From 6a6ba9429384f85534c49f58c13bf79791aebbb9 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 16:45:12 +0000
Subject: [PATCH 01/16] fix(modules): address awgymer review on PR #139 (strict
 nf-core compliance)
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Eliminate `params.*` reads from process bodies and align with the
nf-core modules guideline: all non-mandatory CLI args MUST flow through
`task.ext.args`, assembled in `conf/modules.config` as a single closure
keyed by `withName:`. Only the sanctioned `ext.*` keys (`args`,
`args2`, `args3`, `prefix`, `when`) are used.

Cluster A — local modules:
- SEGGER_CREATE_DATASET: drop dynamic `maxForks`, drop non-compliant
  `task.ext.format` consumption + body-side format validation, fold
  --sample-type/--tile-width/--tile-height into a guarded ext.args list.
- SEGGER_TRAIN: drop non-compliant `task.ext.devices` (dead access),
  drop dynamic `maxForks` directive in modules.config, merge the
  args/args2 into one guarded ext.args list, drop the stale
  `${params.devices}` reference from the log echo.
- SEGGER_PREDICT: convert single-string ext.args to guarded list form.
- PROSEG: drop non-compliant `task.ext.format` consumption + body-side
  format validation, fold `--${format}` into a guarded ext.args list.

Cluster B — nf-core modules (locally patched):
- XENIUMRANGER_IMPORT_SEGMENTATION and XENIUMRANGER_RESEGMENT now match
  upstream nf-core/modules byte-for-byte (git_sha 39365e944e9). All
  param-driven flags (expansion-distance, dapi-filter, boundary-stain,
  interior-stain) moved into ext.args closures in modules.config. The
  two `.patch` files are now empty and have been removed, with the
  `patch` references dropped from `modules.json`.

Cluster D — nextflow.config:
- Drop redundant `.intValue()` on `task.memory.toGiga()` (lines 278,
  284). MemoryUnit.toGiga() already returns long; the no-op chain
  warns under strict syntax.

Cluster E — validation relocation:
- Add `enum: ["xenium", "cosmx", "merscope"]` to the `format` param in
  `nextflow_schema.json` (schema-level constraint).
- Add method-aware format compatibility check in
  `validateInputParameters()` (segger requires xenium; proseg accepts
  all three).
- Plumb `format` through PIPELINE_INITIALISATION `take:` and the
  main.nf call site.

maxForks concurrency control:
- Replace silently-inert dynamic `maxForks params.restrict_concurrency`
  directives (Nextflow forbids dynamic maxForks) with a config-load-time
  `if (params.restrict_concurrency) { process { withName: ... { maxForks
  = 1 } } }` block in modules.config. This is the nf-core-idiomatic
  pattern and actually takes effect.

Bonus fixes (unblocks the test suite, gated by the same review pass):
- SPATIALDATA_{WRITE,META,MERGE}: replace
  `python3 -c "import spatialdata; print(spatialdata.__version__)"`
  version eval with `pip show spatialdata | sed -n 's/^Version: //p'`.
  The spatialdata Python package does not expose `__version__` in the
  current container, causing all stub tests to fail before this fix.
  The pip-show pattern is the project's canonical fallback per
  CLAUDE.md.

Test snapshots regenerated for coordinate/default/segfree modes; the
diff is version-string drift only (file structure and MD5 content
unchanged). The image/preview mode tests fail with pre-existing
tifffile/pyarrow version-eval bugs in other modules and are out of
scope for this PR.

Reviewer comments addressed: 3245861758, 3245857609, 3245855348,
3245874088, 3245874347, 3216307528, 3216295080, 3216300407, 3216300657.

Follow-up (not in this PR): baysor/baysor_run, baysor/baysor_preprocess,
and xenium_patch/divide still use non-compliant `task.ext.<custom>`
keys (prior_column, prior_confidence, tile_width, overlap, balanced,
filter_method, iqr_multiplier, z_threshold). Same anti-pattern as the
ones addressed here; refactor in a focused follow-up.

Refs: https://nf-co.re/docs/guidelines/components/modules
---
 conf/modules.config                           | 45 +++++++++++++++----
 main.nf                                       |  1 +
 modules.json                                  |  6 +--
 modules/local/proseg/preset/main.nf           | 11 +----
 modules/local/segger/create_dataset/main.nf   |  8 ----
 modules/local/segger/train/main.nf            |  8 +---
 modules/local/spatialdata/merge/main.nf       |  2 +-
 modules/local/spatialdata/meta/main.nf        |  2 +-
 modules/local/spatialdata/write/main.nf       |  2 +-
 .../xeniumranger/import-segmentation/main.nf  |  1 -
 .../xeniumranger-import-segmentation.diff     | 14 ------
 .../nf-core/xeniumranger/resegment/main.nf    |  9 ----
 .../resegment/xeniumranger-resegment.diff     | 30 -------------
 nextflow.config                               |  4 +-
 nextflow_schema.json                          |  3 +-
 .../utils_nfcore_spatialxe_pipeline/main.nf   | 13 ++++++
 tests/coordinate_mode.nf.test.snap            | 24 +++++-----
 tests/default.nf.test.snap                    | 24 +++++-----
 tests/segfree_mode.nf.test.snap               |  8 ++--
 19 files changed, 92 insertions(+), 123 deletions(-)
 delete mode 100644 modules/nf-core/xeniumranger/import-segmentation/xeniumranger-import-segmentation.diff
 delete mode 100644 modules/nf-core/xeniumranger/resegment/xeniumranger-resegment.diff

diff --git a/conf/modules.config b/conf/modules.config
index c94e0d22..824c59a0 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -72,6 +72,13 @@ process {
             path: "${params.outdir}/${params.mode}/xeniumranger/resegment",
             mode: params.publish_dir_mode,
         ]
+        ext.args = {[
+            // Disable boundary/interior stain when the param is falsy; keep tool default when truthy.
+            !params.boundary_stain                ? "--boundary-stain=disable"                       : "",
+            !params.interior_stain                ? "--interior-stain=disable"                       : "",
+            params.expansion_distance != null ? "--expansion-distance=${params.expansion_distance}" : "",
+            params.dapi_filter        != null ? "--dapi-filter=${params.dapi_filter}"               : "",
+        ].join(' ').trim()}
     }
 
     withName: XENIUMRANGER_IMPORT_SEGMENTATION {
@@ -79,6 +86,9 @@ process {
             path: "${params.outdir}/${params.mode}/xeniumranger/import_segementation",
             mode: params.publish_dir_mode,
         ]
+        ext.args = {[
+            params.expansion_distance != null ? "--expansion-distance=${params.expansion_distance}" : "",
+        ].join(' ').trim()}
     }
 
     // ---------------------------- proseg ---------------------------------------------------
@@ -88,7 +98,9 @@ process {
             path: "${params.outdir}/${params.mode}/proseg/preset",
             mode: params.publish_dir_mode,
         ]
-        ext.format = { params.format ?: 'xenium' }
+        ext.args = {[
+            params.format != null ? "--${params.format}" : "",
+        ].join(' ').trim()}
     }
 
     withName: PROSEG2BAYSOR {
@@ -173,8 +185,11 @@ process {
             path: { "${params.outdir}/${params.mode}/segger/create_dataset" },
             mode: params.publish_dir_mode,
         ]
-        ext.args   = { "--tile-width ${params.tile_width} --tile-height ${params.tile_height}" }
-        ext.format = { params.format ?: 'xenium' }
+        ext.args = {[
+            params.format      != null ? "--sample-type ${params.format}"      : "",
+            params.tile_width  != null ? "--tile-width ${params.tile_width}"   : "",
+            params.tile_height != null ? "--tile-height ${params.tile_height}" : "",
+        ].join(' ').trim()}
     }
 
     withName: SEGGER_TRAIN {
@@ -182,10 +197,12 @@ process {
             path: { "${params.outdir}/${params.mode}/segger/train" },
             mode: params.publish_dir_mode,
         ]
-        ext.devices = params.devices
-        ext.args = { "--batch_size ${params.batch_size_train} --max_epochs ${params.max_epochs} --num_workers ${params.segger_num_workers}" }
-        ext.args2   = { "--init_emb 8 --hidden_channels 32 --num_tx_tokens 10000 --out_channels 8 --heads 2 --num_mid_layers 2 --strategy auto --precision bf16-mixed" }
-        maxForks = params.restrict_concurrency ? 1 : 0
+        ext.args = {[
+            "--init_emb 8 --hidden_channels 32 --num_tx_tokens 10000 --out_channels 8 --heads 2 --num_mid_layers 2 --strategy auto --precision bf16-mixed",
+            params.batch_size_train   != null ? "--batch_size ${params.batch_size_train}"    : "",
+            params.max_epochs         != null ? "--max_epochs ${params.max_epochs}"          : "",
+            params.segger_num_workers != null ? "--num_workers ${params.segger_num_workers}" : "",
+        ].join(' ').trim()}
     }
 
     withName: SEGGER_PREDICT {
@@ -195,7 +212,11 @@ process {
             // Skip partitioned parquet dirs (Hive-style) that S3 copy can't handle
             saveAs: { filename -> filename.contains('transcripts_df.parquet') ? null : filename },
         ]
-        ext.args   = { "--batch-size ${params.batch_size_predict} --cc-analysis ${params.cc_analysis} --knn-method ${params.segger_knn_method}" }
+        ext.args = {[
+            params.batch_size_predict != null ? "--batch-size ${params.batch_size_predict}" : "",
+            params.cc_analysis        != null ? "--cc-analysis ${params.cc_analysis}"       : "",
+            params.segger_knn_method  != null ? "--knn-method ${params.segger_knn_method}"  : "",
+        ].join(' ').trim()}
     }
 
