SRAtools download seems to insert paired-end suffix into workdir path about fetchngs HOT 6 OPEN

   mkdir -p TEST.OUT TEST_1.OUT TEST_2.OUT
    fasterq-dump \\
        $args \\
        --threads $task.cpus \\
        --outfile TEST.OUT/$outfile \\
        ${key_file} \\
        ${sra}

    mv -v "TEST_1.OUT/${outfile}"  ./${outfile}.1.fastq
    mv -v "TEST_2.OUT/${outfile}"  ./${outfile}.2.fastq

    pigz \\
        $args2 \\
        --no-name \\
        --processes $task.cpus \\
        *.fastq
(...)

process {
    withName: 'SRATOOLS_FASTERQDUMP' {
        container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0'
    }
}

#!/bin/bash -euo pipefail
export NCBI_SETTINGS="$PWD/user-settings.mkfg"

fasterq-dump \
    --split-files --include-technical \
    --threads 6 \
    --outfile SRX10737613_SRR14385311 \
     \
    SRR14385311

pigz \
     \
    --no-name \
    --processes 6 \
    *.fastq

cat <<-END_VERSIONS > versions.yml
"NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP":
    sratools: $(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
    pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS

nf-test test --verbose --tag sra_default_parameters  --profile test,docker