Adding base docker image to all rules

OpenOmics · Jan 25, 2023 · 26fa2a5 · 26fa2a5
1 parent 43c5ebd
commit 26fa2a5
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Showing 3 changed files with 5 additions and 9 deletions.
diff --git a/config/containers.json b/config/containers.json
@@ -1,8 +1,5 @@
 {
     "images": {
-        "fastqc": "docker://nciccbr/ccbr_fastqc_0.11.9:v1.1",
-        "modr": "docker://skchronicles/nanite:v0.1.0",
-        "multiqc": "docker://skchronicles/multiqc:v0.1.0",
-        "nanoplot": "docker://staphb/nanoplot:1.33.0"
+        "modr": "docker://skchronicles/modr:v0.1.0"
     }
 }
diff --git a/workflow/envs/modr.yaml b/workflow/envs/modr.yaml
@@ -7,7 +7,6 @@ channels:
   - anaconda
 dependencies:
  - nanofilt=2.8.0
- - nanoplot=1.38.1
  - minimap2=2.24
  - fastqc=0.11.9
  - nanoplot=1.41.0

diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -17,7 +17,7 @@ rule fastqc_raw:
         rname  = "rawfqc", 
         outdir = join(workpath, "{name}", "fastqc"),
     conda: depending(join(workpath, config['conda']['modr']), use_conda)
-    container: depending(config['images']['fastqc'], use_singularity)
+    container: depending(config['images']['modr'], use_singularity)
     threads: int(allocated("threads", "fastqc_raw", cluster))
     shell: """
     fastqc \\
@@ -44,7 +44,7 @@ rule fastqc_filtered:
         rname  = "filtfqc", 
         outdir = join(workpath, "{name}", "fastqc"),
     conda: depending(join(workpath, config['conda']['modr']), use_conda)
-    container: depending(config['images']['fastqc'], use_singularity)
+    container: depending(config['images']['modr'], use_singularity)
     threads: int(allocated("threads", "fastqc_filtered", cluster))
     shell: """
     fastqc \\
@@ -72,7 +72,7 @@ rule nanoplot:
         rname  = "nanoplot", 
         outdir = join(workpath, "{name}", "nanoplot"),
     conda: depending(join(workpath, config['conda']['modr']), use_conda)
-    container: depending(config['images']['nanoplot'], use_singularity)
+    container: depending(config['images']['modr'], use_singularity)
     threads: int(allocated("threads", "nanoplot", cluster))
     shell: """
     NanoPlot \\
@@ -105,7 +105,7 @@ rule multiqc:
         outdir = join(workpath, "reports"),
         conf   = join(workpath, "resources", "multiqc_config.yaml"),
     conda: depending(join(workpath, config['conda']['modr']), use_conda)
-    container: depending(config['images']['multiqc'], use_singularity)
+    container: depending(config['images']['modr'], use_singularity)
     threads: int(allocated("threads", "mulitqc", cluster))
     shell: """
     multiqc \\