Added thread parameter use in fastqc wrapper (snakemake#117)

* bcftools index * illumina pre.py * Bedtools intersect, slop, merge * cleanup of test results * formatting * Reformatted with black * Update Snakefile * Update Snakefile * added arriba wrapper and black formatted test.py * Moved genome and annotation to input, removed star from dependencies * removed output * removed test output files * wrapper for bcftools reheader * removed duplicates from test.py * added internal bcftools view call to allow changing the output format * Wrapper for downloading snpEff databases * Revert "Update from upstream" This reverts commit c06d165, reversing changes made to 34f09f0. * Added wrapper for downloading snpEff databases * Formatting * Fixed test environment for jannovar + added test for fastq_screen * Updated Strelka wrappers * Formatting * Removed Message * Homer makeTagDirectory, findPeaks, getDifferentialPeaks * Fix shell command getDifferentialPeaks * reformat * Changed snakemake rule names * Fixed error in meta.yaml * Added thread param use in fastqc-wrapper * Added thread param use in fastqc-wrapper Co-authored-by: jafors <[email protected]> Co-authored-by: Johannes Köster <[email protected]>
iromeo · Jun 19, 2020 · 5c11e72 · 5c11e72
1 parent 5c52670
commit 5c11e72
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/bio/fastqc/environment.yaml b/bio/fastqc/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - fastqc ==0.11.8
+  - fastqc ==0.11.9
diff --git a/bio/fastqc/test/Snakefile b/bio/fastqc/test/Snakefile
@@ -7,5 +7,6 @@ rule fastqc:
     params: ""
     log:
         "logs/fastqc/{sample}.log"
+    threads: 1
     wrapper:
         "master/bio/fastqc"
diff --git a/bio/fastqc/wrapper.py b/bio/fastqc/wrapper.py
@@ -29,7 +29,7 @@ def basename_without_ext(file_path):
 # use the same fastqc dir, we create a temp dir.
 with TemporaryDirectory() as tempdir:
     shell(
-        "fastqc {snakemake.params} --quiet "
+        "fastqc {snakemake.params} --quiet -t {snakemake.threads} "
         "--outdir {tempdir} {snakemake.input[0]}"
         " {log}"
     )