🚀 bcftools_markdup, bcftools_stats, fastqc, minimap2_align, picard_ma…

…rkduplicates, pilon
lmtani · Mar 30, 2024 · ff0f008 · ff0f008
1 parent 1ea673a
commit ff0f008
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Showing 6 changed files with 187 additions and 4 deletions.
diff --git a/tasks/bcftools/bcftools_markdup.wdl b/tasks/bcftools/bcftools_markdup.wdl
@@ -0,0 +1,42 @@
+version 1.0
+
+
+task Markdup {
+    input{
+        File vcf
+        String extra_args = "-m-any"
+        Boolean stub = false
+    }
+
+    String outname = basename(vcf, ".vcf.gz")
+
+    command <<<
+        set -e
+
+        bcftools --version | grep bcftools > version.txt
+
+        if [ ~{stub} == "true" ]; then
+            echo "Stubbing out Norm"
+            touch ~{outname}.norm.vcf.gz
+            touch ~{outname}.norm.vcf.gz.tbi
+            exit 0
+        fi
+
+        bcftools norm ~{extra_args} ~{vcf} -Oz -o ~{outname}.norm.vcf.gz
+        bcftools index --tbi ~{outname}.norm.vcf.gz
+    >>>
+
+    runtime {
+        docker: "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        memory: "2 GB"
+        cpu: 1
+        preemptible: 3
+        disks: "local-disk 15 SSD"
+    }
+
+    output {
+        File norm_vcf = "~{outname}.norm.vcf.gz"
+        File norm_vcf_index = "~{outname}.norm.vcf.gz.tbi"
+        File version = "version.txt"
+    }
+}
diff --git a/tasks/bcftools/bcftools_stats.wdl b/tasks/bcftools/bcftools_stats.wdl
@@ -0,0 +1,35 @@
+version 1.0
+
+
+task Stats {
+    input {
+        File vcf
+        File? exons
+        File? fasta
+        File? fasta_idx
+        Boolean stub = false
+    }
+
+    String basename = basename(vcf, ".vcf.gz")
+
+    command <<<
+        set -e
+        bcftools --version | grep bcftools > version.txt
+        if [ ~{stub} == "true" ]; then
+            echo "Stubbing out the task"
+            touch ~{basename}.stats
+            exit 0
+        fi
+
+        bcftools stats ~{"--exons " + exons} ~{"--fasta-ref " + fasta} ~{vcf} > ~{basename}.stats
+    >>>
+
+    runtime {
+        docker: "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+    }
+
+    output {
+        File stats = "~{basename}.stats"
+        File version = "version.txt"
+    }
+}
diff --git a/tasks/fastqc/fastqc.wdl b/tasks/fastqc/fastqc.wdl
@@ -0,0 +1,36 @@
+version 1.0
+
+task FastQC {
+    input {
+        Array[File] input_files
+        Int threads = 2
+        Boolean stub = false
+    }
+
+    Int memory = threads * 250  # 250MB per thread, as per FastQC documentation
+
+    command <<<
+        set -e
+        mkdir -p outputs
+
+        fastqc --version > version.txt
+        if [ ~{stub} == "true" ]; then
+            touch outputs/fastqc_report.zip
+            exit 0
+        fi
+
+
+        fastqc -t ~{threads} -o outputs ~{sep = ' ' input_files}
+    >>>
+
+    runtime {
+        docker: "quay.io/biocontainers/fastqc:0.11.9--0"
+        cpu: threads
+        memory: "~{memory} MB"
+    }
+
+    output {
+        Array[File] zip_files = glob("outputs/*.zip")
+        File version = "version.txt"
+    }
+}
diff --git a/tasks/minimap2/align.wdl b/tasks/minimap2/align.wdl
@@ -11,6 +11,7 @@ task Minimap2Align {
         String sample_id
         String technology
         String library
+        String prefix
 
         Boolean stub = false
     }
@@ -19,12 +20,10 @@ task Minimap2Align {
     Int memory = cpus * 2
     Int disk_size = ceil(size(reads_tar, "GiB") * 8 + size(reference_mmi, "GiB") + 10)
 
-    String prefix = basename(basename(reads_tar, ".gz"), ".tar")
 
     command <<<
 
         minimap2 --version > version.txt
-
         if [ ~{stub} == "true" ]; then
             touch ~{prefix}.sam
             exit 0

diff --git a/tasks/picard/markduplicates.wdl b/tasks/picard/markduplicates.wdl
@@ -26,8 +26,8 @@ task MarkDuplicates {
     java -Xmx4000m -jar /usr/gitc/picard.jar \
       MarkDuplicates \
       INPUT=~{sep=" INPUT="  input_bams} \
-      OUTPUT=~{output_bam_basename}_metrics.txt \
-      METRICS_FILE={} \
+      OUTPUT=~{output_bam_basename}.bam \
+      METRICS_FILE=~{output_bam_basename}_metrics.txt \
       VALIDATION_STRINGENCY=SILENT \
       OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 \
       CREATE_MD5_FILE=true

diff --git a/tasks/pilon/pilon.wdl b/tasks/pilon/pilon.wdl
@@ -0,0 +1,71 @@
+version 1.0
+
+task Pilon {
+    input {
+        File alignment
+        File alignment_index
+        File draft_sequence
+
+        Boolean stub = false
+    }
+
+    command <<<
+
+        pilon --version > version.txt
+        if [ ~{stub} == "true" ]; then
+            mkdir pilon
+            touch pilon/pilon.changes \
+                  pilon/pilon.vcf \
+                  pilon/pilonPilon.bed \
+                  pilon/pilonCoverage.wig \
+                  pilon/pilonDipCoverage.wig \
+                  pilon/pilonDeltaCoverage.wig \
+                  pilon/pilonBadCoverage.wig \
+                  pilon/pilonPctBad.wig \
+                  pilon/pilonClippedAlignments.wig \
+                  pilon/pilonGC.wig \
+                  pilon/pilonWeightedMq.wig \
+                  pilon/pilonWeightedQual.wig \
+                  pilon/pilonPhysicalCoverage.wig \
+                  pilon/pilonCopyNumber.wig \
+                  pilon/pilonUnconfirmed.wig \
+                  pilon/pilon.fasta
+            exit 0
+        fi
+
+        pilon --genome ~{draft_sequence} \
+              --bam ~{alignment} \
+              --output pilon \
+              --outdir pilon \
+              --changes --vcf --tracks \
+              --fix all \
+              --mindepth 0.5 \
+              --minmq 30 \
+              --minqual 20 \
+              --threads 8
+    >>>
+
+    runtime {
+        docker: "quay.io/biocontainers/pilon:1.24--hdfd78af_0"
+    }
+
+    output {
+        File pilon_changes = "pilon/pilon.changes"
+        File pilon_vcf = "pilon/pilon.vcf"
+        File pilon_tracks = "pilon/pilonPilon.bed"
+        File pilon_coverage = "pilon/pilonCoverage.wig"
+        File pilon_dip_coverage = "pilon/pilonDipCoverage.wig"
+        File pilon_delta_coverage = "pilon/pilonDeltaCoverage.wig"
+        File pilon_bad_coverage = "pilon/pilonBadCoverage.wig"
+        File pilon_pct_bad = "pilon/pilonPctBad.wig"
+        File pilon_clipped_alignments = "pilon/pilonClippedAlignments.wig"
+        File pilon_gc = "pilon/pilonGC.wig"
+        File pilon_weighted_mq = "pilon/pilonWeightedMq.wig"
+        File pilon_weighted_qual = "pilon/pilonWeightedQual.wig"
+        File pilon_physical_coverage = "pilon/pilonPhysicalCoverage.wig"
+        File pilon_copy_number = "pilon/pilonCopyNumber.wig"
+        File pilon_unconfirmed = "pilon/pilonUnconfirmed.wig"
+        File pilon_fasta = "pilon/pilon.fasta"
+        File version = "version.txt"
+    }
+}