Merge pull request #26 from TheJacksonLaboratory/spaceranger3-metrics…

….json

For `spaceranger v3`, the metrics.json will be generated by a simple (frankensteinish) check for the tool version

modules/spaceranger.nf

@@ -66,6 +66,7 @@ process SPACERANGER_COUNT {
 
     visium_hd_prefixes = ["H1", "SJ", "14072023", "14082023", "26062023", "RD", "UN"]
     is_visium_hd = visium_hd_prefixes.collect { serial_prefix.startsWith(it) }.any()
+    is_spaceranger3 = record.tool_version[0].toInteger() >= 3
     """
     spaceranger count $main_options --localcores=$task.cpus --localmem=$localmem
 
@@ -99,6 +100,10 @@ process SPACERANGER_COUNT {
         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"
     fi
+
+    if [[ ${is_spaceranger3} ]]; then
+        find ${record.output_id}/SPATIAL_RNA_COUNTER/ -type f -name "metrics_summary_json.json" -exec mv {} ${record.tool_pubdir}/summary.json \\;
+    fi
     """
 }
 

nextflow.config

@@ -17,5 +17,5 @@ manifest {
     homePage = "https://github.com/TheJacksonLaboratory/nf-tenx"
     mainScript = "main.nf"
     nextflowVersion = "!>=20.10.0"
-    version = "0.7.9"
+    version = "0.7.10"
 }