Merge pull request #10 from CCBR/drugz

feat: drugZ

CHANGELOG.md

@@ -6,6 +6,7 @@
 - Run mageck subcommands: count, test, and mle. (#9)
   - `mageck count` only runs if a count table **isn't** given.
   - `mageck mle` only runs if a design matrix **is** given.
+- Optional: run drugZ. (#10)
 
 <!--
 ## CRUISE v0.1.0

conf/modules.config

@@ -33,15 +33,15 @@ process {
     withName: 'MAGECK.*' {
         container = 'quay.io/biocontainers/mageck:0.5.9.5--py39h1f90b4d_3'
     }
+    withName: 'DRUGZ.*' {
+        container = 'nciccbr/cruise_drugz:0.1.0'
+    }
     /*
     withName: 'VISPR.*' {
         container = 'quay.io/biocontainers/mageck-vispr:0.5.6--py_0'
     }
     withName: 'BAGEL.*' {
         container = 'nciccbr/cruise_bagel_2.0:0.1.0'
     }
-    withName: 'DRUGZ.*' {
-        container = 'nciccbr/cruise_drugz:0.1.0'
-    }
     */
 }

conf/test.config

@@ -11,6 +11,10 @@ params {
     max_time   = '12.h'
 
     publish_dir_mode = 'symlink'
+
+    drugz.remove_genes = 'LacZ,luciferase,EGFR'
+    drugz.half_window_size = 5
+
 }
 dag {
     enabled = true

main.nf

@@ -21,6 +21,9 @@ include { INPUT_CHECK } from './submodules/local/input_check.nf'
 include { TRIM_ALIGN  } from './submodules/local/trim_align.nf'
 include { MAGECK      } from './submodules/local/mageck.nf'
 
+// MODULES
+include { DRUGZ } from "./modules/local/drugz.nf"
+
 workflow CRUISE {
     INPUT_CHECK(file(params.input))
     INPUT_CHECK.out
@@ -40,10 +43,14 @@ workflow CRUISE {
         ctrl: meta.treat_or_ctrl == 'control'
             return meta.id
       }
-      .set { treatments }
-
-    MAGECK(ch_count, treatments.treat.collect(), treatments.ctrl.collect())
+      .set { treat_meta }
+    treat = treat_meta.treat.collect()
+    control = treat_meta.ctrl.collect()
+    MAGECK(ch_count, treat, control)
 
+    if (params.drugz.run) {
+        DRUGZ(ch_count, treat, control)
+    }
 }
 
 workflow {

modules/local/drugz.nf

@@ -1,11 +1,31 @@
 
 process DRUGZ {
+
+    input:
+        path(count)
+        val(treatment)
+        val(control)
+
     output:
-        path("output.txt")
+        path("*output.txt"), emit: txt
+        path("*foldchange.txt"), emit: fc
 
     script:
     """
-    uname -a >> output.txt
-    which drugz.py >> output.txt
+    drugz.py \\
+      -i ${count} \\
+      -o ${count.getBaseName(2)}.output.txt \\
+      -f ${count.getBaseName(2)}.foldchange.txt \\
+      -c ${control.join(',')} \\
+      -x ${treatment.join(',')} \\
+      -r ${params.drugz.remove_genes} \\
+      --half_window_size ${params.drugz.half_window_size}
+    """
+
+    stub:
+    """
+    for ext in output foldchange; do
+        touch ${count.getBaseName(2)}.\$ext.txt
+    done
     """
 }

nextflow.config

@@ -19,6 +19,12 @@ params {
         trailingquality = 10
     }
 
+    drugz {
+        run = true
+        remove_genes = null
+        half_window_size = 500 // same as default in drugZ https://github.com/hart-lab/drugz/blob/eb15d34e4dd172965e618d5bb662c053066da799/drugz.py#L305-L306
+    }
+
 }
 
 includeConfig 'conf/base.config'