nf-core · apeltzer · Oct 16, 2019 · Oct 16, 2019 · Oct 16, 2019 · Oct 16, 2019
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,10 @@
 * Add UCSC genomes to `igenomes.config` and add paths to all genome indices
 * Change `maxMultiqcEmailFileSize` parameter to `max_multiqc_email_size`
 * Export conda environment in Docker file [#349](https://github.com/nf-core/tools/issues/349)
+* Change remaining parameters from `camelCase` to `snakeCase` [#39](https://github.com/nf-core/hic/issues/39)
+  * `--singleEnd` to `--single_end`
+  * `--igenomesIgnore` to `--igenomes_ignore`
+* Add `autoMounts=true` to default singularity profile
 
 ### Other
 

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/test.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/test.config
@@ -4,7 +4,7 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run {{ cookiecutter.name }} -profile test
+ *   nextflow run {{ cookiecutter.name }} -profile test,<docker/singularity>
  */
 
 params {
@@ -14,11 +14,11 @@ params {
   max_cpus = 2
   max_memory = 6.GB
   max_time = 48.h
-  
+
   // Input data
   // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
   // TODO nf-core: Give any required params for the test so that command line flags are not needed
-  singleEnd = false
+  single_end = false
   readPaths = [
     ['Testdata', ['https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R1.tiny.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R2.tiny.fastq.gz']],
     ['SRR389222', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']]

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md
@@ -12,11 +12,11 @@
 * [Main arguments](#main-arguments)
   * [`-profile`](#-profile)
   * [`--reads`](#--reads)
-  * [`--singleEnd`](#--singleend)
+  * [`--single_end`](#--single_end)
 * [Reference genomes](#reference-genomes)
   * [`--genome` (using iGenomes)](#--genome-using-igenomes)
   * [`--fasta`](#--fasta)
-  * [`--igenomesIgnore`](#--igenomesignore)
+  * [`--igenomes_ignore`](#--igenomes_ignore)
 * [Job resources](#job-resources)
   * [Automatic resubmission](#automatic-resubmission)
   * [Custom resource requests](#custom-resource-requests)
@@ -125,11 +125,11 @@ Please note the following requirements:
 
 If left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`
 
-### `--singleEnd`
-By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--singleEnd` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
+### `--single_end`
+By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--single_end` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
 
 ```bash
---singleEnd --reads '*.fastq'
+--single_end --reads '*.fastq'
 ```
 
