Adding more stuff to test generator

modules/circularmapper/generator/main.nf

@@ -1,77 +1,45 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
-// 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/software
-//               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 as a string i.e. "options.args"
-//               where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
-//               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.
-
 params.options = [:]
 options        = initOptions(params.options)
 
 process CIRCULARMAPPER_GENERATOR {
-    tag '$bam'
+    tag "$fasta"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
 
-    // TODO nf-core: List required Conda package(s).
+    conda (params.enable_conda ? "bioconda::circularmapper=1.93.5 bioconda::bwa=0.7.17" : null)
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda (params.enable_conda ? "bioconda::circularmapper=1.93.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/circularmapper:1.93.5--h4a94de4_1"
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-9955aa4caccd101358f742fbf51faa7f9105f099:a7be1c066de246d48c344a53c13b18da1f80cb4c-0"
     } else {
-        container "quay.io/biocontainers/circularmapper:1.93.5--h4a94de4_1"
+        container "quay.io/biocontainers/mulled-v2-9955aa4caccd101358f742fbf51faa7f9105f099:a7be1c066de246d48c344a53c13b18da1f80cb4c-0"
     }
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    path fasta
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
-    // 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.
-    path bam
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    path "circularmapper", emit: index
-    path "*.bam", emit: bam
+    path "versions.yml", emit: versions
-    // TODO nf-core: List additional required output channels/values here
-    path "*.version.txt"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     
-    // 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/software/homer/annotatepeaks/main.nf
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$options.args" variable
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
-    samtools \\
+    mkdir circularmapper
-        sort \\
+    circulargenerator \\
-        $options.args \\
+    -i $fasta \\
-        -@ $task.cpus \\
+    $options.args
-        $bam
 
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    bwa index $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(circulargenerator --help 2>&1) | head -n 1')
+        bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
+    END_VERSIONS
     """
 }

modules/circularmapper/generator/meta.yml

@@ -1,37 +1,34 @@
 name: circularmapper_generator
-## TODO nf-core: Add a description of the module and list keywords
+description: CircularMapper Generator Module
-description: write your description here
 keywords:
-  - sort
+  - index
+  - genome
+  - fasta
+  - reference
+
 tools:
   - circularmapper:
-      ## TODO nf-core: Add a description and other details for the software below
       description:  A method to improve mappings on circular genomes, using the BWA mapper.
-      homepage: None
+      homepage: https://github.com/apeltzer/Circularmapper
-      documentation: None
+      documentation: https://circularmapper.readthedocs.io/en/latest/
-      tool_dev_url: None
+      doi: "10.1186/s13059-016-0918-z"
-      doi: ""
       licence: ['GPL v3']
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
-  ## TODO nf-core: Delete / customise this example input
+  - fasta:
-  - bam:
       type: file
-      description: BAM/CRAM/SAM file
+      description: Input genome fasta file
-      pattern: "*.{bam,cram,sam}"
+      pattern: "*.{fasta}"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
-  - version:
+  - index:
       type: file
-      description: File containing software version
+      description: BWA genome index files
-      pattern: "*.{version.txt}"
+      pattern: "*.{amb,ann,bwt,pac,sa}"
-  ## TODO nf-core: Delete / customise this example output
+  - versions:
-  - bam:
       type: file
-      description: Sorted BAM/CRAM/SAM file
+      description: File containing software versions
-      pattern: "*.{bam,cram,sam}"
+      pattern: "versions.yml"
 
 authors:
   - "@apeltzer"

tests/modules/circularmapper/generator/main.nf

@@ -2,11 +2,11 @@
 
 nextflow.enable.dsl = 2
 
-include { CIRCULARMAPPER_GENERATOR } from '../../../../modules/circularmapper/generator/main.nf' addParams( options: [:] )
+include { CIRCULARMAPPER_GENERATOR } from '../../../../modules/circularmapper/generator/main.nf' addParams( options: [publish_dir:'circularmapper'] )
 
 workflow test_circularmapper_generator {
     
-    input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     CIRCULARMAPPER_GENERATOR ( input )
 }

tests/modules/circularmapper/generator/test.yml

@@ -1,5 +1,3 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml circularmapper/generator
 - name: circularmapper generator
   command: nextflow run ./tests/modules/circularmapper/generator -entry test_circularmapper_generator -c tests/config/nextflow.config
   tags: