Minor fixes

README.md

@@ -68,7 +68,7 @@ OPTIONAL ARGUMENTS:
 
 ```bash
 $ bash variantmedium.sh \
-  --samplehsheet <path/to/samplesheet.csv> \
+  --samplesheet <path/to/samplesheet.csv> \
   --outdir <path/to/pipeline-output-directory> \
   --profile conda  
 ```

conf/modules.config

@@ -48,8 +48,6 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
-        clusterOptions = '--gres=gpu:1'
-        accelerator = 'nvidia'
     }
 
     withName: CALL_VARIANTS_SNV {
@@ -58,8 +56,8 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
+        queue = 'GPU'
         clusterOptions = '--gres=gpu:1'
-        accelerator = 'nvidia'
     }
 
     withName: CALL_VARIANTS_INDEL {
@@ -68,8 +66,8 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
+        queue = 'GPU'
         clusterOptions = '--gres=gpu:1'
-        accelerator = 'nvidia'
     }
 
 }

modules/variantmedium/call/environment.yml

@@ -10,4 +10,5 @@ dependencies:
 - pip
 - pip:
   - fire==0.5.0
-  - torch==2.0.1
+  - --extra-index-url https://download.pytorch.org/whl/cu121
+  - torch==2.1.0+cu121

modules/variantmedium/call/main.nf

@@ -1,6 +1,9 @@
 process CALL_VARIANTS {
-    label "process_high_memory"
-
+    label (
+        "${params.use_gpu}" ? "process_gpu" :
+        error("GPU support is required for CALL_VARIANTS process. Please include the 'gpu' profile to run variantmedium call")
+    )
+
     conda "${moduleDir}/environment.yml"
     container "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a7/a73b7de4a8d00029f69b6cef20b74e1a1d6b48c1d7d5a65b5e55cf09c3fe6ce7/data"
 

nextflow.config

@@ -41,12 +41,16 @@ params {
   // version - needs an update with each release
   version = '1.2.0'
 
+  // gpu specific
+  use_gpu = false
+
 }
 
 process {
-  beforeScript = '''
-    echo SLURM_JOB_ID=$SLURM_JOB_ID
-  '''
+  resourceLimits = [
+    cpus: 4,
+    memory: '16.GB',
+  ]
 }
 
 profiles {
@@ -60,9 +64,24 @@ profiles {
   }
   slurm {
     process {
-      executor = 'slurm'  
+      executor = 'slurm' 
     }
   }
+  gpu {
+    params.use_gpu = true
+    apptainer.runOptions    = '--nv'
+    singularity.runOptions  = '--nv'
+  }
+}
+
+// trace file and reports
+report {
+  enabled   = true
+  overwrite = true
+}
+trace {
+  enabled   = true
+  overwrite = true
 }
 
 // Capture exit codes from upstream processes when piping

subworkflows/parse_samplesheet/main.nf

@@ -3,57 +3,75 @@
 // -------------------------------------------------------
 def validateSamplesheet(samplesheet_ch) {
     samplesheet_ch.map { path ->
-        def header = path.text.readLines()[0]
-        def cols = header.split(/,|\t/)  // handle CSV or TSV
+        def sep = path.name.endsWith('.tsv') ? '\t' : ','
 
+        def lines = path.text.readLines()
+        if (!lines) error "Samplesheet is empty: ${path}"
+
+        def header = lines[0].split(sep).collect { colname -> colname.trim() }
         def required = ['sample_name','pair_identifier','tumor_bam','normal_bam']
-        def missing = required.findAll { it !in cols }
+        def missing = required.findAll { colname -> colname !in header }
         if (missing) {
             error "Samplesheet is missing required columns: ${missing.join(', ')}"
         }
 
         // Optional: check BAM files exist
-        path.text.readLines().tail().each { line ->
-            def vals = line.split(/,|\t/)
+        lines.tail().eachWithIndex { line, idx ->
+            def vals = line.split(sep).collect { val -> val.trim() }
+            if (vals.size() < 4) error "Line ${idx + 2} is malformed: ${line}"
+
             def tumor = file(vals[2])
             def normal = file(vals[3])
 
-            if (!tumor.exists()) error "Tumor BAM missing: $tumor"
-            if (!normal.exists()) error "Normal BAM missing: $normal"
+            if (!tumor.exists()) error "Tumor BAM missing: ${tumor}"
+            if (!normal.exists()) error "Normal BAM missing: ${normal}"
         }
+
+        return [path, sep]  // pass separator for downstream use
     }
 }
-    
+
 
 workflow PARSE_SAMPLESHEET {
 
     take:
-    ch_samplesheet // channel ["path-to-samplesheet"]
+    ch_samplesheet  // channel ["path-to-samplesheet"]
 
     main:
 
     validateSamplesheet(ch_samplesheet)
     log.info "[INFO] Samplesheet validated"
 
-    def sep = ch_samplesheet_file.name.endsWith('.tsv') ? '\t' : ','
+    def sep = params.samplesheet.endsWith('.tsv') ? '\t' : ','
     ch_samplesheet
         .splitCsv(header: true, sep: sep)
         .map { row ->
 
