[sratoolkit] Add maxSize option to set -X option of prefetch in case …

…files to download exceed 20 Gb (default limit)

docs/pipelines.rst

@@ -623,7 +623,7 @@ NOTES:
 - If you're a VSC user, you might want to add the ``vsc`` profile.
 - The final output (FASTQ files) will available in ``out/data/sra``
 - If you're downloading 10x Genomics scATAC-seq data, make sure to set ``params.sratoolkit.includeTechnicalReads = true`` and properly set ``params.utils.sra_normalize_fastqs.fastq_read_suffixes``. In the case of downloading the scATAC-seq samples of SRP254409, ``fastq_read_suffixes`` would be set to ``["R1", "R2", "I1", "I2"]``.
-
+- The download of SRA files is by default limited to 20 Gb. If this limit needs to be increased please set ``params.sratoolkit.maxSize`` accordingly. This limit can be removed by setting the parameter to arbitrarily high number (e.g.: 9999999999999).
 
 Now we can run it with the following command:
 

src/sratoolkit/processes/downloadFastQ.nf

@@ -31,7 +31,11 @@ process DOWNLOAD_FASTQS_FROM_SRA_ACC_ID {
             rm \${SRA_FILE_LOCK}
         fi
         # Fetch SRA file
-        prefetch -v -p 1 ${sraId}
+        prefetch \
+           -v \
+           -p 1 \
+           ${params.sratoolkit?.maxSize ? '--max-size '+ params.sratoolkit.maxSize: ''} \
+           ${sraId}
         # Convert SRA file to FASTQ files
         fasterq-dump \
            -S \

src/sratoolkit/processes/fixAndCompressFastQ.nf

@@ -39,7 +39,7 @@ process FIX_AND_COMPRESS_SRA_FASTQ {
         echo "Removing all uncompressed FASTQ files"
         for FASTQ in *.fastq; do
            echo "Removing uncompressed FASTQ file \${FASTQ}..."
-           rm "$(readlink -f \${FASTQ})"
+           rm "\$(readlink -f \${FASTQ})"
         done
         echo "Done."
         """

src/sratoolkit/sratoolkit.config

@@ -4,6 +4,8 @@ params {
         // --include-technical option (fasterq-dump)
         // This option should be set to 'true' if data you're downloading is e.g.: 10x Genomics scATAC-seq
         includeTechnicalReads = false
+        // --max-size (prefetch), maximum file size to download in KB (exclusive). Default: 20G
+        maxSize = 20000000
     }
 }