Merge pull request #1 from theiagen/im-v1.2.0-dev

Update HMAS-wdl to v1.2.0
theiagen · Dec 10, 2024 · d5c860b · d5c860b
2 parents f2aac20 + 0014cd0
commit d5c860b
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Showing 3 changed files with 14 additions and 13 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -9,8 +9,7 @@ WORKDIR /
 
 # Version arguments
 # ARG variables only persist during build time
-# using latest release from 2023/06/20
-ARG HMAS_VERSION="1.0.0"
+ARG HMAS_VERSION="1.2.0"
 ARG HMAS_SRC_URL=https://github.com/ncezid-biome/HMAS-QC-Pipeline2/archive/refs/tags/v${HMAS_VERSION}.zip
 
 # metadata labels
@@ -53,6 +52,8 @@ RUN mamba create -y --name hmas -c conda-forge -c bioconda -c defaults \
     cutadapt=3.5 \
     pear \
     vsearch=2.22.1 \
+    multiqc=1.21 \
+    fastqc=0.12.1 \
     nextflow=22.10.6 && \
     mamba clean -a -y
 

diff --git a/tasks/task_hmas.wdl b/tasks/task_hmas.wdl
@@ -5,10 +5,10 @@ task hmas {
     Array[File] read1
     Array[File] read2
     File primers
-    String docker="us-docker.pkg.dev/general-theiagen/internal/hmas:1.0.0"
-    Int memory = 32
-    Int cpu = 12
-    Int disk_size = 500
+    String docker="us-docker.pkg.dev/general-theiagen/internal/hmas:1.2.0"
+    Int memory = 24
+    Int cpu = 8
+    Int disk_size = 100
   }
   command <<<
     date | tee DATE
@@ -30,16 +30,16 @@ task hmas {
     cp -r /HMAS-QC-Pipeline2/* ./
 
     # Run nextflow
-    nextflow run hmas2.nf --outdir OUT --reads reads --primer ~{primers}
+    nextflow run hmas2.nf --outdir OUT --reads reads --primer ~{primers} 
 
   >>>
   output {
     String hmas_docker = docker
     String analysis_date = read_string("DATE")
     File hmas_report = "OUT/report.csv"
-    Array[File] hmas_clean_read1 = glob("OUT/*/temp/*.1.fastq")
-    Array[File] hmas_clean_read2 = glob("OUT/*/temp/*.2.fastq")
-    Array[File] hmas_consensus_fasta = glob("OUT/*/*final.unique.fasta")
+    File hmas_multiqc_html = "OUT/multiqc_report.html"
+    File hmas_mqc_yaml = "OUT/report_mqc.yaml"
+    Array[File] hmas_final_fasta = glob("OUT/*/*final.unique.fasta")
   }
   runtime {
     docker: "~{docker}"

diff --git a/workflows/hmas.wdl b/workflows/hmas.wdl
@@ -19,9 +19,9 @@ workflow hmas_wf {
   }
   output {
     File hmas_report = hmas.hmas_report
-    Array[File] hmas_clean_read1 = hmas.hmas_clean_read1
-    Array[File] hmas_clean_read2 = hmas.hmas_clean_read2
-    Array[File] hmas_consensus_fasta = hmas.hmas_consensus_fasta
+    File hmas_multiqc_html = hmas.hmas_multiqc_html
+    File hmas_mqc_yaml = hmas.hmas_mqc_yaml
+    Array[File] hmas_final_fasta = hmas.hmas_final_fasta
     String hmas_docker = hmas.hmas_docker
     String analysis_date = hmas.analysis_date
   }