diff --git a/bin/download.sh b/bin/download.sh index b2b63f11..ee4bda10 100755 --- a/bin/download.sh +++ b/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 diff --git a/conf/segmentation-modules.config b/conf/segmentation-modules.config index e68421fc..c7e3046e 100644 --- a/conf/segmentation-modules.config +++ b/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 { diff --git a/examples/medium_sample_params.json b/examples/medium_sample_params.json index 0a86b471..270354a9 100644 --- a/examples/medium_sample_params.json +++ b/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'" } diff --git a/examples/segtest_params.json b/examples/segtest_params.json index 11e164c8..e00cc462 100644 --- a/examples/segtest_params.json +++ b/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'" } diff --git a/examples/tiny_ome_sample_params.json b/examples/tiny_ome_sample_params.json index e3680b29..d23d42c5 100644 --- a/examples/tiny_ome_sample_params.json +++ b/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'" } diff --git a/examples/tiny_sample_params.json b/examples/tiny_sample_params.json index 12f2e551..cb9c7501 100644 --- a/examples/tiny_sample_params.json +++ b/examples/tiny_sample_params.json @@ -1,6 +1,6 @@ { "channels": "c0,c1", - "input": "examples/remote_samplesheets/tiny_samplesheet.csv", + "input": "${projectDir}/examples/remote_samplesheets/tiny_samplesheet.csv", "indir": "/nrs/scicompsoft/goinac/multifish/tiny", "outdir": "/nrs/scicompsoft/goinac/multifish/tiny/results", @@ -55,5 +55,5 @@ "bleeding_channel": "c0", "lsf_opts": "-P scicompsoft", - "cellpose_worker_lsf_opts": "-q gpu_l4 -gpu 'num=1'" + "cellpose_worker_cluster_opts": "-q gpu_l4 -gpu 'num=1'" } diff --git a/nextflow.config b/nextflow.config index e319fa6f..9547c8fa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -208,8 +208,9 @@ timeline { file = "${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_${trace_timestamp}.html" } trace { enabled = true diff --git a/nextflow_schema.json b/nextflow_schema.json index ec57a315..01331142 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,6 +1,6 @@ { - "$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" },