From d39ba08e02b78001f851b737bc832203a60dc7f1 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 31 May 2022 20:19:49 +0200
Subject: [PATCH] Prepare main module code

---
 modules/gatk/realignertargetcreator/main.nf | 64 ++++++---------------
 1 file changed, 16 insertions(+), 48 deletions(-)

diff --git a/modules/gatk/realignertargetcreator/main.nf b/modules/gatk/realignertargetcreator/main.nf
index 59dee1a8..76ac2dd7 100644
--- a/modules/gatk/realignertargetcreator/main.nf
+++ b/modules/gatk/realignertargetcreator/main.nf
@@ -1,46 +1,19 @@
-// 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
-//               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 GATK_REALIGNERTARGETCREATOR {
     tag "$meta.id"
     label 'process_low'
 
-    // TODO nf-core: List required Conda package(s).
-    //               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::gatk=3.8" : null)
+    conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11':
-        'quay.io/biocontainers/gatk:3.8--hdfd78af_11' }"
+        'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11':
+        'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               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/modules/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.
     tuple val(meta), path(bam)
+    tuple val(meta), path(reference)
+    tuple val(meta), path(known_vcf)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
     tuple val(meta), path("*.bam"), emit: bam
-    // TODO nf-core: List additional required output channels/values here
     path "versions.yml"           , emit: versions
 
     when:
@@ -49,27 +22,22 @@ process GATK_REALIGNERTARGETCREATOR {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // 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/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
-    // 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 ;)
+    def known = known_vcf ? "-known ${known_vcf}" ? ""
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
+    gatk3 \\
+        -T RealigerTargetCreator \\
+        -nt ${task.cpus}
+        -I ${bam} \\
+        -R ${reference} \\
         -o ${prefix}.bam \\
-        -T $prefix \\
-        $bam
+        ${known} \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        gatk: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        gatk: \$(echo \$(gatk3 --version))
     END_VERSIONS
     """
 }