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Split mates in fastq-dump retry fallback #11

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Merged
jbrestel merged 1 commit into from
Oct 26, 2026
Merged

Split mates in fastq-dump retry fallback #11

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2 changes: 1 addition & 1 deletion CLAUDE.md
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ Expected CSV format with header:

### Error Handling

- `SRATOOLS_FASTERQDUMP` has retry logic: falls back from `fasterq-dump` to `fastq-dump` on failure
- `SRATOOLS_FASTERQDUMP` has retry logic: falls back from `fasterq-dump` to `fastq-dump --split-3` on failure, keeping the same `_1`/`_2` mate layout
- `SRATOOLS_PREFETCH` uses retry template with exponential backoff
- Maximum 2 concurrent processes (`maxForks = 2`)
- `SKETCH_REFERENCE` fails loudly (rather than producing a bogus genome size) if
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3 changes: 2 additions & 1 deletion modules/nf-core/sratools/fasterqdump/main.nf
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Expand Up @@ -24,7 +24,8 @@ process SRATOOLS_FASTERQDUMP {
task.ext.when == null || task.ext.when

script:
def sraCommand = task.attempt > 1 ? "fastq-dump" : "fasterq-dump";
// fastq-dump does not split mates by default; --split-3 matches fasterq-dump's output layout.
def sraCommand = task.attempt > 1 ? "fastq-dump --split-3" : "fasterq-dump";
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
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