possible fix for name collisions

modules/multiqc/main.nf

@@ -7,7 +7,7 @@ process MULTIQC {
         'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
 
     input:
-    path multiqc_files
+    path "??/*"
 
     output:
     path "*multiqc_report.html", emit: report

tests/modules/multiqc/main.nf

@@ -2,15 +2,30 @@
 
 nextflow.enable.dsl = 2
 
-include { FASTQC  } from '../../../modules/fastqc/main.nf'
-include { MULTIQC } from '../../../modules/multiqc/main.nf'
+include { FASTQC            } from '../../../modules/fastqc/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 ],
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                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] } )
 }
+
+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
-  command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
+- name: multiqc test_multiqc
+  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: