Add nextflow script

.gitignore

@@ -161,4 +161,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
-.DS_Store
+.DS_Store
+
+work/

workflow/main.nf

@@ -0,0 +1,84 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl = 2
+
+params.slide_table = null
+params.tile_px = 256
+params.report_dir = "reports"
+params.models = "resnet50"
+
+process PREPROCESS {
+    publishDir params.report_dir, mode: 'move'
+
+    input:
+    tuple val(wsi), val(storage)
+    val tile_px
+
+    output:
+    path '*_report.txt', emit: report
+    tuple val(wsi), val(storage), emit: slide
+
+    script:
+
+    def wsi_base = wsi.baseName
+
+    """
+    lazyslide preprocess ${wsi} ${tile_px} --output ${storage}
+    touch ${wsi_base}_report.txt
+    """
+}
+
+process FEATURE {
+
+    input:
+    tuple val(wsi), val(storage)
+    each model
+
+    script:
+    """
+    lazyslide feature ${wsi} ${model} --output ${storage}
+    """
+}
+
+
+
+workflow {
+
+    log.info """
+    ██       █████  ███████ ██    ██ ███████ ██      ██ ██████  ███████
+    ██      ██   ██    ███   ██  ██  ██      ██      ██ ██   ██ ██
+    ██      ███████   ███     ████   ███████ ██      ██ ██   ██ █████
+    ██      ██   ██  ███       ██         ██ ██      ██ ██   ██ ██
+    ███████ ██   ██ ███████    ██    ███████ ███████ ██ ██████  ███████
+
+    ===================================================================
+
+    Workflow information:
+    Workflow: ${workflow.projectDir}
+
+    Input parameters:
+    Slide table: ${file(params.slide_table)}
+
+    """
+
+    slides_ch = Channel
+        .fromPath( params.slide_table, checkIfExists: true )
+        .splitCsv( header: true )
+        .map { row -> 
+                def slide_file = file(row.file, checkIfExists: true)
+                def slide_storage = row.storage
+                if (row.storage == null) {  slide_storage = slide_file.parent / slide_file.baseName + ".zarr" }
+                return tuple(slide_file, slide_storage)
+         }
+
+    // slides_ch.view()
+
+    out_ch = PREPROCESS(slides_ch, params.tile_px)
+
+    // println "Ouput of PREPROCESS: "
+    // out_ch.slide.view()
+
+    models = Channel.of(params.models?.split(','))
+
+    FEATURE(out_ch.slide, models)
+
+}

workflow/modules/qc/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl = 2
+
+process SlideQC {
+
+    input:
+        val mpp
+        val
+        path slide
+
+    output:
+        path("*.qc.csv") into qc_ch
+
+    script:
+    """
+    lazyslide qc $slide
+    """
+}