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update sratools/fasterqdump to handle 10X data #3336

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merged 2 commits into from
Apr 26, 2023
Merged

update sratools/fasterqdump to handle 10X data #3336

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CHORES: update sratools/fasterqdump
maxulysse Apr 26, 2023
8a46a95
Merge branch 'master' into master
drpatelh Apr 26, 2023
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9 changes: 2 additions & 7 deletions modules/nf-core/sratools/fasterqdump/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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.
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fastq = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
def outfile = meta.single_end ? "${prefix}.fastq" : prefix
"""
export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
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