add software version

main.nf

@@ -27,7 +27,7 @@ This script is based on :
 ========================================================================================
  GeT/template Analysis Pipeline.
  #### Homepage / Documentation
- https://github.com/nf-core/template
+ https://github.com/get-nf/template
 ----------------------------------------------------------------------------------------
 */
 
@@ -38,7 +38,7 @@ def helpMessage() {
 
     The typical command for running the pipeline is as follows:
 
-    nextflow run nf-core/template --inputdir '/path/to/data' --samplesheet 'samples.csv' -profile docker
+    nextflow run get-nf/template --inputdir '/path/to/data' --samplesheet 'samples.csv' -profile docker
 
     Mandatory arguments:
       --inputdir                    Path to input directory 
@@ -52,6 +52,7 @@ def helpMessage() {
       --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
       --maxMultiqcEmailFileSize     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 [str]                   Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
 
 
@@ -120,6 +121,37 @@ ch_multiqc_config = file(params.multiqc_config, checkIfExists: true)
 ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
 ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
 
+
+
+def summary = [:]
+if (workflow.revision) summary['Pipeline Release'] = workflow.revision
+summary['Run Name']         = custom_runName ?: workflow.runName
+// TODO nf-core: Report custom parameters here
+summary['Input dir']            = params.inputdir
+summary['Sample sheet']        = params.samplesheet
+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 - $workflow.container"
+summary['Output dir']       = params.outdir
+summary['Launch dir']       = workflow.launchDir
+summary['Working dir']      = workflow.workDir
+summary['Script dir']       = workflow.projectDir
+summary['User']             = workflow.userName
+if (workflow.profile == 'awsbatch') {
+  summary['AWS Region']     = params.awsregion
+  summary['AWS Queue']      = params.awsqueue
+}
+summary['Config Profile'] = workflow.profile
+if (params.email || params.email_on_fail) {
+  summary['E-mail Address']    = params.email
+  summary['E-mail on failure'] = params.email_on_fail
+}
+log.info "-\033[2m--------------------------------------------------\033[0m-"
+log.info "-\033[2m---------------- get-nf workflow -----------------\033[0m-"
+log.info "-\033[2m--------------------------------------------------\033[0m-"
+log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
+log.info "-\033[2m--------------------------------------------------\033[0m-"
+
 /* In case of modular pipeline*/
 params.step = "qc"
 availableStepList = 
@@ -136,6 +168,31 @@ for (String a_step: step) {
     assert (a_step in availableStepList)
 }
 
+/*
+ * Parse software version numbers
+ */
+process get_software_versions {
+    publishDir "${params.outdir}/pipeline_info", mode: 'copy',
+        saveAs: { filename ->
+            if (filename.indexOf(".csv") > 0) filename
+            else null
+        }
+
+    output:
+    file 'software_versions_mqc.yaml' into software_versions_yaml
+    file "software_versions.csv"
+
+    script:
+    // TODO nf-core: Get all tools to print their version number here
+    """
+    echo $workflow.manifest.version > v_pipeline.txt
+    echo $workflow.nextflow.version > v_nextflow.txt
+    fastqc --version > v_fastqc.txt
+    multiqc --version > v_multiqc.txt
+    scrape_software_versions.py &> software_versions_mqc.yaml
+    """
+    
+
 /*
  * STEP 1 - FastQC
  */
@@ -194,10 +251,10 @@ process assembly {
     """
 }
 
-/***********
- * MultiQC *
- ***********/
 
+/*
+ * STEP - MultiQC
+ */
 process multiqc {
   
   publishDir "${params.outdir}/MultiQC", mode: 'copy'
@@ -208,7 +265,7 @@ process multiqc {
   input:
   file (multiqc_config) from ch_multiqc_config
   file ('fastqc/*') from fastqc_results_for_multiqc.collect().ifEmpty([])
-  // TODO nf-core: Add in log files from your new processes for MultiQC to find!
+  // TODO get-nf: Add in log files from your new processes for MultiQC to find!
   //file ('softwareVersions/*') from softwareVersionsYamlCh.collect().ifEmpty([])
   //file ('workflowSummary/*') from workflowSummaryYamlCh.collect()
 
