update sratools/fasterqdump to handle 10X data (#3336)

CHORES: update sratools/fasterqdump

Co-authored-by: Harshil Patel <[email protected]>

modules/nf-core/sratools/fasterqdump/main.nf

@@ -12,8 +12,8 @@ process SRATOOLS_FASTERQDUMP {
     path ncbi_settings
 
     output:
-    tuple val(meta), path(fastq), emit: reads
-    path "versions.yml"         , emit: versions
+    tuple val(meta), path('*.fastq.gz'), emit: reads
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,11 +22,6 @@ process SRATOOLS_FASTERQDUMP {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
-    // WARNING: Paired-end data extracted by fasterq-dump (--split-3 the default)
-    // always creates *_1.fastq *_2.fastq files but sometimes also
-    // an additional *.fastq file for unpaired reads which we ignore here.
-    fastq = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
     def outfile = meta.single_end ? "${prefix}.fastq" : prefix
     """
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"