Reduce the number of parameters to the workflow.

Use SLURM_CPUS_PER_NODE for number of threads to use to dynamically scale
better.

Author: viklund

main.nf

@@ -89,7 +89,7 @@ process manta {
     """
     configManta.py --normalBam bamfile --referenceFasta $params.ref_fasta --runDir testRun
     cd testRun
-    ./runWorkflow.py -m local -j $params.threads
+    ./runWorkflow.py -m local -j \$SLURM_CPUS_PER_NODE
     mv results/variants/diploidSV.vcf.gz ../manta.vcf.gz
     cd ..
     gunzip -c manta.vcf.gz > manta.vcf
@@ -155,9 +155,9 @@ process fermikit {
 
     script:
     """
-    fermi2.pl unitig -s$params.genome_size -t$params.threads -l$params.readlen -p sample sample.fq.gz > sample.mak
+    fermi2.pl unitig -s3g -t\$SLURM_CPUS_PER_NODE -l150 -p sample sample.fq.gz > sample.mak
     make -f sample.mak
-    run-calling -t$params.threads $params.ref_fasta sample.mag.gz > calling.sh
+    run-calling -t\$SLURM_CPUS_PER_NODE $params.ref_fasta sample.mag.gz > calling.sh
     bash calling.sh
     vcf-sort -c sample.sv.vcf.gz > fermikit.vcf
     bgzip -c fermikit.vcf > fermikit.vcf.gz

nextflow.config

@@ -3,6 +3,8 @@ params {
     project = "" // Set project or supply on commandline ( --project )
     outdir = "results"
 
+    ref_fasta = "/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37/human_g1k_v37.fasta"
+
     // Modules and their versions on the HPC-system
     modules {
         samtools = 'samtools/0.1.19'
@@ -15,16 +17,6 @@ params {
         snpeff = "snpEff/4.2"
     }
 
-    // Caller specific options
-    threads = 16
-    genome_size = "3g"
-    readlen = 150
-    ref_fasta = "/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37/human_g1k_v37.fasta"
-
-    vep {
-        assembly = "GRCh37"
-    }
-
     runtime {
         simple = '30m'    // Short simple shell jobs
         fermikit = '24h' // Fermikit is the longest running of them all