Merge pull request #10 from TheJacksonLaboratory/gpr-fix

Gpr fix
TheJacksonLaboratory · Jan 3, 2024 · 45abbd2 · 45abbd2
2 parents 9c372ec + 04eacde
commit 45abbd2
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Showing 2 changed files with 18 additions and 1 deletion.
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -410,7 +410,7 @@ def __init__(self):
         for key in (
             "slide", "area", 
             "cyta_image", "dark_image", "color_image", "manual_alignment",
-            "slide_file", "requires_rotation", "roi_json"
+            "slide_file", "requires_rotation", "roi_json", "raw_image"
         ):
             self.allowed_fields.add(key)
 

diff --git a/modules/spaceranger.nf b/modules/spaceranger.nf
@@ -57,6 +57,8 @@ process SPACERANGER_COUNT {
     script:
     main_options = construct_vis_cli_options(record)
     localmem = Math.round(task.memory.toGiga() * 0.95)
+    serial_prefix = record.slide.substring(0, 6)
+    spatial_dir = "${record.tool_pubdir}/spatial"
     """
     spaceranger count $main_options --localcores=$task.cpus --localmem=$localmem
 
@@ -66,6 +68,18 @@ process SPACERANGER_COUNT {
     mv ${record.output_id}/outs/* ${record.tool_pubdir}/
     find ${record.output_id}/SPATIAL_RNA_COUNTER_CS/ -type f -name "metrics_summary_json.json" -exec mv {} ${record.tool_pubdir}/summary.json \\;
     find ${record.output_id}/SPATIAL_RNA_COUNTER_CS/ -type f -name "alignment_metrics.json" -exec mv {} ${record.tool_pubdir}/spatial/alignment_summary.json \\;
+
+    # new 2024-01-02
+    # spaceranger containers wont have gprreader on PATH so build its path manually
+    sr_root=\$(which spaceranger | xargs dirname)
+    gprreader="\${sr_root}/lib/bin/gprreader"
+    \$gprreader fetch ${record.slide} ${spatial_dir} --area=${record.area}
+
+    # the above unfortunately doesn't get the raw GPR file, but just a JSON representation
+    # below is to pull the raw GPR
+
+    url_base="http://s3-us-west-2.amazonaws.com/10x.spatial-slides/gpr"
+    wget -O "${spatial_dir}/${record.slide}.gpr" "\${url_base}/${serial_prefix}/${record.slide}.gpr"
     """
 }
 
@@ -104,6 +118,9 @@ process IMAGE_PROCESS {
     if [ -f "${record.manual_alignment}" ]; then
         cp ${record.manual_alignment} .
     fi
+    if [ -f "${record.raw_image}" ]; then
+        cp ${record.raw_image} .
+    fi
     md5sum * > hashes_img.md5
     """
 }