Mercurial > repos > galaxytrakr > aws_sra
changeset 19:a4186132e1c4 draft
planemo upload for repository https://github.com/CFSAN-Biostatistics/galaxytrakr-tools commit ba119cea4881b4ff3a27470d8b426902977290b3
| author | galaxytrakr |
|---|---|
| date | Mon, 23 Mar 2026 22:01:24 +0000 |
| parents | 5680c31cd031 |
| children | 2b4efa539c71 |
| files | aws_sra.xml |
| diffstat | 1 files changed, 9 insertions(+), 8 deletions(-) [+] |
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--- a/aws_sra.xml Mon Mar 23 20:51:03 2026 +0000 +++ b/aws_sra.xml Mon Mar 23 22:01:24 2026 +0000 @@ -1,4 +1,4 @@ -<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.18" profile="23.0"> +<tool id="aws_sra" name="NCBI SRA AWS Fetch" version="0.3.0+gt_0.19" profile="23.0"> <description>Fetches SRA runs from AWS and converts them to FASTQ</description> <requirements> <requirement type="package" version="2.34.8">awscli</requirement> @@ -33,13 +33,14 @@ aws s3 cp --no-sign-request 's3://sra-pub-run-odp/sra/${acc}/${acc}' ./sra_cache_${acc}/ && fasterq-dump --outdir ./fastq_out_${acc} --temp . --threads \${GALAXY_SLOTS:-4} --split-files ./sra_cache_${acc}/${acc} && pigz -p \${GALAXY_SLOTS:-4} ./fastq_out_${acc}/*.fastq && - #if str($layout) == 'paired' - # Move files to the special path for collection discovery - mv ./fastq_out_${acc}/${acc}_1.fastq.gz '$output_r1_batch.files_path/${acc}_1.fastq.gz' && - mv ./fastq_out_${acc}/${acc}_2.fastq.gz '$output_r2_batch.files_path/${acc}_2.fastq.gz' - #else - mv ./fastq_out_${acc}/*.fastq.gz '$output_r1_batch.files_path/${acc}.fastq.gz' - #end if && + ( + #if str($layout) == 'paired' + mv ./fastq_out_${acc}/${acc}_1.fastq.gz '$output_r1_batch.files_path/${acc}_1.fastq.gz' && + mv ./fastq_out_${acc}/${acc}_2.fastq.gz '$output_r2_batch.files_path/${acc}_2.fastq.gz' + #else + mv ./fastq_out_${acc}/*.fastq.gz '$output_r1_batch.files_path/${acc}.fastq.gz' + #end if + ) && rm -rf sra_cache_${acc} fastq_out_${acc} #end if #end for