diff --git a/data/samples.csv b/data/samples.csv
index bc50be23eabfb1e5cded3f309e7960cd9064008e..aeb593009ae0b519b708750bfeb00dad575c1636 100644
--- a/data/samples.csv
+++ b/data/samples.csv
@@ -1 +1 @@
-1,MT,./data/MT_rep1_1_Ch6.fastq.gz,./data/MT_rep1_2_Ch6.fastq.gz
\ No newline at end of file
+1,MT,./template/data/MT_rep1_1_Ch6.fastq.gz,./template/data/MT_rep1_2_Ch6.fastq.gz
\ No newline at end of file
diff --git a/main.nf b/main.nf
index 08e3abf86af2af0fd171024d76bcd764892b7160..4913ab34a3427f4b4a4d23d5521a831d0ad79cd1 100644
--- a/main.nf
+++ b/main.nf
@@ -1,383 +1,44 @@
-#!/usr/bin/env nextflow
-
-
-/*
-Copyright INRAE 2021
-
-This software is a computer program whose purpose is to
-analyze high-throughput sequencing data.
-You can use, modify and/ or redistribute the software under the terms
-of license (see the LICENSE file for more details).
-The software is distributed in the hope that it will be useful,
-but "AS IS" WITHOUT ANY WARRANTY OF ANY KIND.
-Users are therefore encouraged to test the software's suitability as regards
-their requirements in conditions enabling the security of their systems and/or data.
-The fact that you are presently reading this means that you have had knowledge
-of the license and that you accept its terms.
-This script is based on :
- - the nf-core guidelines . See https://nf-co.re/ for more information
- - the Curie institute template https://github.com/bioinfo-pf-curie/geniac-template/
-
-*/
-
-
-/*
-========================================================================================
- GeT/template
-========================================================================================
- GeT/template Analysis Pipeline.
- #### Homepage / Documentation
- https://github.com/get-nf/template
-----------------------------------------------------------------------------------------
-*/
-
-def helpMessage() {
- log.info"""
-
- Usage:
-
- The typical command for running the pipeline is as follows:
-
- nextflow run get-nf/template --inputdir '/path/to/data' --samplesheet 'samples.csv' -profile docker
-
- Mandatory arguments:
- --inputdir Path to input directory
- -profile Configuration profile to use. Can use multiple (comma separated)
- Available: conda, docker, singularity, path, genotoul, test and more.
-
- Options:
- --samplesheet Default inputdir/samples.csv eg: SAMPLE_ID,SAMPLE_NAME,path/to/R1/fastq/file,path/to/R2/fastq/file (for paired-end only)
- --contaminant Name of iGenomes // To be discussed ????
- --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
- --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.
-
-
- =======================================================
- Available profiles
- -profile test Run the test dataset
- -profile conda Build a new conda environment before running the pipeline. Use `--condaCacheDir` to define the conda cache path
- -profile path Use the installation path defined for all tools. Use `--globalPath` to define the installation path
- -profile docker Use the Docker images for each process
- -profile singularity Use the singularity images for each process
- -profile genologin Run the workflow on the cluster, instead of locally
-
- """.stripIndent()
-}
-
-// Show help message
-if (params.help) {
- helpMessage()
- exit 0
-}
-
-
-// NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
-
-/*
- * Create a channel for input read files
- */
-// If you want to use the channel below in a process, define the following:
-// input:
-// file dir from inputDirCh
-//
-
-
-ch_inputdir = params.inputdir ? Channel.fromPath(params.inputdir, checkIfExists: true) : Channel.empty()
-
-// Create a channel for input read files
-if(params.samplesheet){
- if(params.single_end){
- Channel
- .from(file("${params.samplesheet}"))
- .splitCsv(header: false)
- .map{ row -> [ row[0], [file(row[2])]] }
- .into { ch_read_files_for_fastqc; ch_read_files_for_qc1; ch_read_files_for_assembly}
- }else{
- Channel
- .from(file("${params.samplesheet}"))
- .splitCsv(header: false)
- .map{ row -> [ row[0], [file(row[2]), file(row[3])]] }
- .into { ch_read_files_for_fastqc; ch_read_files_for_qc1; ch_read_files_for_assembly}
- }
- params.reads=false
-} else {
- exit 1, "Expect a samplesheet and an input dir !"
-}
-/*
- * SET UP CONFIGURATION VARIABLES
- */
-// Has the run name been specified by the user?