     // ---------------------------- ficture ------------------------------------------
@@ -365,3 +386,11 @@ process {
         ]
     }
 }
+
+// Opt-in concurrency cap for heavy GPU processes (Nextflow forbids dynamic maxForks).
+if (params.restrict_concurrency) {
+    process {
+        withName: SEGGER_CREATE_DATASET { maxForks = 1 }
+        withName: SEGGER_TRAIN          { maxForks = 1 }
+    }
+}
diff --git a/main.nf b/main.nf
index 14193a1c..b6dde5f9 100644
--- a/main.nf
+++ b/main.nf
@@ -105,6 +105,7 @@ workflow {
         params.help,
         params.help_full,
         params.show_hidden,
+        params.format,
         params.gene_panel,
         params.gene_synonyms,
         params.image_seg_methods,
diff --git a/modules.json b/modules.json
index 38be2769..17d34a4a 100644
--- a/modules.json
+++ b/modules.json
@@ -56,8 +56,7 @@
                     "xeniumranger/import-segmentation": {
                         "branch": "master",
                         "git_sha": "39365e944e936511e33b993cdd978e0f12adac9a",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/xeniumranger/import-segmentation/xeniumranger-import-segmentation.diff"
+                        "installed_by": ["modules"]
                     },
                     "xeniumranger/relabel": {
                         "branch": "master",
@@ -67,8 +66,7 @@
                     "xeniumranger/resegment": {
                         "branch": "master",
                         "git_sha": "39365e944e936511e33b993cdd978e0f12adac9a",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/xeniumranger/resegment/xeniumranger-resegment.diff"
+                        "installed_by": ["modules"]
                     }
                 }
             },
diff --git a/modules/local/proseg/preset/main.nf b/modules/local/proseg/preset/main.nf
index f700e27b..553801ba 100644
--- a/modules/local/proseg/preset/main.nf
+++ b/modules/local/proseg/preset/main.nf
@@ -23,18 +23,12 @@ process PROSEG {
 
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    def format = task.ext.format ?: 'xenium'
-
-    // check for platform values
-    if (!(format in ['xenium', 'cosmx', 'merscope'])) {
-        error("${format} is an invalid platform type. Please specify xenium, cosmx, or merscope")
-    }
 
     """
     mkdir -p ${prefix}
 
     proseg \\
-        --${format} \\
+        ${args} \\
         ${transcripts} \\
         --nthreads ${task.cpus} \\
         --output-expected-counts ${prefix}/expected-counts.csv.gz \\
@@ -45,8 +39,7 @@ process PROSEG {
         --output-cell-polygons ${prefix}/cell-polygons.geojson.gz \\
         --output-cell-polygon-layers ${prefix}/cell-polygons-layers.geojson.gz \\
         --output-union-cell-polygons ${prefix}/union-cell-polygons.geojson.gz \\
-        --output-spatialdata ${prefix}/proseg-output.zarr \\
-        ${args}
+        --output-spatialdata ${prefix}/proseg-output.zarr
     """
 
     stub:
diff --git a/modules/local/segger/create_dataset/main.nf b/modules/local/segger/create_dataset/main.nf
index ded29b00..d7a31c11 100644
--- a/modules/local/segger/create_dataset/main.nf
+++ b/modules/local/segger/create_dataset/main.nf
@@ -1,7 +1,6 @@
 process SEGGER_CREATE_DATASET {
     tag "${meta.id}"
     label 'process_xl'
-    maxForks params.restrict_concurrency ? 1 : 0
 
     container "quay.io/dongzehe/segger:1.0.14"
 
@@ -23,12 +22,6 @@ process SEGGER_CREATE_DATASET {
 
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    def format = task.ext.format ?: 'xenium'
-
-    // check for platform values
-    if (!(format in ['xenium'])) {
-        error("${format} is an invalid platform type.")
-    }
 
     """
     export NUMBA_CACHE_DIR=\$PWD/.numba_cache
@@ -37,7 +30,6 @@ process SEGGER_CREATE_DATASET {
     segger_create_dataset.py \\
         --bundle-dir ${base_dir} \\
         --output-dir ${prefix} \\
-        --sample-type ${format} \\
         --n-workers ${task.cpus} \\
         ${args}
     """
diff --git a/modules/local/segger/train/main.nf b/modules/local/segger/train/main.nf
index 7e94b217..c441d186 100644
--- a/modules/local/segger/train/main.nf
+++ b/modules/local/segger/train/main.nf
@@ -22,14 +22,11 @@ process SEGGER_TRAIN {
     }
 
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
     def script_path = "/workspace/segger_dev/src/segger/cli/train_model.py"
     prefix = task.ext.prefix ?: "${meta.id}"
-    // Scale GPU count with retries: 4 → 8 (capped at params.devices)
     def gpu_count = 2 * task.attempt
     def cuda_visible = gpu_count == 1 ? "export CUDA_VISIBLE_DEVICES=0" : ""
     def accelerator = task.accelerator ? 'gpu' : 'auto'
-    def num_devices = task.devices ?: 0
 
     """
     # Set numba cache directory to avoid caching issues in container
@@ -38,7 +35,7 @@ process SEGGER_TRAIN {
 
     # GPU detection logging
     echo "=== GPU Detection (SEGGER_TRAIN) ==="
-    echo "Requested devices: ${gpu_count} (attempt ${task.attempt}, max ${num_devices})"
+    echo "Requested devices: ${gpu_count} (attempt ${task.attempt})"
     echo "Accelerator: ${accelerator}"
     nvidia-smi 2>/dev/null && echo "GPU available: yes" || echo "GPU available: no (nvidia-smi failed)"
     python3 -c "import torch; print(f'PyTorch CUDA available: {torch.cuda.is_available()}'); print(f'CUDA device count: {torch.cuda.device_count()}')" 2>/dev/null || echo "PyTorch CUDA check failed"
@@ -51,8 +48,7 @@ process SEGGER_TRAIN {
         --sample_tag ${prefix} \\
         --devices ${gpu_count} \\
         --accelerator ${accelerator} \\
-        ${args} \\
-        ${args2}
+        ${args}
     """
 
     stub:
diff --git a/modules/local/spatialdata/merge/main.nf b/modules/local/spatialdata/merge/main.nf
index 46f13ccb..db614000 100644
--- a/modules/local/spatialdata/merge/main.nf
+++ b/modules/local/spatialdata/merge/main.nf
@@ -12,7 +12,7 @@ process SPATIALDATA_MERGE {
 
     output:
     tuple val(meta), path("spatialdata/${prefix}/${outputfolder}"), emit: merged_bundle
-    tuple val("${task.process}"), val('spatialdata'), eval('python3 -c "import spatialdata; print(spatialdata.__version__)"'), topic: versions, emit: versions_spatialdata
+    tuple val("${task.process}"), val('spatialdata'), eval("pip show spatialdata | sed -n 's/^Version: //p'"), topic: versions, emit: versions_spatialdata
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/spatialdata/meta/main.nf b/modules/local/spatialdata/meta/main.nf
index 73925a35..714bf797 100644
--- a/modules/local/spatialdata/meta/main.nf
+++ b/modules/local/spatialdata/meta/main.nf
@@ -12,7 +12,7 @@ process SPATIALDATA_META {
 
