From 18b187d0558726748d83d39f6f6e21b8a67d5a3a Mon Sep 17 00:00:00 2001
From: Bill Flynn <wflynny@gmail.com>
Date: Tue, 2 Jan 2024 14:10:14 -0500
Subject: [PATCH 1/3] added gpr creation to spaceranger pipeline

---
 modules/spaceranger.nf | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/modules/spaceranger.nf b/modules/spaceranger.nf
index 050a694..ced6815 100644
--- 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=${record.area}
+
+    # the above unfortunately doesn't get the raw GPR file, but just a JSON representation
+    # below is to pull the raw GPR
+
+    url_base="http://s3-us-west-2.amazonaws.com/10x.spatial-slides/gpr"
+    curl -L -o "${spatial_dir}/${record.slide}.gpr" "${url_base}/${serial_prefix}/${serial}.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
     """
 }

From d7998c7cf87f12672db337021d12f937508eaa86 Mon Sep 17 00:00:00 2001
From: Bill Flynn <wflynny@gmail.com>
Date: Tue, 2 Jan 2024 14:10:34 -0500
Subject: [PATCH 2/3] added 'raw-image' to visium samplesheets

---
 bin/check_samplesheet.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index ef0eda9..410c20b 100755
--- 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)
 

From 04eacde9efa5bfd3c9542b2e7aaabcb7c7cc2d3f Mon Sep 17 00:00:00 2001
From: Bill Flynn <wflynny@gmail.com>
Date: Tue, 2 Jan 2024 17:25:53 -0500
Subject: [PATCH 3/3] bugfix several issues introduced with gpr-downloading
 code

---
 modules/spaceranger.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/spaceranger.nf b/modules/spaceranger.nf
index ced6815..fecdd10 100644
--- a/modules/spaceranger.nf
+++ b/modules/spaceranger.nf
@@ -71,15 +71,15 @@ process SPACERANGER_COUNT {
 
     # 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}
+    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"
-    curl -L -o "${spatial_dir}/${record.slide}.gpr" "${url_base}/${serial_prefix}/${serial}.gpr"
+    wget -O "${spatial_dir}/${record.slide}.gpr" "\${url_base}/${serial_prefix}/${record.slide}.gpr"
     """
 }