testing segfree methods

Author: khersameesh24

.github/workflows/ci.yml

@@ -82,12 +82,22 @@ jobs:
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: "Run pipeline image mode with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+      - name: "Run pipeline in image mode with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results --mode image -stub
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} -stub --outdir ./results --mode image
 
-      - name: "Run pipeline coordinate mode with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+      - name: "Run pipeline in coordinate mode with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results --mode coordinate -stub
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} -stub --outdir ./results --mode coordinate
+
+      - name: "Run pipeline in preview mode with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} -stub --outdir ./results --mode preview
+
+      - name: "Run pipeline in segfree mode with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} -stub --outdir ./results --mode segfree

conf/test.config

@@ -15,7 +15,7 @@ process {
     resourceLimits = [
         cpus: 4,
         memory: '15.GB',
-        time: '6.h'
+        time: '2.h'
     ]
 
     withName: UNTAR {

modules/local/baysor/create_dataset/templates/create_dataset.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import csv
 import random

subworkflows/local/ficture_preprocess_model/main.nf

@@ -23,7 +23,9 @@ workflow FICTURE_PREPROCESS_MODEL {
     ch_versions = ch_versions.mix ( PARQUET_TO_CSV.out.versions )
 
     // run ficture preprocessing
-    FICTURE_PREPROCESS ( PARQUET_TO_CSV.out.transcripts_csv, ch_features )
+    ch_transcripts = PARQUET_TO_CSV.out.transcripts_csv
+
+    FICTURE_PREPROCESS ( ch_transcripts, ch_features )
     ch_versions = ch_versions.mix ( FICTURE_PREPROCESS.out.versions )
 
     // run the ficture wrapper pipeline

subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf

@@ -255,12 +255,12 @@ def validateXeniumBundle(ch_samplesheet) {
             def missing_files = []
 
             def allExist = xenium_bundle.every { filename ->
-            def fullPath = file("${path}/${filename}")
-            if (!fullPath.exists()) {
-                missing_files.add(filename)
-                return false
-            }
-                return true
+                def fullPath = file("${path}/${filename}")
+                if (!fullPath.exists()) {
+                    missing_files.add(filename)
+                    return false
+                }
+                    return true
             }
 
             if (!allExist) {
@@ -269,7 +269,7 @@ def validateXeniumBundle(ch_samplesheet) {
             }
         }
     }
-    log.info "INFO Xenium bundle validated ✅ "
+    log.info "INFO Xenium bundle validated ✅ \n"
 }
 
 //

workflows/spatialxe.nf

@@ -147,8 +147,9 @@ workflow SPATIALXE {
 
     // get a list of features if provided with the --features for the ficture method
     if ( params.features ) {
-        ch_features = Channel.of (
-            params.features.split(',')
+        ch_features = Channel.fromPath (
+            params.features,
+            checkIfExists: true
         )
     }
 
@@ -383,7 +384,6 @@ workflow SPATIALXE {
                     ch_transcripts_parquet,
                     ch_config
                 )
-                ch_redefined_bundle = BAYSOR_RUN_TRANSCRIPTS_PARQUET.out.redefined_bundle
             }
 
             // run ficture with transcripts.parquet
@@ -393,7 +393,6 @@ workflow SPATIALXE {
                     ch_transcripts_parquet,
                     ch_features
                 )
-                ch_redefined_bundle = BAYSOR_RUN_TRANSCRIPTS_PARQUET.out.redefined_bundle
             }
         }
     }