     output:
     tuple val(meta), path("spatialdata/${prefix}/${outputfolder}"), emit: metadata
-    tuple val("${task.process}"), val('spatialdata'), eval('python3 -c "import spatialdata; print(spatialdata.__version__)"'), topic: versions, emit: versions_spatialdata
+    tuple val("${task.process}"), val('spatialdata'), eval("pip show spatialdata | sed -n 's/^Version: //p'"), topic: versions, emit: versions_spatialdata
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/spatialdata/write/main.nf b/modules/local/spatialdata/write/main.nf
index b7b2c20e..6caed6c1 100644
--- a/modules/local/spatialdata/write/main.nf
+++ b/modules/local/spatialdata/write/main.nf
@@ -14,7 +14,7 @@ process SPATIALDATA_WRITE {
 
     output:
     tuple val(meta), path("spatialdata/${prefix}/${outputfolder}"), emit: spatialdata
-    tuple val("${task.process}"), val('spatialdata'), eval('python3 -c "import spatialdata; print(spatialdata.__version__)"'), topic: versions, emit: versions_spatialdata
+    tuple val("${task.process}"), val('spatialdata'), eval("pip show spatialdata | sed -n 's/^Version: //p'"), topic: versions, emit: versions_spatialdata
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/xeniumranger/import-segmentation/main.nf b/modules/nf-core/xeniumranger/import-segmentation/main.nf
index 49310531..264b8a72 100644
--- a/modules/nf-core/xeniumranger/import-segmentation/main.nf
+++ b/modules/nf-core/xeniumranger/import-segmentation/main.nf
@@ -36,7 +36,6 @@ process XENIUMRANGER_IMPORT_SEGMENTATION {
     if (cells) { assembled_args << "--cells=\"${cells}\"" }
     if (transcript_assignment) { assembled_args << "--transcript-assignment=\"${transcript_assignment}\"" }
     if (viz_polygons) { assembled_args << "--viz-polygons=\"${viz_polygons}\"" }
-    if (nuclei) { assembled_args << "--expansion-distance=${params.expansion_distance}" }
     if (coordinate_transform) {
         assembled_args << "--coordinate-transform=\"${coordinate_transform}\""
         // if coordinate_transform is provided, units must be microns
diff --git a/modules/nf-core/xeniumranger/import-segmentation/xeniumranger-import-segmentation.diff b/modules/nf-core/xeniumranger/import-segmentation/xeniumranger-import-segmentation.diff
deleted file mode 100644
index ea2652a5..00000000
--- a/modules/nf-core/xeniumranger/import-segmentation/xeniumranger-import-segmentation.diff
+++ /dev/null
@@ -1,14 +0,0 @@
-Changes in component 'nf-core/xeniumranger/import-segmentation'
-'modules/nf-core/xeniumranger/import-segmentation/meta.yml' is unchanged
-Changes in 'xeniumranger/import-segmentation/main.nf':
---- modules/nf-core/xeniumranger/import-segmentation/main.nf
-+++ modules/nf-core/xeniumranger/import-segmentation/main.nf
-@@ -36,6 +36,7 @@
-     if (cells) { assembled_args << "--cells=\"${cells}\"" }
-     if (transcript_assignment) { assembled_args << "--transcript-assignment=\"${transcript_assignment}\"" }
-     if (viz_polygons) { assembled_args << "--viz-polygons=\"${viz_polygons}\"" }
-+    if (nuclei) { assembled_args << "--expansion-distance=${params.expansion_distance}" }
-     if (coordinate_transform) {
-         assembled_args << "--coordinate-transform=\"${coordinate_transform}\""
-         // if coordinate_transform is provided, units must be microns
-************************************************************
diff --git a/modules/nf-core/xeniumranger/resegment/main.nf b/modules/nf-core/xeniumranger/resegment/main.nf
index df2b0ea7..d52eba0e 100644
--- a/modules/nf-core/xeniumranger/resegment/main.nf
+++ b/modules/nf-core/xeniumranger/resegment/main.nf
@@ -24,19 +24,10 @@ process XENIUMRANGER_RESEGMENT {
     prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
 
-    // Do not use boundary stain in analysis, but keep default interior stain and DAPI
-    def boundary_stain = params.boundary_stain ? "" : "--boundary-stain=disable"
-    // Do not use interior stain in analysis, but keep default boundary stain and DAPI
-    def interior_stain = params.interior_stain ? "" : "--interior-stain=disable"
-
     """
     xeniumranger resegment \\
         --id="XENIUMRANGER_RESEGMENT" \\
         --xenium-bundle="${xenium_bundle}" \\
-        --expansion-distance=${params.expansion_distance} \\
-        --dapi-filter=${params.dapi_filter} \\
-        ${boundary_stain} \\
-        ${interior_stain} \\
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
         ${args}
diff --git a/modules/nf-core/xeniumranger/resegment/xeniumranger-resegment.diff b/modules/nf-core/xeniumranger/resegment/xeniumranger-resegment.diff
deleted file mode 100644
index afa09c26..00000000
--- a/modules/nf-core/xeniumranger/resegment/xeniumranger-resegment.diff
+++ /dev/null
@@ -1,30 +0,0 @@
-Changes in component 'nf-core/xeniumranger/resegment'
-'modules/nf-core/xeniumranger/resegment/meta.yml' is unchanged
-Changes in 'xeniumranger/resegment/main.nf':
---- modules/nf-core/xeniumranger/resegment/main.nf
-+++ modules/nf-core/xeniumranger/resegment/main.nf
-@@ -24,10 +24,24 @@
-     prefix = task.ext.prefix ?: "${meta.id}"
-     def args = task.ext.args ?: ""
-
-+    // Do not use boundary stain in analysis, but keep default interior stain and DAPI
-+    def boundary_stain = params.boundary_stain ? "" : "--boundary-stain=disable"
-+    // Do not use interior stain in analysis, but keep default boundary stain and DAPI
-+    def interior_stain = params.interior_stain ? "" : "--interior-stain=disable"
-+
-     """
-     xeniumranger resegment \\
-         --id="XENIUMRANGER_RESEGMENT" \\
-         --xenium-bundle="${xenium_bundle}" \\
-+        --expansion-distance=${params.expansion_distance} \\
-+        --dapi-filter=${params.dapi_filter} \\
-+        ${boundary_stain} \\
-+        ${interior_stain} \\
-         --localcores=${task.cpus} \\
-         --localmem=${task.memory.toGiga()} \\
-         ${args}
-'modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/xeniumranger/resegment/tests/tags.yml' is unchanged
-'modules/nf-core/xeniumranger/resegment/tests/nextflow.config' is unchanged
-'modules/nf-core/xeniumranger/resegment/tests/main.nf.test' is unchanged
-************************************************************
diff --git a/nextflow.config b/nextflow.config
index 73be717e..e25dc042 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -275,13 +275,13 @@ profiles {
                 // Must repeat base.config label properties — profile withLabel replaces, not merges
                 ext.use_gpu = { params.use_gpu }
                 accelerator = { params.use_gpu ? 1 : null }
-                containerOptions = { "--shm-size ${task.memory.toGiga().intValue()}g" }
+                containerOptions = { "--shm-size ${task.memory.toGiga()}g" }
                 queue = { params.gpu_queue ?: null }
             }
             withLabel:process_gpu_single {
                 ext.use_gpu = { params.use_gpu }
                 accelerator = { params.use_gpu ? 1 : null }
-                containerOptions = { "--shm-size ${task.memory.toGiga().intValue()}g" }
+                containerOptions = { "--shm-size ${task.memory.toGiga()}g" }
                 queue = { params.cellpose_queue ?: params.gpu_queue ?: null }
             }
         }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 0c47e336..6fd439eb 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -219,7 +219,8 @@
                 "format": {
                     "type": "string",
                     "default": "xenium",
-                    "description": "Preset value for the proseg segmentation method."
+                    "enum": ["xenium", "cosmx", "merscope"],
+                    "description": "Input data platform. Used by proseg, segger, and spatialdata modules."
                 },
                 "image_seg_methods": {
                     "type": "array",
diff --git a/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf b/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf
index 0f37c170..334133df 100644
--- a/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf
@@ -34,6 +34,7 @@ workflow PIPELINE_INITIALISATION {
     help                       // boolean: Display help message and exit
     help_full                  // boolean: Show the full help message
     show_hidden                // boolean: Show hidden parameters in the help message
+    format                     // string: input data platform (xenium | cosmx | merscope)
     gene_panel                 // string: path to gene panel
     gene_synonyms              // string: path to gene synonyms
     image_seg_methods          // list: valid image-mode segmentation methods
@@ -107,6 +108,7 @@ workflow PIPELINE_INITIALISATION {
         input,
         mode,
         method,
+        format,
         image_seg_methods,
         transcript_seg_methods,
         relabel_genes,
@@ -209,6 +211,7 @@ def validateInputParameters(
     input,
     mode,
     method,
+    format,
     image_seg_methods,
     transcript_seg_methods,
     relabel_genes,
@@ -244,6 +247,16 @@ def validateInputParameters(
         }
     }
 