-// this has the bonus effect of catching both -name and --name
-custom_runName = params.name
-if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
- custom_runName = workflow.runName
-}
-// Stage config files
-ch_multiqc_config = file(params.multiqc_config, checkIfExists: true)
-ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
-
-
-def summary = [:]
-if (workflow.revision) summary['Pipeline Release'] = workflow.revision
-summary['Run Name'] = custom_runName ?: workflow.runName
-// TODO nf-core: Report custom parameters here
-summary['Input dir'] = params.inputdir
-summary['Sample sheet'] = params.samplesheet
-summary['Data Type'] = params.single_end ? 'Single-End' : 'Paired-End'
-summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
-if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
-summary['Output dir'] = params.outdir
-summary['Launch dir'] = workflow.launchDir
-summary['Working dir'] = workflow.workDir
-summary['Script dir'] = workflow.projectDir
-summary['User'] = workflow.userName
-if (workflow.profile == 'awsbatch') {
- summary['AWS Region'] = params.awsregion
- summary['AWS Queue'] = params.awsqueue
-}
-summary['Config Profile'] = workflow.profile
-if (params.email || params.email_on_fail) {
- summary['E-mail Address'] = params.email
- summary['E-mail on failure'] = params.email_on_fail
-}
-log.info "-\033[2m--------------------------------------------------\033[0m-"
-log.info "-\033[2m----------------"+ workflow.manifest.name +" --\033[0m-"
-log.info "-\033[2m--------------------------------------------------\033[0m-"
-log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
-log.info "-\033[2m--------------------------------------------------\033[0m-"
-
-/*
- * Parse software version numbers
- */
-process get_software_versions {
- publishDir "${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 $workflow.nextflow.version > v_nextflow.txt
- fastqc --version > v_fastqc.txt
- multiqc --version > v_multiqc.txt
- scrape_software_versions.py &> software_versions_mqc.yaml
- """
-}
-/*
- * STEP 1 - FastQC
- */
-process fastqc {
- tag "$name"
- label 'process_medium'
- publishDir "${params.outdir}/fastqc", mode: 'copy',
- saveAs: { filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename" }
-
- input:
- set val(name), file(reads) from ch_read_files_for_fastqc
-
- output:
- file "*_fastqc.{zip,html}" into ch_fastqc_results_for_multiqc
-
- script:
- """
- fastqc --quiet --threads $task.cpus $reads
- """
-}
-
-/*
- * STEP 2 - Fake QC
- */
-process qc1 {
- input:
- set replicate_id, file(reads) from ch_read_files_for_qc1
-
- output:
- file("${replicate_id}.qc1") into ch_fastqc_raw_for_assembly
-
- script:
- """
- echo "mkdir ${replicate_id} ; fastqc --nogroup --quiet -o ${replicate_id} --threads ${task.cpus} ${reads[0]} ${reads[1]}" > ${replicate_id}.qc1
- """
-}
-
-/*
- * STEP 3 - Fake assembly
- */
-process assembly {
- input:
- file (qc) from ch_fastqc_raw_for_assembly
- set replicate_id, file(reads) from ch_read_files_for_assembly
-
- output:
- file("${replicate_id}.assembly") into ch_assembly_for_multiqc
-
- script:
- """
- echo "ASSEMBLY ${replicate_id} ; " > ${replicate_id}.assembly
- """
-}
-
-process workflow_summary {
-
- output:
- file 'workflow_summary_mqc.yaml' into ch_workflow_summary_yaml
-
- exec:
- def yaml_file = task.workDir.resolve('workflow_summary_mqc.yaml')
- yaml_file.text = """
- id: 'summary'
- description: " - this information is collected when the pipeline is started."
- section_name: 'Workflow Summary'
- section_href: "${workflow.manifest.homePage}"
- plot_type: 'html'
- data: |
- <dl class=\"dl-horizontal\">
- ${summary.collect { k,v -> " <dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }.join("\n")}
- </dl>
- """.stripIndent()
-}
-
-/*
- * STEP - MultiQC
- */
-process multiqc {
-
- publishDir "${params.outdir}/MultiQC", mode: 'copy'
-
- when:
- !params.skip_multiQC
-
- input:
- file (multiqc_config) from ch_multiqc_config
- file ('fastqc/*') from ch_fastqc_results_for_multiqc.collect().ifEmpty([])
- // TODO get-nf: Add in log files from your new processes for MultiQC to find!
- file ('software_versions/*') from software_versions_yaml.collect()
- file ('workflowSummary/*') from ch_workflow_summary_yaml.collect()
-
- output:
- file "*report.html" into ch_multiqc_report
- file "*_data"
- file "multiqc_plots"
-
- script:
- rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
- rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
- """
- 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 $output_docs -t html -o results_description.html
- """
-}
-
-/*
- * Completion e-mail notification
- */
-workflow.onComplete {
-
- // Set up the e-mail variables
- def name_wf = workflow.manifest.name
- def subject = "[$name_wf] Successful: $workflow.runName"
- if (!workflow.success) {
- subject = "[$name_wf] 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
- try {
- def sending = [ 'echo', '-e' , email_txt ].execute() | [ 'mail', '-s', subject, email_address ].execute()
- log.debug "[$name_wf] Sent summary e-mail to $email_address (mail)"
- } catch (all) {
- log.error "[$name_wf] ERROR ON EMAIL SENDING TO $email_address !!"
