update smoke test datasets and smoke_test.yml

Author: ch99l

.github/workflows/smoke_test.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   smoke_test:
-    name: "${{ matrix.profile }} (NF ${{ matrix.nextflow_version }})"
+    name: "${{ matrix.profile }} (NF ${{ matrix.nextflow_version }})${{ matrix.quantification_mode && format(' [{0}]', matrix.quantification_mode) || '' }}${{ matrix.bam_only && ' [bam_only]' || '' }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -19,10 +19,26 @@ jobs:
           - test_sc_multi
           - test_visium
           - test_custom
+        include:
+          - nextflow_version: "latest-stable"
+            profile: test_sc_fastq
+            quantification_mode: EM
+          - nextflow_version: "latest-stable"
+            profile: test_sc_multi
+            quantification_mode: EM
+          - nextflow_version: "latest-stable"
+            profile: test_sc_fastq
+            quantification_mode: no_quant
+          - nextflow_version: "latest-stable"
+            profile: test_sc_fastq
+            bam_only: true
     steps:
       - uses: actions/checkout@v4
       - uses: nf-core/setup-nextflow@v2
         with:
           version: ${{ matrix.nextflow_version }}
       - name: Run ${{ matrix.profile }}
-        run: nextflow run . -profile test_base,${{ matrix.profile }},docker
+        run: |
+          nextflow run . -profile test_base,${{ matrix.profile }},docker \
+            ${{ matrix.quantification_mode && format('--quantification_mode {0}', matrix.quantification_mode) || '' }} \
+            ${{ matrix.bam_only && '--bam_only true' || '' }}

README.md

@@ -83,6 +83,7 @@ sample,path,chemistry,technology
 ```csv
 sample,path,chemistry,technology
 10x5v2_ONT_example,examples/10x5v2_ONT_example.fastq.gz,10x5v2,ONT
+10x5v2_PacBio_example,examples/10x5v2_PacBio_example.fastq.gz,10x5v2,PacBio
 10x5v3_ONT_example,examples/10x5v3_ONT_example_demultiplexed.bam,10x5v3,ONT
 ```
 
@@ -238,7 +239,7 @@ Example data and pre-configured profiles are provided in `examples/` to run the
 |---|---|
 | `test_sc_fastq` | Single-cell, single-sample ONT run from raw reads |
 | `test_sc_bam` | Single-cell, single-sample ONT run from demultiplexed BAM |
-| `test_sc_multi` | Single-cell, multi-sample ONT run across two chemistries (10x5v2 FASTQ + 10x5v3 BAM) |
+| `test_sc_multi` | Single-cell, multiple-sample run with different chemistries and technologies |
 | `test_visium` | Spatial (Visium), single-sample ONT run from raw reads |
 | `test_custom` | Custom chemistry, single-sample ONT run from demultiplexed BAM |
 

examples/10x5v2_PacBio_example.fastq.gz

@@ -1,3 +1,4 @@
 sample,path,chemistry,technology
 10x5v2_ONT_example,examples/10x5v2_ONT_example.fastq.gz,10x5v2,ONT
+10x5v2_PacBio_example,examples/10x5v2_PacBio_example.fastq.gz,10x5v2,PacBio
 10x5v3_ONT_example,examples/10x5v3_ONT_example_demultiplexed.bam,10x5v3,ONT