From 37472c3ac2fc9eb3e83e08a7a0e035333ab7f77d Mon Sep 17 00:00:00 2001
From: Tim Sackton <timsackton@gmail.com>
Date: Mon, 6 Apr 2026 17:03:36 -0400
Subject: [PATCH 1/2] Fix ffq fallback for SRA downloads

---
 tests/tests.py           | 2 ++
 workflow/rules/fastq.smk | 8 +++++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/tests/tests.py b/tests/tests.py
index 4c724be9..4cb3b1bb 100644
--- a/tests/tests.py
+++ b/tests/tests.py
@@ -339,6 +339,8 @@ def test_mixed_srr_and_fastq_same_sample_dry_run(request):
         output = result.stdout + result.stderr
         assert "unsupported mixed input_type values" not in output
         assert "download_sra" in output
+        assert "while IFS= read -r url; do" in output
+        assert 'curl -fSL "$url"' in output
         assert "merge_library_bams" in output
         assert "library=libA" in output
         assert "input_unit=u1" in output
diff --git a/workflow/rules/fastq.smk b/workflow/rules/fastq.smk
index 854324b3..9e4fe8f9 100644
--- a/workflow/rules/fastq.smk
+++ b/workflow/rules/fastq.smk
@@ -64,7 +64,13 @@ rule download_sra:
             echo "Prefetch failed, trying ENA via ffq..." >> {log}
             ffq --ftp {wildcards.accession} 2>> {log} \
                 | jq -r '.[].url' \
-                | xargs -I {{}} curl -fSL -o {params.outdir}/$(basename {{}}) {{}} 2>> {log}
+                | while IFS= read -r url; do
+                    [[ -n "$url" ]] || continue
+                    echo "Downloading: $url" >> {log}
+                    curl -fSL "$url" \
+                        -o {params.outdir}/$(basename "$url") \
+                        >> {log} 2>&1
+                done
         fi
         
         [[ -f {output.r1} ]] && [[ -f {output.r2} ]]

From 4d3dc50e97946aaef78503b7195d733dba02b801 Mon Sep 17 00:00:00 2001
From: Tim Sackton <timsackton@gmail.com>
Date: Mon, 6 Apr 2026 17:45:37 -0400
Subject: [PATCH 2/2] Pin sra-tools to 3.2.1

---
 workflow/envs/sra.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/envs/sra.yaml b/workflow/envs/sra.yaml
index 64209b5c..22e99a9d 100644
--- a/workflow/envs/sra.yaml
+++ b/workflow/envs/sra.yaml
@@ -2,7 +2,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - sra-tools>=3.0
+  - sra-tools=3.2.1
   - pigz>=2.6
   - curl>=7.73
   - ffq >=0.3.1