test mageck mle w/ demo data

.gitignore

@@ -41,3 +41,6 @@ results/
 # code editors
 .vscode/
 *.code-workspace
+
+# user-specific dev files
+*KLS*

conf/ci_stub.config

@@ -5,6 +5,7 @@ params {
     input = 'tests/assets/samplesheet.csv' // adapted from https://github.com/nf-core/test-datasets/blob/chipseq/samplesheet/v2.0/samplesheet_test.csv
     library = 'assets/lib/yusa_library.csv'
     outdir = 'results/test'
+    design_matrix = 'tests/data/designmat.txt'
 
     max_cpus = 2        // for GitHub Actions https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
     max_memory = '6.GB'

conf/test_mle.config

@@ -0,0 +1,21 @@
+params {
+    config_profile_name = 'Test dataset for MAGECK_MLE'
+    config_profile_description = 'Minimal test dataset for MAGECK_MLE only on biowulf'
+
+    input = 'assets/samplesheet_test_mle.csv'
+    library = 'assets/lib/yusa_library.csv'
+    outdir = 'results/test_mle'
+    exp_name = 'leukemia'
+
+    count_table   = '/data/CCBR_Pipeliner/testdata/CRUISE/leukemia.new.csv'
+    design_matrix = '/data/CCBR_Pipeliner/testdata/CRUISE/designmat.txt'
+
+    mageck.run = true
+    drugz.run = false
+    bagel.run = false
+
+    max_cpus = 32
+}
+dag {
+    enabled = false
+}

modules/local/mageck.nf

@@ -65,6 +65,7 @@ process TEST {
 
 process MLE {
     label 'mageck'
+    label 'process_higher'
     container 'quay.io/biocontainers/mageck:0.5.9.5--py39h1f90b4d_3'
 
     input:
@@ -77,10 +78,12 @@ process MLE {
 
     script:
     """
+    export OMP_NUM_THREADS=${task.cpus}
     mageck mle \\
       -k ${count} \\
       -d ${design} \\
-      -n ${count.getBaseName(2)}
+      -n ${count.getBaseName(2)} \\
+      --threads ${task.cpus}
     """
 
     stub:

nextflow.config

@@ -66,6 +66,9 @@ profiles {
     test {
         includeConfig "conf/test.config"
     }
+    test_mle {
+        includeConfig "conf/test_mle.config"
+    }
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container

tests/data/designmat.txt

@@ -0,0 +1,5 @@
+Samples        baseline        HL60        KBM7
+HL60.initial   1               0           0
+KBM7.initial   1               0           0
+HL60.final     1               1           0
+KBM7.final     1               0           1