Module only accepts fasta

Use seqtk downstream to convert fastqs

modules/nf-core/metabuli/classify/main.nf

@@ -1,20 +1,3 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-// https://github.com/nf-core/modules/tree/master/modules/nf-core/
-// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-// https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-// All other parameters MUST be provided using the "task.ext" directive, see here:
-// https://www.nextflow.io/docs/latest/process.html#ext
-// where "task.ext" is a string.
-// Any parameters that need to be evaluated in the context of a particular sample
-// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-// unless there is a run-time, storage advantage in implementing in this way
-// e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-// bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-// list (`[]`) instead of a file can be used to work around this issue.
-
 process METABULI_CLASSIFY {
  tag "$meta.id"
  label 'process_medium'
@@ -25,8 +8,6 @@ process METABULI_CLASSIFY {
  'biocontainers/1.0.0--pl5321hf1761c0_0' }"
 
  input:
- // TODO nf-core: Where applicable please provide/convert compressed files as input/output
- // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
  tuple val(meta), path(fastas)
  path(db)
 
@@ -42,18 +23,13 @@ process METABULI_CLASSIFY {
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def input = meta.single_end ? "--seq_mode 1 ${fastas}" : "${fastas}"
- // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
- // If the software is unable to output a version number on the command-line then it can be manually specified
- // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
- // Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
- // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
  """
  metabuli \\
  classify \\
  $args \\
  --threads $task.cpus \\
  ${input}
- ${database}
+ ${db}
  ${prefix} \\
  ${prefix}
 

modules/nf-core/metabuli/classify/meta.yml

@@ -1,5 +1,4 @@
 name: "metabuli_classify"
-## TODO nf-core: Add a description of the module and list keywords
 description: Classify FASTA files against a metabuli database
 keywords:
  - metabuli
@@ -15,7 +14,7 @@ tools:
  homepage: "https://github.com/steineggerlab/Metabuli"
  documentation: "https://github.com/steineggerlab/Metabuli#readme"
  tool_dev_url: "https://github.com/steineggerlab/Metabuli"
- doi: "https://doi.org/10.1101/2023.05.31.543018"
+ doi: "10.1101/2023.05.31.543018"
  licence: "['GPL v3']"
 
 input:
@@ -24,13 +23,13 @@ input:
  description: |
  Groovy Map containing sample information
  e.g. [ id:'test', single_end:false ]
-  - fastas:
+ - fastas:
  type: file
- description: single or paired FASTA files, optionally gzipped
- pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}"
-  - db:
+ description: single or paired FASTA files
+ pattern: "*.{fa,fasta,fna}"
+ - db:
  type: file
- description: Metabuli databse file from build or custom made.
+ description: Metabuli database file, prebuild or custom made.
 
 output:
  - meta: