Merge pull request #57 from genomic-medicine-sweden/fix-R-error

Update R version in dockerfile
genomic-medicine-sweden · May 28, 2022 · c4edf92 · c4edf92
2 parents 27eb193 + 8b8e50a
commit c4edf92
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Showing 3 changed files with 8 additions and 2 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -13,6 +13,7 @@ params{
     profile = false
     cleanup = true
     scheme = false
+    tmpdir = "~/tmp"
 
     // Repo to download your primer scheme from
     schemeRepoURL = 'https://github.com/genomic-medicine-sweden/gms-artic.git'

diff --git a/environments/illumina/environment.yml b/environments/illumina/environment.yml
@@ -3,6 +3,7 @@ channels:
   - conda-forge
   - bioconda
   - defaults
+  - r
 dependencies:
   - biopython=1.74
   - libxcb
@@ -27,6 +28,7 @@ dependencies:
   - fastqc=0.11.9
   - multiqc=1.11
   - nextclade=1.10.2
+  - r=3.6.0
   - pip:
       - pandas >= 1.1
       - scikit-learn >= 0.23.1

diff --git a/modules/qc.nf b/modules/qc.nf
@@ -48,7 +48,7 @@ process fastqc {
     file "*fastqc*"
 
     """
-    fastqc ${forward} ${reverse} --format fastq --threads ${task.cpus}
+    fastqc ${forward} ${reverse} --format fastq --threads ${task.cpus} --dir ${params.tmpdir}
     """
 }
 
@@ -75,6 +75,8 @@ process statsInsert {
     tag { sampleName }
 
     label 'largemem'
+    errorStrategy 'retry'
+    maxRetries 5
 
     publishDir "${params.outdir}/QCStats/${task.process.replaceAll(":","_")}", pattern: "*.txt", mode: 'copy'
     publishDir "${params.outdir}/QCStats/${task.process.replaceAll(":","_")}", pattern: "*.pdf", mode: 'copy'
@@ -91,7 +93,8 @@ process statsInsert {
     if [[ \$( samtools view -F 12 ${bam} | cut -f1 | sort -T ./tmp | uniq -c | awk '\$1 > 1 { count++ } END { print count }' ) > 0 ]]
     then
        picard CollectInsertSizeMetrics I=${bam} O=${sampleName}_insert_size.metrics.txt \
-       H=${sampleName}_insert_size.distribution.pdf
+       H=${sampleName}_insert_size.distribution.pdf \
+       TMP_DIR=${params.tmpdir}
     else
        echo "Skipping sample ${sampleName} - no usable paired reads"
        touch ${sampleName}_insert_size.metrics.txt