Refactor genrich to avoid params in main (#981)

* Refactor genrich to avoid params in main

* Missed to commit test.yml file

modules/genrich/main.nf

@@ -22,6 +22,10 @@ process GENRICH {
     tuple val(meta), path(treatment_bam)
     path  control_bam
     path  blacklist_bed
+    val   save_pvalues
+    val   save_pileup
+    val   save_bed
+    val   save_duplicates
 
     output:
     tuple val(meta), path("*narrowPeak")                     , emit: peaks
@@ -32,14 +36,14 @@ process GENRICH {
     path "versions.yml"                                      , emit: versions
 
     script:
-    def prefix     = options.suffix              ? "${meta.id}${options.suffix}"   : "${meta.id}"
+    def prefix     = options.suffix ? "${meta.id}${options.suffix}"   : "${meta.id}"
-    def control    = params.control_bam          ? "-c $control_bam"               : ''
+    def control    = control_bam    ? "-c $control_bam"               : ''
-    def pvalues    = params.pvalues              ? "-f ${prefix}.pvalues.bedGraph" : ""
+    def blacklist  = blacklist_bed  ? "-E $blacklist_bed"             : ""
-    def pileup     = params.pileup               ? "-k ${prefix}.pileup.bedGraph"  : ""
+    def pvalues    = save_pvalues   ? "-f ${prefix}.pvalues.bedGraph" : ""
-    def bed        = params.bed                  ? "-b ${prefix}.intervals.bed"    : ""
+    def pileup     = save_pileup    ? "-k ${prefix}.pileup.bedGraph"  : ""
-    def blacklist  = params.blacklist_bed        ? "-E $blacklist_bed"             : ""
+    def bed        = save_bed       ? "-b ${prefix}.intervals.bed"    : ""
     def duplicates = ""
-    if (params.save_duplicates) {
+    if (save_duplicates) {
         if (options.args.contains('-r')) {
             duplicates = "-R ${prefix}.duplicates.txt"
         } else {
@@ -58,7 +62,6 @@ process GENRICH {
         $pileup \\
         $bed \\
         $duplicates \\
-        $blacklist \\
         $control
 
     cat <<-END_VERSIONS > versions.yml

modules/genrich/meta.yml

@@ -15,7 +15,6 @@ tools:
       tool_dev_url: https://github.com/jsh58/Genrich
       doi: ""
       licence: ['MIT']
-
 input:
   - meta:
       type: map
@@ -34,7 +33,18 @@ input:
       type: file
       description: Bed file containing genomic intervals to exclude from the analysis
       pattern: "*.{bed}"
-
+  - save_pvalues:
+      type: boolean
+      description: Create bedgraph-ish file for p/q-values file
+  - save_pileup:
+      type: boolean
+      description: Create bedgraph-ish file for pileups and p-values
+  - save_bed:
+      type: boolean
+      description: Create BED file for reads/fragments/intervals
+  - save_duplicates:
+      type: boolean
+      description: Create PCR duplicates file (only works if -r option is set)
 output:
   - meta:
       type: map
@@ -65,7 +75,6 @@ output:
       type: file
       description: File containing software version
       pattern: "*.{version.txt}"
-
 authors:
   - "@JoseEspinosa"
 

tests/modules/genrich/main.nf

@@ -2,10 +2,10 @@
 
 nextflow.enable.dsl = 2
 
-include { GENRICH } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:false, save_duplicates:false, options: ["args": "-p 0.1"] )
+include { GENRICH } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-p 0.1"] )
-include { GENRICH as GENRICH_BLACKLIST   } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:true, save_duplicates:false, options: ["args": "-p 0.1"] )
+include { GENRICH as GENRICH_CTRL    } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-p 0.9"] )
-include { GENRICH as GENRICH_ALL_OUTPUTS } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: true, pileup:true, bed:true, blacklist_bed:false, save_duplicates:true, options: ["args": "-r -p 0.1"] )
+include { GENRICH as GENRICH_ALL     } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-r -p 0.1"] )
-include { GENRICH as GENRICH_ATACSEQ     } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:false, save_duplicates:false, options: ["args": "-j -p 0.1"] )
+include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-j -p 0.1"] )
 
 workflow test_genrich {
     input     = [ [ id:'test', single_end:false ], // meta map
@@ -13,7 +13,12 @@ workflow test_genrich {
     control   = [ ]
     blacklist = [ ]
 
-    GENRICH ( input, control, blacklist )
+    save_pvalues    = false
+    save_pileup     = false
+    save_bed        = false
+    save_duplicates = false
+
+    GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
 }
 
 workflow test_genrich_ctrl {
@@ -22,7 +27,12 @@ workflow test_genrich_ctrl {
     control   = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
     blacklist = [ ]
 
-    GENRICH ( input, control, blacklist )
+    save_pvalues    = false
+    save_pileup     = false
+    save_bed        = false
+    save_duplicates = false
+
+    GENRICH_CTRL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
 }
 
 workflow test_genrich_all_outputs {
@@ -31,14 +41,39 @@ workflow test_genrich_all_outputs {
     control   = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
     blacklist = [ ]
 
-    GENRICH_ALL_OUTPUTS ( input, control, blacklist )
+    save_pvalues    = true
+    save_pileup     = true
+    save_bed        = true
+    save_duplicates = true
+
+    GENRICH_ALL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+}
+
+workflow test_genrich_blacklist {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
+    control   = [ ]
+    blacklist = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
+
+    save_pvalues    = false
+    save_pileup     = false
+    save_bed        = false
+    save_duplicates = false
+
+    GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
 }
 
 workflow test_genrich_atacseq {
     input     = [ [ id:'test', single_end:false ], // meta map
                   [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
+    control   = [ ]
     blacklist = [ ]
 
-    GENRICH_ATACSEQ ( input, control, blacklist )
+    save_pvalues    = false
+    save_pileup     = false
+    save_bed        = false
+    save_duplicates = false
+
+    GENRICH_ATACSEQ ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
 }
+

tests/modules/genrich/test.yml

@@ -12,7 +12,7 @@
     - genrich
   files:
     - path: output/genrich/test.narrowPeak
-      md5sum: 6afabdd3f691c7c84c66ff8a23984681
+      md5sum: 2fcc392360b317f5ebee88cdbc149e05
 
 - name: genrich test_genrich_all_outputs
   command: nextflow run tests/modules/genrich -entry test_genrich_all_outputs -c tests/config/nextflow.config
@@ -20,15 +20,23 @@
     - genrich
   files:
     - path: output/genrich/test.duplicates.txt
-      md5sum: a92893f905fd8b3751bc6a960fbfe7ba
+      md5sum: 159d557af7c23bc3cfb802d87fa96c34
     - path: output/genrich/test.intervals.bed
-      md5sum: 52edf47e6641c0cc03f9cca7324f7eaa
+      md5sum: 4bea65caa3f4043d703af4b57161112e
     - path: output/genrich/test.narrowPeak
-      md5sum: e45eb7d000387975050c2e85c164e5be
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/genrich/test.pileup.bedGraph
-      md5sum: e4f7fa664cd4ed2cf3a1a3a9eb415e71
+      md5sum: 03e53848de695b5794f32f15b2709203
     - path: output/genrich/test.pvalues.bedGraph
-      md5sum: 564859953704983393d4b7d6317060cd
+      md5sum: b14feef34b6d2379a173a734ca963cde
+
+- name: genrich test_genrich_blacklist
+  command: nextflow run tests/modules/genrich -entry test_genrich_blacklist -c tests/config/nextflow.config
+  tags:
+    - genrich
+  files:
+    - path: output/genrich/test.narrowPeak
+      md5sum: 6afabdd3f691c7c84c66ff8a23984681
 
 - name: genrich test_genrich_atacseq
   command: nextflow run tests/modules/genrich -entry test_genrich_atacseq -c tests/config/nextflow.config