@@ -224,3 +281,104 @@ process multiqc {
   multiqc -f $rtitle $rfilename  --config $multiqc_config .
   """
 }
+
+/*
+ * STEP - Output Description HTML
+ */
+process output_documentation {
+    publishDir "${params.outdir}/pipeline_info", mode: 'copy'
+
+    input:
+    file output_docs from ch_output_docs
+
+    output:
+    file "results_description.html"
+
+    script:
+    """
+    pandoc $output_docs -t html -o results_description.html
+    """
+}
+
+/*
+ * Completion e-mail notification
+ */
+workflow.onComplete {
+
+    // Set up the e-mail variables
+    def subject = "[get-nf/template] Successful: $workflow.runName"
+    if (!workflow.success) {
+      subject = "[get-nf/template] FAILED: $workflow.runName"
+    }
+    def email_fields = [:]
+    email_fields['version'] = workflow.manifest.version
+    email_fields['runName'] = custom_runName ?: workflow.runName
+    email_fields['success'] = workflow.success
+    email_fields['dateComplete'] = workflow.complete
+    email_fields['duration'] = workflow.duration
+    email_fields['exitStatus'] = workflow.exitStatus
+    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    email_fields['errorReport'] = (workflow.errorReport ?: 'None')
+    email_fields['commandLine'] = workflow.commandLine
+    email_fields['projectDir'] = workflow.projectDir
+    email_fields['summary'] = summary
+    println(workflow)
+    
+    email_fields['summary']['Date Started'] = 11 // workflow.start
+    email_fields['summary']['Date Completed'] = 11 // workflow.complete
+    email_fields['summary']['Pipeline script file path'] = 'aaa' //workflow.scriptFile
+    email_fields['summary']['Pipeline script hash ID'] = 'aaa' //workflow.scriptId 
+    if (workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
+    if (workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
+    if (workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
+    if (workflow.container) email_fields['summary']['Docker image'] = workflow.container
+    email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
+    email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
+    email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+    // Check if we are only sending emails on failure
+    email_address = params.email
+    if (!params.email && params.email_on_fail && !workflow.success) {
+        email_address = params.email_on_fail
+    }
+
+    // Render the TXT template
+    def engine = new groovy.text.GStringTemplateEngine()
+    def tf = new File("$baseDir/assets/email_template.txt")
+    def txt_template = engine.createTemplate(tf).make(email_fields)
+    def email_txt = txt_template.toString()
+
+    // Send the HTML e-mail
+    if (email_address) {
+      // Catch failures and try with plaintext
+      [ 'mail', '-s', subject, email_address ].execute() << email_txt
+      log.info "[get-nf/template] Sent summary e-mail to $email_address (mail)"
+      log.info "$email_txt"
+    }
+
+    // Write summary e-mail HTML to a file
+    def output_d = new File( "${params.outdir}/pipeline_info/" )
+    if (!output_d.exists()) {
+      output_d.mkdirs()
+    }
+    def output_tf = new File( output_d, "pipeline_report.txt" )
+    output_tf.withWriter { w -> w << email_txt }
+
+    c_reset = params.monochrome_logs ? '' : "\033[0m";
+    c_purple = params.monochrome_logs ? '' : "\033[0;35m";
+    c_green = params.monochrome_logs ? '' : "\033[0;32m";
+    c_red = params.monochrome_logs ? '' : "\033[0;31m";
+
+    if (workflow.stats.ignoredCount > 0 && workflow.success) {
+      log.info "${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}"
+      log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCount} ${c_reset}"
+      log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}"
+    }
+
+    if (workflow.success) {
+        log.info "${c_purple}[get-nf/template]${c_green} Pipeline completed successfully${c_reset}"
+    } else {
+        log.info "${c_purple}[get-nf/template]${c_red} Pipeline completed with errors${c_reset}"
+    }
+
+}
\ No newline at end of file

nextflow.config

@@ -14,6 +14,7 @@ params {
   samplesheet = "${params.inputdir}/samples.csv"
   single_end = false
   outdir = './results'
+  skip_multiQC = false
 
   // Boilerplate options
   name = false
@@ -21,8 +22,6 @@ params {
   tracedir = "${params.outdir}/pipeline_info"
   email = false
   email_on_fail = false
-  maxMultiqcEmailFileSize = 25.MB
-  plaintext_email = false
   monochrome_logs = false
   help = false
   config_profile_description = false
@@ -40,7 +39,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = "$baseDir/img.sif"
+process.container = "$baseDir/template-nf.sif"
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'