-            def tumorPath = row.tumor_bam.trim()
-            def normalPath = row.normal_bam.trim()
+    // Validate samplesheet
+    def validated_ch = validateSamplesheet(ch_samplesheet)
+    log.info "[INFO] Samplesheet validated"
 
-            // get file object
-            def tumorFile = file(tumorPath)
-            def normalFile = file(normalPath)
+    // Split samplesheet into sample info
+    validated_ch
+        .map { path, sep ->
+            path.text.readLines().tail().collect { line ->
+                def vals = line.split(sep).collect { val -> val.trim() }
 
-            tuple(row.sample_name, row.pair_identifier, tumorFile, normalFile)
+                tuple(
+                    vals[0],                     // sample_name
+                    vals[1],                     // pair_identifier
+                    file(vals[2]),               // tumor_bam
+                    file(vals[3])                // normal_bam
+                )
+            }
         }
+        .flatten()
         .set { sample_info_ch }
 
 
     emit:
 
+    emit:
     ch_samples = sample_info_ch
 
 }

variantmedium.sh

@@ -287,6 +287,7 @@ CMD=(nextflow run tron-bioinformatics/VariantMedium
     --samplesheet "${SAMPLESHEET}"
     --outdir "${OUTDIR}"
     --execution_step "${PIPELINE_STEP}"
+    -work-dir "${OUTDIR}/nxfwork"
 )
 # add report/trace args if requested
 CMD+=("${REPORT_ARGS[@]}")
@@ -312,6 +313,7 @@ else
         --samplesheet "${SAMPLESHEET}"
         --outdir "${OUTDIR}"
         --execution_step "${PIPELINE_STEP}"
+        -work-dir "${OUTDIR}/nxfwork"
     )
     CMD+=("${REPORT_ARGS[@]}")
     [[ -n "$MOUNT_PATH" ]] && CMD+=(--mount_path "${MOUNT_PATH}")
@@ -329,7 +331,7 @@ else
     readarray -t REPORT_ARGS < <(generate_nf_report "$PIPELINE_STEP")
 
     CMD=(nextflow run tron-bioinformatics/tronflow-bam-preprocessing
-        -r v2.1.0
+        -r v2.2.2
         -profile "${PROFILE}"
         --input_files "${TSV_FOLDER}/preproc.tsv"
         --reference "${REF}"
@@ -339,6 +341,7 @@ else
         --output "${OUTDIR}/output_01_01_preprocessed_bams"
         --skip_deduplication
         --skip_metrics
+        -work-dir "${OUTDIR}/nxfwork"
     )
     CMD+=("${REPORT_ARGS[@]}")
 
@@ -363,11 +366,12 @@ else
     [[ -f "$EXOME_BED" ]] && INTERVALS_PARAM=(--intervals "$EXOME_BED")
 
     CMD=(nextflow run tron-bioinformatics/tronflow-strelka2
+        -r v0.2.4
         -profile "${PROFILE}"
         --input_files "${TSV_FOLDER}/pairs_wo_reps.tsv"
         --reference "${REF}"
         --output "${OUTDIR}/output_01_02_candidates_strelka2"
-        -r v0.2.4
+        -work-dir "${OUTDIR}/nxfwork"
     )
     CMD+=("${REPORT_ARGS[@]}")
 
@@ -394,12 +398,13 @@ else
     readarray -t REPORT_ARGS < <(generate_nf_report "$PIPELINE_STEP")
 
     CMD=(nextflow run tron-bioinformatics/tronflow-vcf-postprocessing
-        -r v3.1.2
+        -r v3.1.4
         -profile "${PROFILE}"
         --input_vcfs "${TSV_FOLDER}/vcfs.tsv"
         --input_bams "${TSV_FOLDER}/bams.tsv"
         --reference "${REF}"
         --output "${OUTDIR}/output_01_03_vcf_postprocessing"
+        -work-dir "${OUTDIR}/nxfwork"
     )
     CMD+=("${REPORT_ARGS[@]}")
 
@@ -425,6 +430,7 @@ else
         --samplesheet "${SAMPLESHEET}"
         --outdir "${OUTDIR}"
         --execution_step "${PIPELINE_STEP}"
+        -work-dir "${OUTDIR}/nxfwork"
     )
     CMD+=("${REPORT_ARGS[@]}")
     [[ -n "$RESUME" ]] && CMD+=("$RESUME")
@@ -452,6 +458,7 @@ else
         --read_length 50
         --max_mapq 60
         --max_baseq 82
+        -work-dir "${OUTDIR}/nxfwork"
     )
     CMD+=("${REPORT_ARGS[@]}")
 
@@ -474,11 +481,12 @@ CMD=(nextflow run tron-bioinformatics/VariantMedium
     --samplesheet "${SAMPLESHEET}"
     --outdir "${OUTDIR}"
     --execution_step "${PIPELINE_STEP}"
+    -work-dir "${OUTDIR}/nxfwork"
 )
 CMD+=("${REPORT_ARGS[@]}")
 [[ -n "$RESUME" ]] && CMD+=("$RESUME")
 [[ -n "$MOUNT_PATH" ]] && CMD+=(--mount_path "${MOUNT_PATH}")
 run_step "3D DenseNet SNV/Indel calling" "${CMD[@]}"
 #---------------------------------------
 log "🎉 Pipeline completed successfully!"
-#---------------------------------------
+#---------------------------------------