Add new input to multiqc module for use with --rename_samples

modules/nf-core/multiqc/main.nf

@@ -11,6 +11,8 @@ process MULTIQC {
  path(multiqc_config)
  path(extra_multiqc_config)
  path(multiqc_logo)
+ path(replace_names)
+ path(sample_names)
 
  output:
  path "*multiqc_report.html", emit: report
@@ -26,13 +28,17 @@ process MULTIQC {
  def config = multiqc_config ? "--config $multiqc_config" : ''
  def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
  def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+ def replace = replace_names ? "--replace-names ${replace_names}" : ''
+ def samples = sample_names ? "--sample-names ${sample_names}" : ''
  """
  multiqc \\
  --force \\
  $args \\
  $config \\
  $extra_config \\
  $logo \\
+ $replace \\
+ $samples \\
  .
 
  cat <<-END_VERSIONS > versions.yml

modules/nf-core/multiqc/meta.yml

@@ -29,6 +29,19 @@ input:
  type: file
  description: Optional logo file for MultiQC
  pattern: "*.{png}"
+ - replace_names:
+ type: file
+ description: |
+ Optional two-column sample renaming file. First column a set of
+ patterns, second column a set of corresponding replacements. Passed via
+ MultiQC's `--replace-names` option.
+ pattern: "*.{tsv}"
+ - sample_names:
+ type: file
+ description: |
+ Optional TSV file with headers, passed to the MultiQC --sample_names
+ argument.
+ pattern: "*.{tsv}"
 output:
  - report:
  type: file

modules/nf-core/multiqc/tests/main.nf.test

@@ -17,6 +17,8 @@ nextflow_process {
  input[1] = []
  input[2] = []
  input[3] = []
+ input[4] = []
+ input[5] = []
  """
  }
  }
@@ -41,6 +43,8 @@ nextflow_process {
  input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
  input[2] = []
  input[3] = []
+ input[4] = []
+ input[5] = []
  """
  }
  }
@@ -66,6 +70,8 @@ nextflow_process {
  input[1] = []
  input[2] = []
  input[3] = []
+ input[4] = []
+ input[5] = []
  """
  }
  }