From 9483c8b5085ad690009e3d90cef8e4000ef0a62e Mon Sep 17 00:00:00 2001
From: Abhinav Sharma <abhi18av@users.noreply.github.com>
Date: Tue, 28 Jul 2020 10:07:57 +0530
Subject: [PATCH] sync with develop (#7)

* general formatting

* add the usage doc, update the code

* add stub for the snippy core
---
 LICENSE   |  2 +-
 README.md | 64 +++++++++++++++++++++++++++++++++++++++-
 main.nf   | 87 ++++++++++++++++++++++++++++++++++++++++---------------
 3 files changed, 127 insertions(+), 26 deletions(-)

diff --git a/LICENSE b/LICENSE
index c9e63b4..2d1d3f0 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 BioDragao-Org
+Copyright (c) 2020 Abhinav Sharma (@abhi18av)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index 20c7881..fc78b9f 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,63 @@
-# nf_process
+# Nextflow wrapper for `snippy` process.
+
+## Pre-requisites
+
+- Nextflow
+- Docker 
+
+**NOTE** If you plan to setup a basic server, then you can refer [minimal-nextflow-setup](https://github.com/nextflow-hub/minimal-nextflow-setup)
+
+## Usage
+
+```
+nextflow run https://github.com/nextflow-hub/snippy
+```
+
+## Options
+
+- `refGbk`
+
+By default, the process assumes the reference file to be `NC000962_3.gbk` which could be customized using this option
+
+```
+nextflow run https://github.com/nextflow-hub/snippy --refGbk NCxxxxxx.gbk
+```
+
+- `filePattern`
+
+By default, the process assumes the files to follow the `*_{R1,R2}.fastq.gz` pattern, which could be customized using this option
+
+```
+nextflow run https://github.com/nextflow-hub/snippy --filePattern './*_{1,2}.fastq.gz'
+```
+
+- `resultsDir`
+
+By default, it stores the result files locally inside the `results` directory.
+
+```
+nextflow run https://github.com/nextflow-hub/snippy --resultsDir /path/to/custom/resultsDir
+```
+
+- `saveMode`
+
+By default, the pipeline publishes the results in the `resultsDir` by copying the relevant output.
+
+You can update this behavior by simply specifying the alternative such as `move` or `link` etc. 
+
+```
+nextflow run https://github.com/nextflow-hub/snippy --saveMode move
+```
+
+For more information please refer [Nextflow documentation](https://www.nextflow.io/docs/latest/process.html#publishdir)
+
+## Customizing the script
+
+The sole purpose of process wrappers in `nextflow-hub` is to keep the code small, clean and hackable with some basic knowledge of `nextflow` scripting.
+
+If you have specific requirements, you are encouraged to fork/clone and update your version to accomodate your needs. 
+
+
+## Contribution
+
+Contribution, in all forms, is most welcome!
diff --git a/main.nf b/main.nf
index 5b0007f..7768830 100644
--- a/main.nf
+++ b/main.nf
@@ -1,40 +1,46 @@
 #!/usr/bin/env nextflow
 
+
 /*
-################
+#==============================================
+code documentation
+#==============================================
+*/
+
+/*
+#==============================================
 params
-################
+#==============================================
 */
 
-params.trimmed= true
-params.saveBy= 'copy'
-params.ram= 7
-params.cpus= 4
+params.resultsDir = 'results/snippy'
+params.filePattern = "./*_{R1,R2}.fastq.gz"
+params.saveMode = 'copy'
+params.ram = 4
+params.cpus = 4
+params.snippyCore = false
 
-params.refGbk = "NC000962_3.gbk"
 
-inputUntrimmedRawFilePattern = "./*_{R1,R2}.fastq.gz"
-inputTrimmedRawFilePattern = "./*_{R1,R2}.p.fastq.gz"
-
-inputRawFilePattern = params.trimmed ? inputTrimmedRawFilePattern : inputUntrimmedRawFilePattern
+params.refGbk = "NC000962_3.gbk"
 
-Channel.fromFilePairs(inputRawFilePattern)
+Channel.fromFilePairs(params.filePattern)
         .set { ch_in_snippy }
 
 Channel.value("$workflow.launchDir/NC000962_3.gbk")
-       .set {ch_refGbk}
+        .set { ch_refGbk }
 
 /*
-###############
-snippy_command
-###############
+#==============================================
+snippy
+#==============================================
 */
 
 process snippy {
-    container 'ummidock/snippy_tseemann:4.6.0-02'
-    publishDir 'results/snippy', mode: params.saveBy
+    container 'quay.io/biocontainers/snippy:4.6.0--0'
+    publishDir params.resultsDir, mode: params.saveMode
     stageInMode 'symlink'
-    errorStrategy 'ignore'
+    errorStrategy 'retry'
+    maxRetries 3
 
 
     input:
@@ -44,15 +50,48 @@ process snippy {
     output:
     path("""${genomeName}""") into ch_out_snippy
 
+    when:
+    !params.snippyCore
+
     script:
-    genomeName= genomeFileName.toString().split("\\_")[0]
+    genomeName = genomeFileName.toString().split("\\_")[0]
 
     """
-
     snippy --cpus ${params.cpus} --ram ${params.ram} --outdir $genomeName --ref $refGbk --R1 ${genomeReads[0]} --R2 ${genomeReads[1]}
     """
-    
+
 }
 
-// alternative container 
-// container 'quay.io/biocontainers/snippy:4.6.0--0'
+// TODO implement the snippy-core process
+process snippyCore {
+    container 'ummidock/snippy_tseemann:4.6.0-02'
+    publishDir params.resultsDir, mode: params.saveBy
+
+    when:
+    params.snippyCore
+
+    input:
+    path refGbk from ch_refGbk
+    set genomeFileName, file(genomeReads) from ch_in_snippy
+
+    output:
+    path("""${genomeName}""") into ch_out_snippy
+
+    script:
+
+    """
+    snippy-core 
+    """
+
+}
+
+
+/*
+#==============================================
+# extra
+#==============================================
+*/
+
+
+// alternative container
+//container 'ummidock/snippy_tseemann:4.6.0-02'