (
             ch_sra_reads.aspera,
-            'era-fasp'
+            'era-fasp',
+            params.aspera_cli_args ?: ''
         )
         ch_versions = ch_versions.mix(ASPERA_CLI.out.versions.first())