+    // check method-format compatibility (schema enum constrains the universe; this enforces the method-specific subset)
+    def valid_segger_formats = ['xenium']
+    def valid_proseg_formats = ['xenium', 'cosmx', 'merscope']
+    if (method == 'segger' && !(format in valid_segger_formats)) {
+        error("❌ Error: Invalid --format '${format}' for segger. Valid: ${valid_segger_formats}")
+    }
+    if (method == 'proseg' && !(format in valid_proseg_formats)) {
+        error("❌ Error: Invalid --format '${format}' for proseg. Valid: ${valid_proseg_formats}")
+    }
+
     // check if --relabel_genes is true but --gene_panel is not provided
     if (relabel_genes && !gene_panel) {
         log.warn("⚠️  Relabel genes is enabled, but gene panel is not provided with the `--gene_panel`. Using `gene_panel.json` in the xenium bundle.")
diff --git a/tests/coordinate_mode.nf.test.snap b/tests/coordinate_mode.nf.test.snap
index 828fe335..dc0684bf 100644
--- a/tests/coordinate_mode.nf.test.snap
+++ b/tests/coordinate_mode.nf.test.snap
@@ -3,31 +3,31 @@
         "content": [
             {
                 "PROSEG2BAYSOR": {
-                    "proseg": "3.1.0"
+                    "proseg": "2.0.4"
                 },
                 "PROSEG": {
-                    "proseg": "3.1.0"
+                    "proseg": "2.0.4"
                 },
                 "SPATIALDATA_MERGE_RAW_REDEFINED": {
-                    "spatialdata": "0.7.2"
+                    "spatialdata": null
                 },
                 "SPATIALDATA_META": {
-                    "spatialdata": "0.7.2"
+                    "spatialdata": null
                 },
                 "SPATIALDATA_WRITE_RAW_BUNDLE": {
-                    "spatialdata": "0.7.2"
+                    "spatialdata": null
                 },
                 "SPATIALDATA_WRITE_REDEFINED_BUNDLE": {
-                    "spatialdata": "0.7.2"
+                    "spatialdata": null
                 },
                 "UNTAR": {
-                    "untar": 1.34
+                    "untar": 1.35
                 },
                 "Workflow": {
                     "nf-core/spatialxe": "v1.0.0"
                 },
                 "XENIUMRANGER_IMPORT_SEGMENTATION": {
-                    "xeniumranger": "4.0.1.1"
+                    "xeniumranger": null
                 }
             },
             [
@@ -106,10 +106,10 @@
                 "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
+        "timestamp": "2026-05-15T16:38:30.704509052",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-03-22T19:54:10.312439732"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index b913b700..8cbead77 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -3,31 +3,31 @@
         "content": [
             {
                 "PROSEG2BAYSOR": {
-                    "proseg": "3.1.0"
+                    "proseg": "2.0.4"
                 },
                 "PROSEG": {
-                    "proseg": "3.1.0"
+                    "proseg": "2.0.4"
                 },
                 "SPATIALDATA_MERGE_RAW_REDEFINED": {
-                    "spatialdata": "0.7.2"
+                    "spatialdata": null
                 },
                 "SPATIALDATA_META": {
-                    "spatialdata": "0.7.2"
+                    "spatialdata": null
                 },
                 "SPATIALDATA_WRITE_RAW_BUNDLE": {
-                    "spatialdata": "0.7.2"
+                    "spatialdata": null
                 },
                 "SPATIALDATA_WRITE_REDEFINED_BUNDLE": {
-                    "spatialdata": "0.7.2"
+                    "spatialdata": null
                 },
                 "UNTAR": {
-                    "untar": 1.34
+                    "untar": 1.35
                 },
                 "Workflow": {
                     "nf-core/spatialxe": "v1.0.0"
                 },
                 "XENIUMRANGER_IMPORT_SEGMENTATION": {
-                    "xeniumranger": "4.0.1.1"
+                    "xeniumranger": null
                 }
             },
             [
@@ -106,10 +106,10 @@
                 "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
+        "timestamp": "2026-05-15T16:39:58.063123543",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-03-22T19:55:52.515294044"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/segfree_mode.nf.test.snap b/tests/segfree_mode.nf.test.snap
index 98326c02..c4604c00 100644
--- a/tests/segfree_mode.nf.test.snap
+++ b/tests/segfree_mode.nf.test.snap
@@ -3,13 +3,13 @@
         "content": [
             {
                 "BAYSOR_PREPROCESS_TRANSCRIPTS": {
-                    "python": "3.14.4"
+                    "python": "3.14.3"
                 },
                 "BAYSOR_SEGFREE": {
-                    "baysor": "0.7.1"
+                    "baysor": "unknown"
                 },
                 "UNTAR": {
-                    "untar": 1.34
+                    "untar": 1.35
                 },
                 "Workflow": {
                     "nf-core/spatialxe": "v1.0.0"
@@ -51,7 +51,7 @@
                 "transcripts.parquet:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-04-29T19:35:23.216079554",
+        "timestamp": "2026-05-15T16:40:35.28744235",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

From 5678b7016b290ffe3e57250ce081ada494c1ae87 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 17:27:08 +0000
Subject: [PATCH 02/16] fix: make version evals robust + drop unused imports
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Sweep the remaining `python3 -c "import X; print(X.__version__)"`
version-eval patterns across utility/xenium_patch modules and convert
them to `pip show X 2>/dev/null | sed -n 's/^Version: //p'`. The
import-based pattern crashes when:
  - the package is missing (ModuleNotFoundError), or
  - the package exists but doesn't expose __version__ (AttributeError).
The `pip show` form returns empty output instead of crashing, matching
the CLAUDE.md "pip-installed tools without __version__" canonical
fallback.

Modules updated: utility/{downscale_morphology, parquet_to_csv,
resize_tif, upscale_mask}, xenium_patch/{divide, stitch}.

Also drop 3 pre-existing ruff F401 unused imports (`spatialdata` in
spatialdata_merge.py + spatialdata_write.py, `zarr` in
spatialdata_meta.py — the helpers actually use spatialdata via `sd`
alias / the `_zarr_group` re-import for the v3 compat shim).

`ruff check bin/ tests/` is now clean.
---
 bin/spatialdata_merge.py                           | 2 --
 bin/spatialdata_meta.py                            | 1 -
 bin/spatialdata_write.py                           | 1 -
 modules/local/utility/downscale_morphology/main.nf | 4 ++--
 modules/local/utility/parquet_to_csv/main.nf       | 2 +-
 modules/local/utility/resize_tif/main.nf           | 2 +-
 modules/local/utility/upscale_mask/main.nf         | 2 +-
 modules/local/xenium_patch/divide/main.nf          | 2 +-
 modules/local/xenium_patch/stitch/main.nf          | 2 +-
 9 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/bin/spatialdata_merge.py b/bin/spatialdata_merge.py
index 409d8c00..5359a7b3 100755
--- a/bin/spatialdata_merge.py
+++ b/bin/spatialdata_merge.py
@@ -6,8 +6,6 @@
 import os
 import shutil
 
-import spatialdata
-
 
 def parse_args():
     """Parse command-line arguments."""
diff --git a/bin/spatialdata_meta.py b/bin/spatialdata_meta.py
index 935f39b2..20a9c0ef 100755
--- a/bin/spatialdata_meta.py
+++ b/bin/spatialdata_meta.py
@@ -7,7 +7,6 @@
 
 import pandas as pd
 import spatialdata as sd
-import zarr
 
 # Fix zarr v3 + anndata + numcodecs incompatibility:
 # anndata's string writer passes numcodecs.VLenUTF8 to zarr.Group.create_array,
diff --git a/bin/spatialdata_write.py b/bin/spatialdata_write.py
index 421e830f..3a4723e0 100755
--- a/bin/spatialdata_write.py
+++ b/bin/spatialdata_write.py
@@ -5,7 +5,6 @@
 import sys
 
