Schema fixes

bin/download.sh

@@ -6,7 +6,7 @@ md5=$3
 
 if [ ! -e $filepath ]; then
     echo "Downloading $uri to $filepath"
-    curl -skL $uri -o $filepath
+    curl -skL --user-agent 'Mozilla/5.0' $uri -o $filepath
 fi
 
 if [ "$md5" ]; then

conf/segmentation-modules.config

@@ -54,8 +54,7 @@ params {
     cellpose_dashboard_port            = 0
 
     cellpose_worker_runtime_opts       = ''
-    cellpose_worker_cluster_opts       = ''
-    cellpose_worker_lsf_opts           = '-q gpu_l4 -gpu "num=1"'
+    cellpose_worker_cluster_opts       = '-q gpu_l4 -gpu "num=1"'
 }
 
 process {

examples/medium_sample_params.json

@@ -57,5 +57,5 @@
     "bleeding_channel": "c3",
 
     "lsf_opts": "-P scicompsoft",
-    "cellpose_worker_lsf_opts": "-q gpu_l4 -gpu 'num=1'"
+    "cellpose_worker_cluster_opts": "-q gpu_l4 -gpu 'num=1'"
 }

examples/segtest_params.json

@@ -45,5 +45,5 @@
     "cellpose_dask_workers": 8,
     "runtime_opts": "",
     "lsf_opts": "-P scicompsoft",
-    "cellpose_worker_lsf_opts": "-q gpu_l4 -gpu 'num=1'"
+    "cellpose_worker_cluster_opts": "-q gpu_l4 -gpu 'num=1'"
 }

examples/tiny_ome_sample_params.json

@@ -58,5 +58,5 @@
     "bleeding_channel": "c0",
 
     "lsf_opts": "-P scicompsoft",
-    "cellpose_worker_lsf_opts": "-q gpu_l4 -gpu 'num=1'"
+    "cellpose_worker_cluster_opts": "-q gpu_l4 -gpu 'num=1'"
 }

examples/tiny_sample_params.json

@@ -1,6 +1,6 @@
 {
     "channels": "c0,c1",
-    "input": "examples/remote_samplesheets/tiny_samplesheet.csv",
+    "input": "${projectDir}/examples/remote_samplesheets/tiny_samplesheet.csv",
     "indir": "/nrs/scicompsoft/goinac/multifish/tiny",
     "outdir": "/nrs/scicompsoft/goinac/multifish/tiny/results",
 
@@ -55,5 +55,5 @@
     "bleeding_channel": "c0",
 
     "lsf_opts": "-P scicompsoft",
-    "cellpose_worker_lsf_opts": "-q gpu_l4 -gpu 'num=1'"
+    "cellpose_worker_cluster_opts": "-q gpu_l4 -gpu 'num=1'"
 }

nextflow.config

@@ -208,8 +208,9 @@ timeline {
     file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
 }
 report {
-    enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+    enabled   = true
+    overwrite = true
+    file      = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
 }
 trace {
     enabled = true

nextflow_schema.json

@@ -1,6 +1,6 @@
 {
-    "$schema": "https://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/JaneliaSciComp/easifish/master/nextflow_schema.json",
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/JaneliaSciComp/easifish/main/nextflow_schema.json",
     "title": "JaneliaSciComp/easifish pipeline parameters",
     "description": "Lightsheet microscopy image reconstruction",
     "type": "object",
@@ -440,7 +440,7 @@
                 },
                 "bigstream_inv_step": {
                     "type": "number",
-                    "default": 1.0,
+                    "default": 1,
                     "hidden": true,
                     "description": "Step used for generating inverse displacement vector"
                 },
@@ -534,6 +534,10 @@
                     "type": "string",
                     "description": "rounds used for extracting spots"
                 },
+                "distributed_spot_extraction": {
+                    "type": "boolean",
+                    "description": "if set uses a spark cluster to run spot extraction otherwise it uses spark-local"
+                },
                 "spot_channels": {
                     "type": "string",
                     "description": "Comma delimited list of spot channels. This together with spot_scales is used for determining the datasets used for spot extraction."
@@ -643,7 +647,7 @@
                     "description": "Name of the DAPI channel.",
                     "help_text": "The DAPI channel is used as a reference channel for registration, segmentation, and spot extraction."
                 },
-                "bleed_channel": {
+                "bleeding_channel": {
                     "type": "string",
                     "fa_icon": "fas fa-asterisk",
                     "description": "Channel (other than DAPI) that needs bleedthrough correction."
@@ -866,11 +870,11 @@
                 },
                 "sample_anisotropy": {
                     "type": "number",
-                    "default": 1.0
+                    "default": 1
                 },
                 "sample_expansion_factor": {
                     "type": "number",
-                    "default": 1.0
+                    "default": 1
                 },
                 "sample_voxel_spacing": {
                     "type": "string"
@@ -958,7 +962,7 @@
                 },
                 "cellprob_threshold": {
                     "type": "number",
-                    "default": 1.0,
+                    "default": 1,
                     "description": "Probabilty threshold to control cellpose mask size."
                 },
                 "cellpose_iou_threshold": {
@@ -1038,12 +1042,42 @@
                 "cellpose_worker_runtime_opts": {
                     "type": "string"
                 },
-                "cellpose_worker_lsf_opts": {
+                "cellpose_worker_cluster_opts": {
                     "type": "string",
                     "default": "-q gpu_l4 -gpu \"num=1"
                 }
             }
         },
+        "warp_spots": {
+            "title": "Warp spots parameters",
+            "type": "object",
+            "description": "Parameters for warping spots",
+            "fa_icon": "far fa-map",
+            "properties": {
+                "skip_warp_spots": {
+                    "type": "boolean",
+                    "description": "If set skip spots warping",
+                    "default": false
+                },
+                "warped_spots_subdir": {
+                    "type": "string",
+                    "description": "Subdirectory for warped spots results",
+                    "default": "warped-spots"
+                },
+                "warp_spots_cpus": {
+                    "type": "integer",
+                    "fa_icon": "fas fa-microchip",
+                    "description": "Number of cpus needed for warping spots.",
+                    "default": 1
+                },
+                "warp_spots_mem_in_gb": {
+                    "type": "integer",
+                    "fa_icon": "fas fa-memory",
+                    "description": "Amount of memory needed for warping spots",
+                    "default": 15
+                }
+            }
+        },
         "generic_options": {
             "title": "Generic options",
             "type": "object",
@@ -1193,6 +1227,9 @@
         {
             "$ref": "#/definitions/spot_extraction"
         },
+        {
+            "$ref": "#/definitions/warp_spots"
+        },
         {
             "$ref": "#/definitions/spots_features"
         },