fix: use fastqc & multiqc containers

CCBR · Apr 12, 2024 · 5664d0a · 5664d0a
1 parent 9fcb3ee
commit 5664d0a
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -121,7 +121,9 @@ containers:
   clear: "docker://nciccbr/ccbr_clear:latest"
   cutadapt: 'nciccbr/ncigb_cutadapt_v1.18:latest'
   dcc: "docker://nciccbr/charlie_dcc:v0.1.0"
+  fastqc: 'nciccbr/ccrgb_qctools:v4.0'
   mapsplice: "docker://cgrlab/mapsplice2:latest"
+  multiqc: 'nciccbr/ccbr_multiqc_1.15:v1'
   nclscan: "docker://nciccbr/charlie_nclscan:v0.1.0"
   picard: 'docker://nciccbr/ccbr_picard_2.27.5:v1'
   R: 'docker://nciccbr/ccbr_r_4.3.0:v1'

diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -33,8 +33,7 @@ rule fastqc:
     params:
         outdir=join(WORKDIR, "qc", "fastqc"),
     threads: getthreads("fastqc")
-    envmodules:
-        TOOLS["fastqc"]["version"],
+    container: config['containers']['fastqc']
     shell:
         """
 set -exo pipefail
@@ -85,8 +84,7 @@ rule multiqc:
         html=join(WORKDIR, "multiqc_report.html"),
     params:
         outdir=WORKDIR,
-    envmodules:
-        TOOLS["multiqc"]["version"],
+    container: config['containers']['multiqc']
     shell:
         """
 cd {params.outdir}