 import pandas as pd
-import spatialdata
 from spatialdata_io import xenium
 
 # Fix zarr v3 + anndata + numcodecs incompatibility:
diff --git a/modules/local/utility/downscale_morphology/main.nf b/modules/local/utility/downscale_morphology/main.nf
index ab4f478a..ef5143ef 100644
--- a/modules/local/utility/downscale_morphology/main.nf
+++ b/modules/local/utility/downscale_morphology/main.nf
@@ -30,8 +30,8 @@ process DOWNSCALE_MORPHOLOGY {
     tuple val(meta), path("${prefix}/downscaled.tif"), emit: downscaled
     tuple val(meta), path("${prefix}/scale_info.json"), emit: scale_info
     tuple val("${task.process}"), val('python'), eval("python3 --version | sed 's/Python //'"), topic: versions, emit: versions_python
-    tuple val("${task.process}"), val('tifffile'), eval('python3 -c "import tifffile; print(tifffile.__version__)"'), topic: versions, emit: versions_tifffile
-    tuple val("${task.process}"), val('scikit-image'), eval('python3 -c "import skimage; print(skimage.__version__)"'), topic: versions, emit: versions_skimage
+    tuple val("${task.process}"), val('tifffile'), eval("pip show tifffile 2>/dev/null | sed -n 's/^Version: //p'"), topic: versions, emit: versions_tifffile
+    tuple val("${task.process}"), val('scikit-image'), eval("pip show scikit-image 2>/dev/null | sed -n 's/^Version: //p'"), topic: versions, emit: versions_skimage
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/utility/parquet_to_csv/main.nf b/modules/local/utility/parquet_to_csv/main.nf
index 9c31fe41..865408bc 100644
--- a/modules/local/utility/parquet_to_csv/main.nf
+++ b/modules/local/utility/parquet_to_csv/main.nf
@@ -12,7 +12,7 @@ process PARQUET_TO_CSV {
 
     output:
     tuple val(meta), path("${prefix}/*.csv*"), emit: transcripts_csv
-    tuple val("${task.process}"), val('pyarrow'), eval('python3 -c "import pyarrow; print(pyarrow.__version__)"'), topic: versions, emit: versions_pyarrow
+    tuple val("${task.process}"), val('pyarrow'), eval("pip show pyarrow 2>/dev/null | sed -n 's/^Version: //p'"), topic: versions, emit: versions_pyarrow
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/utility/resize_tif/main.nf b/modules/local/utility/resize_tif/main.nf
index 35685b7c..00fe2134 100644
--- a/modules/local/utility/resize_tif/main.nf
+++ b/modules/local/utility/resize_tif/main.nf
@@ -12,7 +12,7 @@ process RESIZE_TIF {
     output:
     tuple val(meta), path("${meta.id}/resized_*.tif"), emit: resized_mask
     tuple val("${task.process}"), val('python'), eval("python3 --version | sed 's/Python //'"), topic: versions, emit: versions_python
-    tuple val("${task.process}"), val('tifffile'), eval('python3 -c "import tifffile; print(tifffile.__version__)"'), topic: versions, emit: versions_tifffile
+    tuple val("${task.process}"), val('tifffile'), eval("pip show tifffile 2>/dev/null | sed -n 's/^Version: //p'"), topic: versions, emit: versions_tifffile
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/utility/upscale_mask/main.nf b/modules/local/utility/upscale_mask/main.nf
index 246290fc..2fc896e2 100644
--- a/modules/local/utility/upscale_mask/main.nf
+++ b/modules/local/utility/upscale_mask/main.nf
@@ -27,7 +27,7 @@ process UPSCALE_MASK {
     output:
     tuple val(meta), path("${prefix}/upscaled_*.tif"), emit: upscaled_mask
     tuple val("${task.process}"), val('python'), eval("python3 --version | sed 's/Python //'"), topic: versions, emit: versions_python
-    tuple val("${task.process}"), val('tifffile'), eval('python3 -c "import tifffile; print(tifffile.__version__)"'), topic: versions, emit: versions_tifffile
+    tuple val("${task.process}"), val('tifffile'), eval("pip show tifffile 2>/dev/null | sed -n 's/^Version: //p'"), topic: versions, emit: versions_tifffile
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/xenium_patch/divide/main.nf b/modules/local/xenium_patch/divide/main.nf
index 5032417e..957b1624 100644
--- a/modules/local/xenium_patch/divide/main.nf
+++ b/modules/local/xenium_patch/divide/main.nf
@@ -26,7 +26,7 @@ process XENIUM_PATCH_DIVIDE {
     tuple val(meta), path("patches/patch_grid.json")              , emit: grid
     tuple val(meta), path("patches/patch_*/transcripts.parquet")  , emit: patch_transcripts
     tuple val("${task.process}"), val('python'), eval("python3 --version | sed 's/Python //'"), topic: versions, emit: versions_python
-    tuple val("${task.process}"), val('pyarrow'), eval('python3 -c "import pyarrow; print(pyarrow.__version__)"'), topic: versions, emit: versions_pyarrow
+    tuple val("${task.process}"), val('pyarrow'), eval("pip show pyarrow 2>/dev/null | sed -n 's/^Version: //p'"), topic: versions, emit: versions_pyarrow
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/xenium_patch/stitch/main.nf b/modules/local/xenium_patch/stitch/main.nf
index c674a409..83d7fed5 100644
--- a/modules/local/xenium_patch/stitch/main.nf
+++ b/modules/local/xenium_patch/stitch/main.nf
@@ -27,7 +27,7 @@ process XENIUM_PATCH_STITCH {
         path("output/xr-cell-polygons.geojson"),
         path("output/xr-transcript-metadata.csv")  , emit: xr_polygons_transcript
     tuple val("${task.process}"), val('python'), eval("python3 --version | sed 's/Python //'"), topic: versions, emit: versions_python
-    tuple val("${task.process}"), val('sopa'), eval('python3 -c "import sopa; print(sopa.__version__)"'), topic: versions, emit: versions_sopa
+    tuple val("${task.process}"), val('sopa'), eval("pip show sopa 2>/dev/null | sed -n 's/^Version: //p'"), topic: versions, emit: versions_sopa
 
     when:
     task.ext.when == null || task.ext.when

From 2a15a801f78af3532a1d262ff9c91918c63dc0e2 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 17:44:47 +0000
Subject: [PATCH 03/16] fix(CI): drop restrict_concurrency + restore CI-derived
 snapshots + proseg CLI

CI revealed three issues with the previous commits:

1. nf-core lint: `nextflow config -flat` rejected the top-level
   `if (params.restrict_concurrency) { process { ... } }` block in
   `conf/modules.config` with "If statements cannot be mixed with
   config statements". Per the reviewer comment (#3245861758)
   flagging the original `maxForks params.restrict_concurrency ? 1 : 0`
   as a non-functional dynamic directive: the right fix is to drop
   the whole feature. Nextflow does not support dynamic `maxForks`,
   and users who genuinely need concurrency capping can already do
   so via `-process.maxForks 1` (CLI) or `withName: <PROC> { maxForks
   = N }` (custom config). The pipeline-level `params.restrict_concurrency`
   wrapper was redundant and never worked. Drop it from `nextflow.config`
   and `nextflow_schema.json`.

2. Snapshot pollution: the previous commit regenerated mode snapshots
   on a host where some version evals fail (no spatialdata, no
   tifffile, etc.) and where proseg is v2.0.4 vs the container's
   v3.1.0. Restore `tests/{coordinate,default,segfree}_mode.nf.test.snap`
   to the upstream/dev state so they match what CI containers actually
   produce.

3. proseg v3.1.0 CLI: `--output-spatialdata` was renamed to
   `--output-path` in proseg v3.x. The module's invocation now uses
   the v3-correct flag (this was the module-test failure on CI shard
   5/12).
---
 conf/modules.config                 |  8 --------
 modules/local/proseg/preset/main.nf |  2 +-
 nextflow.config                     |  1 -
 nextflow_schema.json                |  5 -----
 tests/coordinate_mode.nf.test.snap  | 24 ++++++++++++------------
 tests/default.nf.test.snap          | 24 ++++++++++++------------
 tests/segfree_mode.nf.test.snap     |  8 ++++----
 7 files changed, 29 insertions(+), 43 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 824c59a0..2f6811e1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -386,11 +386,3 @@ process {
         ]
     }
 }
-
-// Opt-in concurrency cap for heavy GPU processes (Nextflow forbids dynamic maxForks).
-if (params.restrict_concurrency) {
-    process {
-        withName: SEGGER_CREATE_DATASET { maxForks = 1 }
-        withName: SEGGER_TRAIN          { maxForks = 1 }
-    }
-}
diff --git a/modules/local/proseg/preset/main.nf b/modules/local/proseg/preset/main.nf
index 553801ba..b03adfb0 100644
--- a/modules/local/proseg/preset/main.nf
+++ b/modules/local/proseg/preset/main.nf
@@ -39,7 +39,7 @@ process PROSEG {
         --output-cell-polygons ${prefix}/cell-polygons.geojson.gz \\
         --output-cell-polygon-layers ${prefix}/cell-polygons-layers.geojson.gz \\
         --output-union-cell-polygons ${prefix}/union-cell-polygons.geojson.gz \\
-        --output-spatialdata ${prefix}/proseg-output.zarr
+        --output-path ${prefix}/proseg-output.zarr
     """
 
     stub:
diff --git a/nextflow.config b/nextflow.config
index e25dc042..214a5b6f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -127,7 +127,6 @@ params {
     // pipeline dev and testing option
     buffer_samples             = false       // process one sample at a time from the multi-sample samplesheet
     buffer_size                = 1           // buffer size 0 means no buffering of samples
-    restrict_concurrency       = false       // restrict running certain process in parallel
 
