Merge pull request #69 from rki-mf1/replacing_static_PBSIM3

Replacing static pbsim3
rki-mf1 · Aug 23, 2024 · 0bbf22e · 0bbf22e
2 parents b802523 + 1f1c999
commit 0bbf22e
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/bin/pbsim b/bin/pbsim
diff --git a/modules/pbsim/main.nf b/modules/pbsim/main.nf
@@ -6,6 +6,8 @@ process PBSIM {
     // Store results
     publishDir "${params.outdir}", mode: 'copy', pattern: "simulated_hap${sample}.ONTWGS*.fastq"
 
+    conda "bioconda::pbsim3=3.0.4"
+
     // Process I/O
     input:
     tuple val(sample), path(fasta)
@@ -17,7 +19,7 @@ process PBSIM {
     script:
     unique_seed = (params.seed * sample) % 2147483647       // that's (2^31)-1, the upper bound for mason
     """
-    ${projectDir}/${params.pbsim_bin} \
+    pbsim \
         --seed         ${unique_seed} \
         --strategy     ${params.pbsim_strategy} \
         --prefix       simulated_hap${sample}.ONTWGS \

diff --git a/nextflow.config b/nextflow.config
@@ -35,7 +35,6 @@ params {
     nb_reads        = 10000
 
     // PBSIM Oxford Nanopore (WGS) - Read simulation parameters
-    pbsim_bin         = 'bin/pbsim'
     pbsim_method      = 'qshmm'
     pbsim_model       = 'aux/pbsim_model/QSHMM-ONT-HQ.model'
     pbsim_depth       = 500