 It is not possible to run a mixture of single-end and paired-end files in one run.
@@ -180,7 +180,7 @@ If you prefer, you can specify the full path to your reference genome when you r
 --fasta '[path to Fasta reference]'
 ```
 
-### `--igenomesIgnore`
+### `--igenomes_ignore`
 Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.
 
 ## Job resources

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
@@ -23,21 +23,21 @@ def helpMessage() {
     Mandatory arguments:
       --reads                       Path to input data (must be surrounded with quotes)
       -profile                      Configuration profile to use. Can use multiple (comma separated)
-                                    Available: conda, docker, singularity, awsbatch, test and more.
+                                    Available: conda, docker, singularity, awsbatch, test and more
 
     Options:
       --genome                      Name of iGenomes reference
-      --singleEnd                   Specifies that the input is single end reads
+      --single_end                  Specifies that the input is single-end reads
 
-    References                      If not specified in the configuration file or you wish to overwrite any of the references.
-      --fasta                       Path to Fasta reference
+    References                      If not specified in the configuration file or you wish to overwrite any of the references
+      --fasta                       Path to fasta reference
 
     Other options:
       --outdir                      The output directory where the results will be saved
       --email                       Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
       --email_on_fail               Same as --email, except only send mail if the workflow is not successful
       --max_multiqc_email_size      Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
-      -name                         Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
+      -name                         Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic
 
     AWSBatch options:
       --awsqueue                    The AWSBatch JobQueue that needs to be set when running on AWSBatch
@@ -78,7 +78,7 @@ if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
     custom_runName = workflow.runName
 }
 
-if ( workflow.profile == 'awsbatch') {
+if (workflow.profile == 'awsbatch') {
     // AWSBatch sanity checking
     if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
     // Check outdir paths to be S3 buckets if running on AWSBatch
@@ -96,7 +96,7 @@ ch_output_docs = file("$baseDir/docs/output.md", checkIfExists: true)
  * Create a channel for input read files
  */
 if (params.readPaths) {
-    if (params.singleEnd) {
+    if (params.single_end) {
         Channel
             .from(params.readPaths)
             .map { row -> [ row[0], [ file(row[1][0], checkIfExists: true) ] ] }
@@ -111,8 +111,8 @@ if (params.readPaths) {
     }
 } else {
     Channel
-        .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
-        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --singleEnd on the command line." }
+        .fromFilePairs(params.reads, size: params.single_end ? 1 : 2)
+        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --single_end on the command line." }
         .into { ch_read_files_fastqc; ch_read_files_trimming }
 }
 
@@ -124,7 +124,7 @@ summary['Run Name']         = custom_runName ?: workflow.runName
 // TODO nf-core: Report custom parameters here
 summary['Reads']            = params.reads
 summary['Fasta Ref']        = params.fasta
-summary['Data Type']        = params.singleEnd ? 'Single-End' : 'Paired-End'
+summary['Data Type']        = params.single_end ? 'Single-End' : 'Paired-End'
 summary['Max Resources']    = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
 if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
 summary['Output dir']       = params.outdir
@@ -334,7 +334,7 @@ workflow.onComplete {
     // Send the HTML e-mail
     if (email_address) {
         try {
-            if ( params.plaintext_email ){ throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
             [ 'sendmail', '-t' ].execute() << sendmail_html
             log.info "[{{ cookiecutter.name }}] Sent summary e-mail to $email_address (sendmail)"
@@ -346,13 +346,13 @@ workflow.onComplete {
     }
 
     // Write summary e-mail HTML to a file
-    def output_d = new File( "${params.outdir}/pipeline_info/" )
+    def output_d = new File("${params.outdir}/pipeline_info/")
     if (!output_d.exists()) {
         output_d.mkdirs()
     }
-    def output_hf = new File( output_d, "pipeline_report.html" )
+    def output_hf = new File(output_d, "pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    def output_tf = new File( output_d, "pipeline_report.txt" )
+    def output_tf = new File(output_d, "pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
 
     c_reset = params.monochrome_logs ? '' : "\033[0m";
@@ -376,7 +376,7 @@ workflow.onComplete {
 }
 
 
-def nfcoreHeader(){
+def nfcoreHeader() {
     // Log colors ANSI codes
     c_reset = params.monochrome_logs ? '' : "\033[0m";
     c_dim = params.monochrome_logs ? '' : "\033[2m";
@@ -399,7 +399,7 @@ def nfcoreHeader(){
     """.stripIndent()
 }
 
-def checkHostname(){
+def checkHostname() {
     def c_reset = params.monochrome_logs ? '' : "\033[0m"
     def c_white = params.monochrome_logs ? '' : "\033[0;37m"
     def c_red = params.monochrome_logs ? '' : "\033[1;91m"

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -12,7 +12,7 @@ params {
   // TODO nf-core: Specify your pipeline's command line flags
   genome = false
   reads = "data/*{1,2}.fastq.gz"
-  singleEnd = false
+  single_end = false
   outdir = './results'
 
   // Boilerplate options
@@ -28,7 +28,7 @@ params {
   tracedir = "${params.outdir}/pipeline_info"
   awsqueue = false
   awsregion = 'eu-west-1'
-  igenomesIgnore = false
+  igenomes_ignore = false
   custom_config_version = 'master'
   custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
   hostnames = false
@@ -56,7 +56,8 @@ profiles {
   conda { process.conda = "$baseDir/environment.yml" }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   docker { docker.enabled = true }
-  singularity { singularity.enabled = true }
+  singularity { singularity.enabled = true
+                singularity.autoMounts = true }
   test { includeConfig 'conf/test.config' }
 }
 
@@ -66,7 +67,7 @@ profiles {
 docker.runOptions = '-u \$(id -u):\$(id -g)'
 
 // Load igenomes.config if required
-if (!params.igenomesIgnore) {
+if (!params.igenomes_ignore) {
   includeConfig 'conf/igenomes.config'
 }