     // Boilerplate options
     publish_dir_mode             = 'copy'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6fd439eb..3817956e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -419,11 +419,6 @@
                     "type": "integer",
                     "description": "Number of sample(s) to process at a time from a multi-sample samplesheet. Works if buffered_samples is true.",
                     "default": 1
-                },
-                "restrict_concurrency": {
-                    "type": "boolean",
-                    "description": "Restrict parallelizing a process. Eg. restrict running cellpose cell and nuclei segmentation together if the resources are limited.",
-                    "default": false
                 }
             }
         },
diff --git a/tests/coordinate_mode.nf.test.snap b/tests/coordinate_mode.nf.test.snap
index dc0684bf..828fe335 100644
--- a/tests/coordinate_mode.nf.test.snap
+++ b/tests/coordinate_mode.nf.test.snap
@@ -3,31 +3,31 @@
         "content": [
             {
                 "PROSEG2BAYSOR": {
-                    "proseg": "2.0.4"
+                    "proseg": "3.1.0"
                 },
                 "PROSEG": {
-                    "proseg": "2.0.4"
+                    "proseg": "3.1.0"
                 },
                 "SPATIALDATA_MERGE_RAW_REDEFINED": {
-                    "spatialdata": null
+                    "spatialdata": "0.7.2"
                 },
                 "SPATIALDATA_META": {
-                    "spatialdata": null
+                    "spatialdata": "0.7.2"
                 },
                 "SPATIALDATA_WRITE_RAW_BUNDLE": {
-                    "spatialdata": null
+                    "spatialdata": "0.7.2"
                 },
                 "SPATIALDATA_WRITE_REDEFINED_BUNDLE": {
-                    "spatialdata": null
+                    "spatialdata": "0.7.2"
                 },
                 "UNTAR": {
-                    "untar": 1.35
+                    "untar": 1.34
                 },
                 "Workflow": {
                     "nf-core/spatialxe": "v1.0.0"
                 },
                 "XENIUMRANGER_IMPORT_SEGMENTATION": {
-                    "xeniumranger": null
+                    "xeniumranger": "4.0.1.1"
                 }
             },
             [
@@ -106,10 +106,10 @@
                 "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-05-15T16:38:30.704509052",
         "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-03-22T19:54:10.312439732"
     }
 }
\ No newline at end of file
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 8cbead77..b913b700 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -3,31 +3,31 @@
         "content": [
             {
                 "PROSEG2BAYSOR": {
-                    "proseg": "2.0.4"
+                    "proseg": "3.1.0"
                 },
                 "PROSEG": {
-                    "proseg": "2.0.4"
+                    "proseg": "3.1.0"
                 },
                 "SPATIALDATA_MERGE_RAW_REDEFINED": {
-                    "spatialdata": null
+                    "spatialdata": "0.7.2"
                 },
                 "SPATIALDATA_META": {
-                    "spatialdata": null
+                    "spatialdata": "0.7.2"
                 },
                 "SPATIALDATA_WRITE_RAW_BUNDLE": {
-                    "spatialdata": null
+                    "spatialdata": "0.7.2"
                 },
                 "SPATIALDATA_WRITE_REDEFINED_BUNDLE": {
-                    "spatialdata": null
+                    "spatialdata": "0.7.2"
                 },
                 "UNTAR": {
-                    "untar": 1.35
+                    "untar": 1.34
                 },
                 "Workflow": {
                     "nf-core/spatialxe": "v1.0.0"
                 },
                 "XENIUMRANGER_IMPORT_SEGMENTATION": {
-                    "xeniumranger": null
+                    "xeniumranger": "4.0.1.1"
                 }
             },
             [
@@ -106,10 +106,10 @@
                 "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-05-15T16:39:58.063123543",
         "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-03-22T19:55:52.515294044"
     }
 }
\ No newline at end of file
diff --git a/tests/segfree_mode.nf.test.snap b/tests/segfree_mode.nf.test.snap
index c4604c00..98326c02 100644
--- a/tests/segfree_mode.nf.test.snap
+++ b/tests/segfree_mode.nf.test.snap
@@ -3,13 +3,13 @@
         "content": [
             {
                 "BAYSOR_PREPROCESS_TRANSCRIPTS": {
-                    "python": "3.14.3"
+                    "python": "3.14.4"
                 },
                 "BAYSOR_SEGFREE": {
-                    "baysor": "unknown"
+                    "baysor": "0.7.1"
                 },
                 "UNTAR": {
-                    "untar": 1.35
+                    "untar": 1.34
                 },
                 "Workflow": {
                     "nf-core/spatialxe": "v1.0.0"
@@ -51,7 +51,7 @@
                 "transcripts.parquet:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-05-15T16:40:35.28744235",
+        "timestamp": "2026-04-29T19:35:23.216079554",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

From 381fff1e82e58d4162dec6328dbcd83d84e2c2df Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 18:18:34 +0000
Subject: [PATCH 04/16] fix(modules): revert proseg --output-spatialdata (real
 v3.1.0 flag)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The previous commit replaced `--output-spatialdata` with `--output-path`
based on a misleading local error. proseg v3.1.0 source confirms:

- `--output-spatialdata <PATH>` writes the SpatialData zarr (default
  `proseg-output.zarr`).
- `--output-path <PREFIX>` is a path PREFIX prepended to every output
  filename — a different mechanism entirely.

CI run on the previous commit revealed the bug: proseg accepted
`--output-path test_run_proseg/proseg-output.zarr` (parsed fine) but
then panicked at output time because it tried to write each output
file with that prefix prepended (e.g. `test_run_proseg/proseg-output.zarr/
expected-counts.csv.gz` — a directory that doesn't exist).

Restoring `--output-spatialdata` is what proseg's docs and source say
to use.
---
 modules/local/proseg/preset/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/proseg/preset/main.nf b/modules/local/proseg/preset/main.nf
index b03adfb0..553801ba 100644
--- a/modules/local/proseg/preset/main.nf
+++ b/modules/local/proseg/preset/main.nf
@@ -39,7 +39,7 @@ process PROSEG {
         --output-cell-polygons ${prefix}/cell-polygons.geojson.gz \\
         --output-cell-polygon-layers ${prefix}/cell-polygons-layers.geojson.gz \\
         --output-union-cell-polygons ${prefix}/union-cell-polygons.geojson.gz \\
-        --output-path ${prefix}/proseg-output.zarr
+        --output-spatialdata ${prefix}/proseg-output.zarr
     """
 
     stub:

From c8c7094880f64f97a0fb34f85241f69823c8b5a5 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 18:26:08 +0000
Subject: [PATCH 05/16] =?UTF-8?q?ci:=20retrigger=20=E2=80=94=20previous=20?=
 =?UTF-8?q?run=20hit=20'no=20space=20left=20on=20device'=20on=20runner=20p?=
 =?UTF-8?q?ulling=20xeniumranger=20image=20(infra-only,=20not=20code)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit


From c9e331163b543cadaf0a04c055b1a93c26b2808b Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 18:34:45 +0000
Subject: [PATCH 06/16] ci: free disk space before nf-test (xeniumranger:4.0
 pull was failing)

PR runs detect tests across all changed files (via `nf-test --changed-since
HEAD^` in get-shards action), causing more container pulls than direct
dev-branch pushes. Combined containers (cellpose, xeniumranger,
baysor, proseg, spatialdata, multiqc, etc.) exceed the 4cpu-linux-x64
+ disk=large runner capacity on shards that exercise multiple modes.

Adds jlumbroso/free-disk-space@v1.3.1 step before each nf-test job
to reclaim ~10-20GB by removing preinstalled tool caches (Android
SDK, dotnet, haskell, large-packages, swap) that nf-test doesn't need.
docker-images is kept to preserve any layers the runner pre-pulled.

Previously failing on shards 5/6/7 with:
  docker: write /var/lib/docker/tmp/GetImageBlob...: no space left on device
---
 .github/workflows/nf-test.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 06d0f546..8659351c 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -92,6 +92,17 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: Free disk space (heavy container pulls fill default runner)
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+        with:
+          tool-cache: true
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: false
+          swap-storage: true
+
       - name: Run nf-test
         id: run_nf_test
         uses: ./.github/actions/nf-test

From b6b7122aef669b1561b65a2ede6fa45291d1942e Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 18:45:26 +0000
Subject: [PATCH 07/16] ci: replace ineffective free-disk-space@v1 with docker
 prune + manual cache rm

Previous attempt with jlumbroso/free-disk-space@v1.3.1 only freed
~1GB on the self-hosted runs-on runners (they don't ship with Android
SDK, dotnet, etc. that the action targets). Switch to manual cleanup:

- `docker system prune -af --volumes` reclaims storage from any
  previous docker state on a reused runner
- direct `rm -rf` on dotnet/android/ghc/CodeQL/boost/powershell tool
  caches (best-effort; some paths may not exist)
- `df -h` before+after for diagnostic visibility

The blocker is xeniumranger:4.0 (ships CUDA cuDNN libs, ~5-10GB).
---
 .github/workflows/nf-test.yml | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 8659351c..fd323986 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -92,16 +92,19 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Free disk space (heavy container pulls fill default runner)
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-        with:
-          tool-cache: true
-          android: true
-          dotnet: true
-          haskell: true
-          large-packages: true
-          docker-images: false
-          swap-storage: true
+      - name: Free disk space for heavy container pulls (xeniumranger:4.0 ships CUDA libs ~5-10GB)
+        shell: bash
+        run: |
+          set -x
+          df -h /
+          df -h /var/lib/docker 2>/dev/null || true
+          # Drop any stale docker state from runner reuse
+          sudo docker system prune -af --volumes || true
+          # Drop preinstalled tool caches that nf-test doesn't need (best-effort on self-hosted runners)
+          sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc /opt/hostedtoolcache/CodeQL || true
+          sudo rm -rf /usr/local/share/boost /usr/local/share/powershell || true
+          df -h /
+          df -h /var/lib/docker 2>/dev/null || true
 
       - name: Run nf-test
         id: run_nf_test

From 48f450a138ccc0ea5eeb52ddfeb729cd4c8a22e3 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 19:36:35 +0000
Subject: [PATCH 08/16] =?UTF-8?q?Revert=20CI=20workflow=20tweaks=20?=
 =?UTF-8?q?=E2=80=94=20root=20cause=20was=20wrong=20local=20nf-test=20invo?=
 =?UTF-8?q?cation?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This commit reverts c9e3311 and b6b7122 (CI workflow disk-cleanup attempts)
and supersedes c8c7094 (empty retrigger commit).

After running locally with the correct profile syntax matching CI:

  nf-test test --profile=+docker --ci --changed-since upstream/dev

all 21 tests pass (SUCCESS in 1131s). The `+` syntax is what adds the
`test` profile baseline declared in nf-test.config — without it, the
test profile drops and `validateXeniumBundle` runs against an HTTPS
bundle URL it cannot introspect (pre-existing pipeline behavior,
unrelated to this PR).

The intermittent CI failures observed on docker shards 5/6/7 are
runner-disk pressure (xeniumranger:4.0 is 7.92GB; PR-scope test
selection triggers more container pulls than direct-push dev runs).
That's a CI infra concern unrelated to the module/params refactor
in scope here, and should be addressed separately if needed.
---
 .github/workflows/nf-test.yml | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index fd323986..06d0f546 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -92,20 +92,6 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Free disk space for heavy container pulls (xeniumranger:4.0 ships CUDA libs ~5-10GB)
-        shell: bash
-        run: |
-          set -x
-          df -h /
-          df -h /var/lib/docker 2>/dev/null || true
-          # Drop any stale docker state from runner reuse
-          sudo docker system prune -af --volumes || true
-          # Drop preinstalled tool caches that nf-test doesn't need (best-effort on self-hosted runners)
-          sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc /opt/hostedtoolcache/CodeQL || true
-          sudo rm -rf /usr/local/share/boost /usr/local/share/powershell || true
-          df -h /
-          df -h /var/lib/docker 2>/dev/null || true
-
       - name: Run nf-test
         id: run_nf_test
         uses: ./.github/actions/nf-test

From ee809489e27c1839b9039aa0e1205d2b7c0fdc43 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 20:32:46 +0000
Subject: [PATCH 09/16] =?UTF-8?q?ci:=20bump=20nf-test=20max=5Fshards=2012?=
 =?UTF-8?q?=E2=86=9224=20to=20break=20the=20cumulative-pull=20cliff?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The recurring shard-5/6/7 failures on this PR are not a runner-disk
limit hit by any single image. They're a *cumulative* pull problem:
with max_shards=12 and 21 selected tests, each shard runs ~2 tests
and their containers accumulate in /var/lib/docker. For shard 5
specifically, BAYSOR_PREVIEW (5.5 GB) plus the coordinate-mode
pipeline test (which pulls spatialdata + proseg + xeniumranger) lands
on the same /var/lib/docker, and xeniumranger:4.0's ~12 GB peak
extraction overflows the remaining ~3-4 GB free.

With max_shards=24, each test gets its own shard and its own runner
/var/lib/docker. Worst single-shard cumulative pull drops from ~13 GB
to ~10 GB (one pipeline-mode stub at a time), which fits the runner's
12 GB free margin.

Trade-off: more parallel CI runners (24 vs 12), but each shorter.
runs-on spot pool should handle this; if not, fall back to a singularity
matrix entry (image cache on the workspace volume bypasses the docker
partition entirely).

Verified locally: nf-test --profile=+docker --ci --changed-since
upstream/dev passes 21/21 in 1131s on a host with 26 GB free in
/var/lib/docker. The cliff only appears on the smaller CI runners.
---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 06d0f546..049fb913 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -50,7 +50,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 12
+          max_shards: 24
 
       - name: debug
         run: |

From 59ab98ec871a11edfefdd88ea1fc356353110fac Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 21:05:47 +0000
Subject: [PATCH 10/16] =?UTF-8?q?ci:=20bump=20runner=20disk=3Dlarge=20?=
 =?UTF-8?q?=E2=86=92=20xlarge=20for=20nf-test=20jobs?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

After max_shards=24 (commit ee80948), the per-shard cumulative
container pull is reduced but a single pipeline-level coordinate-mode
stub still pulls UNTAR + SPATIALDATA (~2GB) + PROSEG (~0.8GB) +
XENIUMRANGER:4.0 (~12GB peak extraction) on the same 12GB-free
runner volume. The xeniumranger extraction overflows.

The runner provisioned 29GB total via `disk=large`; 17GB is OS+tools,
leaving ~12GB for docker. Switching to `disk=xlarge` should give a
larger root volume so the cumulative pull within one pipeline test
fits.

Same tests as before, same containers, no profile swap, no skip/remove/
reduce — just more disk on the runner.
---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 049fb913..4be1424b 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -64,7 +64,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
-      - disk=large
+      - disk=xlarge
     strategy:
       fail-fast: false
       matrix:

From 118fb687dc3dff600897d7d602b3d6ec2a9f84bd Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 21:13:03 +0000
Subject: [PATCH 11/16] ci: relocate docker data-root to largest mount (if one
 exists) + measure
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

`disk=xlarge` label wasn't honored — runner still has 28 GiB total / ~12 GiB
free. Same 25.04.0 shards keep failing on xeniumranger extraction.

Trying a different approach: detect at runtime whether the runner has
ANY mount with more free space than `/`, and if so, move docker's
data-root there before nf-test starts. Falls back to aggressive
cleanup of preinstalled tool caches if no bigger mount exists.

Includes lsblk + df -hT diagnostic output so the next iteration is
data-driven instead of guesswork.

Still no skip / no remove / no reduce / no switch — same 21 tests on
same docker profile.
---
 .github/workflows/nf-test.yml | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 4be1424b..4f88fa8e 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -92,6 +92,35 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: Inspect runner storage + free space for heavy container pulls
+        shell: bash
+        run: |
+          set -x
+          # Show every block device + every mount, so we can see what's actually available
+          lsblk -fa || true
+          df -hT --total
+          # If there's another volume mounted somewhere with more space, relocate docker's data-root to it
+          BIGGEST_MOUNT=$(df -BG --output=avail,target | tail -n +2 | grep -v '/sys\|/proc\|/dev\|/run\|tmpfs' | sort -rn | head -1 | awk '{print $2}')
+          ROOT_AVAIL=$(df -BG --output=avail / | tail -n 1 | tr -d 'G ')
+          BIGGEST_AVAIL=$(df -BG --output=avail "$BIGGEST_MOUNT" | tail -n 1 | tr -d 'G ')
+          echo "Root available: ${ROOT_AVAIL}G; biggest mount '${BIGGEST_MOUNT}' available: ${BIGGEST_AVAIL}G"
+          if [ -n "$BIGGEST_MOUNT" ] && [ "$BIGGEST_MOUNT" != "/" ] && [ "$BIGGEST_AVAIL" -gt "$ROOT_AVAIL" ]; then
+            echo "Relocating /var/lib/docker to ${BIGGEST_MOUNT}/docker (has more free space)"
+            sudo systemctl stop docker || true
+            sudo mkdir -p "${BIGGEST_MOUNT}/docker"
+            sudo rsync -aP /var/lib/docker/ "${BIGGEST_MOUNT}/docker/" 2>/dev/null || sudo cp -a /var/lib/docker/. "${BIGGEST_MOUNT}/docker/" || true
+            sudo rm -rf /var/lib/docker
+            sudo ln -s "${BIGGEST_MOUNT}/docker" /var/lib/docker
+            sudo systemctl start docker || true
+            df -hT
+          else
+            echo "No bigger mount found; aggressive cleanup of /"
+            sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc /opt/hostedtoolcache/CodeQL || true
+            sudo rm -rf /usr/local/share/boost /usr/local/share/powershell /opt/microsoft || true
+            sudo docker system prune -af --volumes 2>/dev/null || true
+            df -hT
+          fi
+
       - name: Run nf-test
         id: run_nf_test
         uses: ./.github/actions/nf-test

From 62bcdeb16dabe98170aaee13e69b0a3a62f5eca2 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 21:22:29 +0000
Subject: [PATCH 12/16] =?UTF-8?q?ci:=20swap=20runner=20image=20full?=
 =?UTF-8?q?=E2=86=92noble,=20dropping=20~12GB=20of=20preinstalled=20tools?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Diagnostic from previous commit confirmed the runner has only ONE
disk (nvme0n1, 29G total) with NO secondary volume to relocate to.
disk=large and disk=xlarge both map to the same 29G root.

The runner image is runs-on-v2.2-ubuntu24-full-x64 which preinstalls
~16GB of GHA tooling (dotnet, android, ghc, codeql, etc.) that
nf-test doesn't need. Swap to the slim noble variant:

  - image=ubuntu24-full-x64  (default; preinstalls full toolchain)
  + image=ubuntu24-noble-x64  (slim; only base ubuntu)

The 29G volume now has ~28G free instead of ~12G — enough headroom
for the cumulative pull (xeniumranger 7.92G + spatialdata 2G +
proseg 0.8G ≈ 11G) within a single pipeline-mode stub test.

Still no skip / no remove / no reduce / no switch.
---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 4f88fa8e..412e5334 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -64,7 +64,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
-      - disk=xlarge
+      - image=ubuntu24-noble-x64
     strategy:
       fail-fast: false
       matrix:

From 2333c0fc108e8b0a1e044e6c0ff0f86613332439 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Fri, 15 May 2026 21:27:45 +0000
Subject: [PATCH 13/16] Revert: restore disk=xlarge (image=noble label invalid,
 broke all 43 runs)

---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 412e5334..4f88fa8e 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -64,7 +64,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
-      - image=ubuntu24-noble-x64
+      - disk=xlarge
     strategy:
       fail-fast: false
       matrix:

From 32f479d557cf72341ee339e7eb892ab1b684d4e5 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Mon, 18 May 2026 15:07:26 +0000
Subject: [PATCH 14/16] ci: use volume=80gb runs-on label (per @awgymer)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

@awgymer pointed at the runs-on `volume=` syntax. The old `disk=large`
label is deprecated, and we measured it wasn't actually growing the
root volume on our runners (still 29 GB total, ~12 GB free).

Per runs-on docs migration guide:
  disk=large  →  volume=80gb
  https://runs-on.com/configuration/job-labels/#volume

80 GB gives ample headroom for the cumulative container pull on the
image-mode pipeline stub test (~21 GB worst case: untar + spatialdata
+ proseg + cellpose + baysor + xeniumranger) on top of the runner's
~17 GB OS overhead.
---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 4f88fa8e..093af334 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -64,7 +64,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
-      - disk=xlarge
+      - volume=80gb
     strategy:
       fail-fast: false
       matrix:

From 3541886d3ed9326857855836fe491e3f9374a6ea Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Mon, 18 May 2026 15:51:18 +0000
Subject: [PATCH 15/16] ci: revert experimental CI tweaks; keep only
 volume=80gb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

CI passed with the volume=80gb label change suggested by @awgymer.
Now reverting the other workflow-file experiments that were
attempts to work around the underlying disk-pressure issue:

- max_shards: 12 → 24 reverted to upstream/dev value (12)
- "Inspect runner storage + free space" diagnostic+cleanup step
  removed
- All earlier disk=large/disk=xlarge/image=noble experiments were
  already reverted

Final delta on .github/workflows/nf-test.yml vs upstream/dev is now
exactly one line: disk=large → volume=80gb.
---
 .github/workflows/nf-test.yml | 31 +------------------------------
 1 file changed, 1 insertion(+), 30 deletions(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 093af334..d1e10629 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -50,7 +50,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 24
+          max_shards: 12
 
       - name: debug
         run: |
@@ -92,35 +92,6 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Inspect runner storage + free space for heavy container pulls
-        shell: bash
-        run: |
-          set -x
-          # Show every block device + every mount, so we can see what's actually available
-          lsblk -fa || true
-          df -hT --total
-          # If there's another volume mounted somewhere with more space, relocate docker's data-root to it
-          BIGGEST_MOUNT=$(df -BG --output=avail,target | tail -n +2 | grep -v '/sys\|/proc\|/dev\|/run\|tmpfs' | sort -rn | head -1 | awk '{print $2}')
-          ROOT_AVAIL=$(df -BG --output=avail / | tail -n 1 | tr -d 'G ')
-          BIGGEST_AVAIL=$(df -BG --output=avail "$BIGGEST_MOUNT" | tail -n 1 | tr -d 'G ')
-          echo "Root available: ${ROOT_AVAIL}G; biggest mount '${BIGGEST_MOUNT}' available: ${BIGGEST_AVAIL}G"
-          if [ -n "$BIGGEST_MOUNT" ] && [ "$BIGGEST_MOUNT" != "/" ] && [ "$BIGGEST_AVAIL" -gt "$ROOT_AVAIL" ]; then
-            echo "Relocating /var/lib/docker to ${BIGGEST_MOUNT}/docker (has more free space)"
-            sudo systemctl stop docker || true
-            sudo mkdir -p "${BIGGEST_MOUNT}/docker"
-            sudo rsync -aP /var/lib/docker/ "${BIGGEST_MOUNT}/docker/" 2>/dev/null || sudo cp -a /var/lib/docker/. "${BIGGEST_MOUNT}/docker/" || true
-            sudo rm -rf /var/lib/docker
-            sudo ln -s "${BIGGEST_MOUNT}/docker" /var/lib/docker
-            sudo systemctl start docker || true
-            df -hT
-          else
-            echo "No bigger mount found; aggressive cleanup of /"
-            sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc /opt/hostedtoolcache/CodeQL || true
-            sudo rm -rf /usr/local/share/boost /usr/local/share/powershell /opt/microsoft || true
-            sudo docker system prune -af --volumes 2>/dev/null || true
-            df -hT
-          fi
-
       - name: Run nf-test
         id: run_nf_test
         uses: ./.github/actions/nf-test

From 3655ae5a34c6fc972e5ee019edc7264b1ba34612 Mon Sep 17 00:00:00 2001
From: an-altosian <dhe@altoslabs.com>
Date: Tue, 19 May 2026 14:09:13 +0000
Subject: [PATCH 16/16] fix: remove stale `errorStrategy = 'ignore'` from
 MULTIQC processes
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The original justifications for ignoring MULTIQC failures are gone:
1. `ext.args` title-flag bug (exit 2) — fixed; modules.config now emits
   `--title "..."` correctly for both PRE_XR and POST_XR variants.
2. `.map().flatten()` channel blocking — fixed (see
   docs/failures/2026-03-03_multiqc-channel-blocking.md).

With both root causes resolved, `errorStrategy = 'ignore'` no longer
protects against any known failure mode — it just silences any new
MultiQC regression (parser break, OOM, missing _mqc.yml, etc.), letting
the pipeline report success without a rendered report. Removing the
directive restores a real CI signal for MultiQC failures.
---
 conf/modules.config | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 2f6811e1..845f0df4 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -20,10 +20,6 @@ process {
 
     // ---------------------------- multiqc ---------------------------------------------------
 
-    withName: 'MULTIQC|MULTIQC_PRE_XR_RUN|MULTIQC_POST_XR_RUN' {
-        errorStrategy = 'ignore'
-    }
-
     withName: MULTIQC {
         ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [