Merge branch 'master' into haplocheck

modules/bcftools/roh/main.nf

@@ -9,7 +9,7 @@ process BCFTOOLS_ROH {
 
     input:
     tuple val(meta), path(vcf), path(tbi)
-    path af_file
+    tuple path(af_file), path(af_file_tbi)
     path genetic_map
     path regions_file
     path samples_file

modules/bcftools/roh/meta.yml

@@ -23,6 +23,9 @@ input:
   - af_file:
       type: file
       description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF."
+  - af_file_tbi:
+      type: file
+      description: "tbi index of af_file."
   - genetic_map:
       type: file
       description: "Genetic map in the format required also by IMPUTE2."

modules/multiqc/main.nf

@@ -7,7 +7,8 @@ process MULTIQC {
         'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
 
     input:
-    path multiqc_files
+    path  multiqc_files, stageAs: "?/*"
+    tuple path(multiqc_config), path(multiqc_logo)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -20,8 +21,13 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def config = multiqc_config ? "--config $multiqc_config" : ''
     """
-    multiqc -f $args .
+    multiqc \\
+        --force \\
+        $config \\
+        $args \\
+        .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/multiqc/meta.yml

@@ -17,6 +17,14 @@ input:
       type: file
       description: |
         List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - multiqc_config:
+      type: file
+      description: Config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - multiqc_logo:
+      type: file
+      description: Logo file for MultiQC
+      pattern: "*.{png}"
 output:
   - report:
       type: file

tests/modules/bcftools/roh/main.nf

@@ -10,7 +10,7 @@ workflow test_bcftools_roh {
              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
              file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
 
-    af_file = []
+    af_file = [[],[]]
     gen_map = []
     regions = []
     targets = []
@@ -25,7 +25,7 @@ workflow test_bcftools_roh_stub {
              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
              file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
 
-    af_file = []
+    af_file = [[],[]]
     gen_map = []
     regions = []
     targets = []

tests/modules/multiqc/main.nf

@@ -2,15 +2,32 @@
 
 nextflow.enable.dsl = 2
 
-include { FASTQC  } from '../../../modules/fastqc/main.nf'
+include { FASTQC            } from '../../../modules/fastqc/main.nf'
-include { MULTIQC } from '../../../modules/multiqc/main.nf'
+include { FASTQC as FASTQC2 } from '../../../modules/fastqc/main.nf'
+include { MULTIQC           } from '../../../modules/multiqc/main.nf'
 
 workflow test_multiqc {
-    input = [ [ id: 'test', single_end: false ],
+    input = [
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        [ id: 'test', single_end: false ],
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-            ]
+    ]
 
     FASTQC  ( input )
-    MULTIQC ( FASTQC.out.zip.collect { it[1] } )
+    MULTIQC ( FASTQC.out.zip.collect { it[1] }, [[],[]] )
+}
+
+workflow test_multiqc_fn_collision {
+    fqc_input = [
+        [ id: 'test', single_end: false ],
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+    ]
+    mqc_input = Channel.empty()
+
+    FASTQC  ( fqc_input  )
+    mqc_input = mqc_input.mix(FASTQC.out.zip.collect { it[1] })
+
+    FASTQC2  ( fqc_input )
+    mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] })
+
+    MULTIQC ( mqc_input, [[],[]] )
 }

tests/modules/multiqc/nextflow.config

@@ -1,5 +1,7 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+    withName: "FASTQC*" {
+         publishDir = [ enabled: false ]
+     }
 }

tests/modules/multiqc/test.yml

@@ -1,5 +1,12 @@
-- name: multiqc
+- name: multiqc test_multiqc
-  command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
+  command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config  -c ./tests/modules/multiqc/nextflow.config
+  tags:
+    - multiqc
+  files:
+    - path: output/multiqc/multiqc_report.html
+
+- name: multiqc test_multiqc_fn_collision
+  command: nextflow run ./tests/modules/multiqc -entry test_multiqc_fn_collision -c ./tests/config/nextflow.config  -c ./tests/modules/multiqc/nextflow.config
   tags:
     - multiqc
   files: