[DO NOT MERGE] Test gpu runners

.github/workflows/nf-test-gpu.yml

@@ -104,6 +104,46 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           fetch-depth: 0
+
+      - name: Basic GPU Check
+        run: |
+          whoami
+          groups
+          nvidia-smi
+          docker info | grep -i runtime
+        # This should succeed based on your output
+
+      - name: Run Application (Will Fail)
+        run: |
+          # Run your actual application command here
+          # For example: python my_gpu_script.py
+          # Or: docker run your_image your_command
+          # ADD "set -x" TO SEE EXACTLY WHAT'S HAPPENING
+          set -x
+          your_actual_command_that_fails
+        continue-on-error: true # This allows the workflow to continue even if this step fails
+
+      - name: Debug Environment
+        run: |
+          echo "=== Debug After Failure ==="
+          env | grep -i cuda
+          env | grep -i nvidia
+          ls -la /dev/nvidia*
+          ldconfig -p | grep cuda
+        continue-on-error: true # This allows the workflow to continue even if this step fails
+
+      - name: Test Different CUDA Versions
+        run: |
+          # Test with CUDA 12.0
+          docker run --rm --gpus all nvidia/cuda:12.0.1-base-ubuntu22.04 nvidia-smi
+
+          # Test with CUDA 11.8
+          docker run --rm --gpus all nvidia/cuda:11.8.0-base-ubuntu22.04 nvidia-smi
+
+          # Try running your application inside a CUDA container
+          docker run --rm --gpus all -v $(pwd):/app -w /app nvidia/cuda:11.8.0-runtime-ubuntu22.04 your_application_command
+        continue-on-error: true # This allows the workflow to continue even if this step fails
+
       - name: Run nf-test Action
         uses: ./.github/actions/nf-test-action
         env:

modules/nf-core/parabricks/fq2bam/main.nf

@@ -7,19 +7,22 @@ process PARABRICKS_FQ2BAM {
     container "nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta) , path(reads)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(index)
     tuple val(meta4), path(interval_file)
-    path(known_sites)
+    tuple val(meta5), path(known_sites)
+    val(output_fmt) // either bam or cram
 
     output:
-    tuple val(meta), path("*.bam")  , emit: bam
-    tuple val(meta), path("*.bai")  , emit: bai
-    tuple val(meta), path("*.table"), emit: bqsr_table         , optional:true
-    path("versions.yml")            , emit: versions
-    path("qc_metrics")              , emit: qc_metrics          , optional:true
-    path("duplicate-metrics.txt")   , emit: duplicate_metrics  , optional:true
+    tuple val(meta), path("*.bam")                  , emit: bam              , optional:true
+    tuple val(meta), path("*.bai")                  , emit: bai              , optional:true
+    tuple val(meta), path("*.cram")                 , emit: cram             , optional:true
+    tuple val(meta), path("*.crai")                 , emit: crai             , optional:true
+    tuple val(meta), path("*.table")                , emit: bqsr_table       , optional:true
+    tuple val(meta), path("*_qc_metrics")           , emit: qc_metrics       , optional:true
+    tuple val(meta), path("*.duplicate-metrics.txt"), emit: duplicate_metrics, optional:true
+    path("versions.yml")                            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,10 +34,14 @@ process PARABRICKS_FQ2BAM {
     }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+
     def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads"
-    def known_sites_command = known_sites ? known_sites.collect{"--knownSites $it"}.join(' ') : ""
-    def known_sites_output = known_sites ? "--out-recal-file ${prefix}.table" : ""
-    def interval_file_command = interval_file ? interval_file.collect{"--interval-file $it"}.join(' ') : ""
+    def extension = "$output_fmt"
+
+    def known_sites_command = known_sites ? (known_sites instanceof List ? known_sites.collect { "--knownSites $it" }.join(' ') : "--knownSites ${known_sites}") : ""
+    def known_sites_output_cmd = known_sites ? "--out-recal-file ${prefix}.table" : ""
+    def interval_file_command = interval_file ? (interval_file instanceof List ? interval_file.collect { "--interval-file $it" }.join(' ') : "--interval-file ${interval_file}") : ""
+
     def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
@@ -44,9 +51,9 @@ process PARABRICKS_FQ2BAM {
         fq2bam \\
         --ref \$INDEX \\
         $in_fq_command \\
-        --out-bam ${prefix}.bam \\
+        --out-bam ${prefix}.${extension} \\
         $known_sites_command \\
-        $known_sites_output \\
+        $known_sites_output_cmd \\
         $interval_file_command \\
         $num_gpus \\
         $args
@@ -62,10 +69,19 @@ process PARABRICKS_FQ2BAM {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
+    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = "$output_fmt"
+    def extension_index = "$output_fmt" == "cram" ? "crai" : "bai"
+    def known_sites_output = known_sites ? "touch ${prefix}.table" : ""
+    def qc_metrics_output = args.contains("--out-qc-metrics-dir") ? "mkdir ${prefix}_qc_metrics" : ""
+    def duplicate_metrics_output = args.contains("--out-duplicate-metrics") ? "touch ${prefix}.duplicate-metrics.txt" : ""
     """
-    touch ${prefix}.bam
-    touch ${prefix}.bam.bai
+    touch ${prefix}.${extension}
+    touch ${prefix}.${extension}.${extension_index}
+    $known_sites_output
+    $qc_metrics_output
+    $duplicate_metrics_output
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/parabricks/fq2bam/meta.yml

@@ -49,11 +49,19 @@ input:
         description: (optional) file(s) containing genomic intervals for use in base
           quality score recalibration (BQSR)
         pattern: "*.{bed,interval_list,picard,list,intervals}"
-  - - known_sites:
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing known sites information
+    - known_sites:
         type: file
         description: (optional) known sites file(s) for calculating BQSR. markdups must
           be true to perform BQSR.
         pattern: "*.vcf.gz"
+  - - output_fmt:
+        type: string
+        description: Output format for the alignment. Options are 'bam' or 'cram'
+        pattern: "{bam,cram}"
 output:
   - bam:
       - meta:
@@ -75,6 +83,26 @@ output:
           type: file
           description: index corresponding to sorted BAM file
           pattern: "*.bai"
+  - cram:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.cram":
+          type: file
+          description: Sorted CRAM file
+          pattern: "*.cram"
+  - crai:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.crai":
+          type: file
+          description: index corresponding to sorted CRAM file
+          pattern: "*.crai"
   - bqsr_table:
       - meta:
           type: map
@@ -86,22 +114,30 @@ output:
           description: (optional) table from base quality score recalibration calculation,
             to be used with parabricks/applybqsr
           pattern: "*.table"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
   - qc_metrics:
-      - qc_metrics:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+      - "*_qc_metrics":
           type: directory
           description: (optional) optional directory of qc metrics
-          pattern: "qc_metrics"
+          pattern: "*_qc_metrics"
   - duplicate_metrics:
-      - duplicate-metrics.txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+      - "*.duplicate-metrics.txt":
           type: file
           description: (optional) metrics calculated from marking duplicates in the bam
             file
-          pattern: "*-duplicate-metrics.txt"
+          pattern: "*.duplicate-metrics.txt"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@bsiranosian"
   - "@adamrtalbot"