Merge remote-tracking branch 'nf-core/master'

modules/seacr/callpeak/main.nf

@@ -13,29 +13,30 @@ process SEACR_CALLPEAK {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.29.2" : null)
+    conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0"
     } else {
-        container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0'
+        container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0'
     }
 
     input:
     tuple val(meta), path(bedgraph), path(ctrlbedgraph)
+    val (threshold)
 
     output:
     tuple val(meta), path("*.bed"), emit: bed
     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 function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold"
     """
     SEACR_1.3.sh \\
         $bedgraph \\
-        $ctrlbedgraph \\
+        $function_switch \\
         $options.args \\
         $prefix
-
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo $VERSION)

modules/seacr/callpeak/meta.yml

@@ -1,3 +1,4 @@
+
 name: seacr_callpeak
 description: Call peaks using SEACR on sequenced reads in bedgraph format
 keywords:
@@ -30,6 +31,10 @@ input:
         type: file
         description: |
             Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
+    - threshold:
+        type: value
+        description: |
+            Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph
 output:
     - meta:
         type: map

tests/config/test_data.config

@@ -200,6 +200,9 @@ params {
 
                 test_yak                                      = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
                 test2_yak                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
+
+                cutandrun_bedgraph_test_1                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
+                cutandrun_bedgraph_test_2                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
             }
             'pacbio' {
                 primers                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"

tests/modules/seacr/callpeak/main.nf

@@ -5,11 +5,19 @@ nextflow.enable.dsl = 2
 include { SEACR_CALLPEAK } from '../../../../modules/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
 
 workflow test_seacr_callpeak {
-    input = [
+    input = [ [ id:'test_1'],
-        [ id:'test_1'],
+              file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_1'], checkIfExists: true),
-        file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_2'], checkIfExists: true) 
-        file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true)
+            ]
-    ]
 
-    SEACR_CALLPEAK ( input )
+    SEACR_CALLPEAK ( input, 0.05 )
+}
+
+workflow test_seacr_callpeak_threshold {
+    input = [ [ id:'test_1'],
+              file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_1'], checkIfExists: true),
+              []
+            ]
+
+    SEACR_CALLPEAK ( input, 0.05 )
 }

tests/modules/seacr/callpeak/test.yml

@@ -5,4 +5,13 @@
     - seacr/callpeak
   files:
     - path: output/seacr/test_1.stringent.bed
-      md5sum: 3ac70475669eb6a7b8ca89e19a08a28e
+      md5sum: a3cb0c7c4ffa895788da3f0d6371b7df
+
+- name: seacr callpeak threshold
+  command: nextflow run ./tests/modules/seacr/callpeak -entry test_seacr_callpeak_threshold -c tests/config/nextflow.config
+  tags:
+    - seacr
+    - seacr/callpeak
+  files:
+    - path: output/seacr/test_1.stringent.bed
+      md5sum: 1d23015c7087f7b48cc3139d53fd3463