Fix 'dir' handling for cloud file systems

CHANGELOG.md

@@ -18,6 +18,7 @@ compatible with further downstream analyses and/or exploration in _e.g._
 
 ### `Added`
 
+- Fix 'dir' handling for cloud file systems [[#122](https://github.com/nf-core/spatialvi/pull/122)]
 - Follow the new Nextflow strict syntax for local (sub-) workflows [[#115](https://github.com/nf-core/spatialvi/pull/115)]
 - Add ability to use unknown slides for Space Ranger-based analyses [[#99](https://github.com/nf-core/spatialvi/issues/99) and [#109](https://github.com/nf-core/spatialvi/pull/109)]
 - Add subworkflow for merging per-sample SpatialData into one [[#96](https://github.com/nf-core/spatialvi/pull/96)]

subworkflows/local/input_check/main.nf

@@ -38,11 +38,9 @@ workflow INPUT_CHECK {
 
     // Combine extracted and directory inputs into one channel
     ch_spaceranger_combined = UNTAR_SPACERANGER_INPUT.out.untar
-        .mix ( ch_spaceranger.dir )
-        .map { meta, dir -> meta + [fastq_dir: dir] }
-
+        .mix ( ch_spaceranger.dir.map { meta, dir -> [meta, file(dir)] } )
     // Create final meta map and check input existance
-    ch_spaceranger_input = ch_spaceranger_combined.map { it -> create_channel_spaceranger(it) }
+    ch_spaceranger_input = ch_spaceranger_combined.map { meta, dir -> create_channel_spaceranger(meta, dir) }
 
     // Downstream analysis: ----------------------------------------------------
 
@@ -112,12 +110,13 @@ def check_downstream_dir(input, hd_bin_size) {
 }
 
 // Function to get list of [ meta, [ fastq_dir, tissue_hires_image, slide, area ]]
-def create_channel_spaceranger(meta) {
+def create_channel_spaceranger(meta, fastq_dir) {
     meta["id"] = meta.remove("sample")
     def slide = meta.remove("slide")
     def area = meta.remove("area")
-    def fastq_dir = meta.remove("fastq_dir")
-    def fastq_files = file("${fastq_dir}/${meta['id']}*.fastq.gz")
+    def fastq_files = fastq_dir.listFiles().findAll { file ->
+        file.name.startsWith(meta['id']) && file.name.endsWith('.fastq.gz')
+    }
 
     // Convert a path in `meta` to a file object and return it. If key `k` is
     // not contained in `meta` return an empty list which is recognized as 'no

tower.yml

@@ -1,3 +1,13 @@
 reports:
-  samplesheet.csv:
-    display: "Auto-created samplesheet with collated metadata and FASTQ paths"
+  "multiqc_report.html":
+    display: "MultiQC report with comprehensive quality control metrics and summary statistics"
+  "**/reports/quality_controls.html":
+    display: "Quality control analysis report with filtering metrics and visualizations"
+  "**/reports/clustering.html":
+    display: "Clustering analysis report with dimensionality reduction and cell type identification"
+  "**/reports/spatially_variable_genes.html":
+    display: "Spatially variable genes analysis report with spatial autocorrelation results"
+  "**/fastqc/*.html":
+    display: "FastQC quality control reports for raw sequencing data"
+  "**/spaceranger/outs/web_summary.html":
+    display: "Space Ranger web summary with count statistics and quality metrics"