- }
- log.info "$email_txt"
- }
-
- // Write summary e-mail HTML to a file
- def output_d = new File( "${params.outdir}/pipeline_info/" )
- if (!output_d.exists()) {
- output_d.mkdirs()
- }
- def output_tf = new File( output_d, "pipeline_report.txt" )
- output_tf.withWriter { w -> w << email_txt }
- c_green = params.monochrome_logs ? '' : "\033[0;32m";
- c_purple = params.monochrome_logs ? '' : "\033[0;35m";
- c_red = params.monochrome_logs ? '' : "\033[0;31m";
- c_reset = params.monochrome_logs ? '' : "\033[0m";
-
- if (workflow.stats.ignoredCount > 0 && workflow.success) {
- log.info "-${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}[${name_wf}]${c_green} Pipeline completed successfully${c_reset}"
- } else {
- log.info "-${c_purple}[${name_wf}]${c_red} Pipeline completed with errors${c_reset}"
- }
-
-}
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+/*
+Copyright INRAE 2021
+
+This software is a computer program whose purpose is to
+analyze high-throughput sequencing data.
+You can use, modify and/ or redistribute the software under the terms
+of license (see the LICENSE file for more details).
+The software is distributed in the hope that it will be useful,
+but "AS IS" WITHOUT ANY WARRANTY OF ANY KIND.
+Users are therefore encouraged to test the software's suitability as regards
+their requirements in conditions enabling the security of their systems and/or data.
+The fact that you are presently reading this means that you have had knowledge
+of the license and that you accept its terms.
+This script is based on :
+ - the nf-core guidelines . See https://nf-co.re/ for more information
+ - the Curie institute template https://github.com/bioinfo-pf-curie/geniac-template/
+
+*/
+
+/*
+========================================================================================
+ NAMED WORKFLOW FOR PIPELINE
+========================================================================================
+*/
+
+include { techno_qc } from './workflow/techno_qc.nf'
+
+workflow QC_ANALYSIS {
+ techno_qc()
+}
+
+/*
+========================================================================================
+ RUN ALL WORKFLOWS
+========================================================================================
+*/
+
+workflow {
+ QC_ANALYSIS()
+}
diff --git a/modules/local/modules_report.nf b/modules/local/modules_report.nf
new file mode 100644
index 0000000000000000000000000000000000000000..b8c01c1c900bf08ce066129fbd30b801de0efd48
--- /dev/null
+++ b/modules/local/modules_report.nf
@@ -0,0 +1,75 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+process workflow_summary {
+
+ output:
+ path('workflow_summary_mqc.yaml')
+
+ exec:
+ def yaml_file = task.workDir.resolve('workflow_summary_mqc.yaml')
+ yaml_file.text = """
+ id: 'summary'
+ description: " - this information is collected when the pipeline is started."
+ section_name: 'Workflow Summary'
+ section_href: "${workflow.manifest.homePage}"
+ plot_type: 'html'
+ data: |
+ <dl class=\"dl-horizontal\">
+ ${params.summary.collect { k,v -> " <dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }.join("\n")}
+ </dl>
+ """.stripIndent()
+}
+
+/*
+ * STEP - MultiQC
+ */
+process multiqc {
+
+ publishDir "${params.outdir}/MultiQC", mode: 'copy'
+
+ module 'bioinfo/MultiQC-v1.7'
+
+ when:
+ !params.skip_multiQC
+
+ input:
+ path(multiqc_config)
+ path('fastqc/*') //.collect().ifEmpty([])
+ // TODO get-nf: Add in log files from your new processes for MultiQC to find!
+ //path('software_versions/*') //.collect()
+ path('workflowSummary/*') //.collect()
+
+ output:
+ path("*report.html")
+ path("*_data")
+ path("multiqc_plots")
+
+ script:
+ rtitle = params.custom_runName ? "--title \"$params.custom_runName\"" : ''
+ rfilename = params.custom_runName ? "--filename " + params.custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
+ """
+ multiqc -f $rtitle $rfilename --config $multiqc_config .
+ """
+}
+
+/*
+ * STEP - Output Description HTML
+ */
+process output_documentation {
+ publishDir "${params.outdir}/pipeline_info", mode: 'copy'
+
+ module 'system/pandoc-2.1.3'
+
+ input:
+ path(output_docs)
+
+ output:
+ path("results_description.html")
+
+ script:
+ """
+ pandoc $output_docs -t html -o results_description.html
+ """
+}
\ No newline at end of file
diff --git a/modules/local/utils.nf b/modules/local/utils.nf
new file mode 100644
index 0000000000000000000000000000000000000000..349252dfa675f828fe025683cb59eaea62d2881f
--- /dev/null
+++ b/modules/local/utils.nf
@@ -0,0 +1,82 @@
+/*
+ * Parse software version numbers
+ */
+process get_software_versions {
+ publishDir "${params.outdir}/pipeline_info", mode: 'copy',
+ saveAs: { filename ->
+ if (filename.indexOf(".csv") > 0) filename
+ else null
+ }
+
+ output:
+ path('software_versions_mqc.yaml')
+ path("software_versions.csv")
+
+ script:
+ // TODO nf-core: Get all tools to print their version number here
+ """
+ echo $workflow.manifest.version > v_pipeline.txt
+ echo $workflow.nextflow.version > v_nextflow.txt
+ fastqc --version > v_fastqc.txt
+ multiqc --version > v_multiqc.txt
+ scrape_software_versions.py &> software_versions_mqc.yaml
+ """
+}
+
+/*
+ * STEP 1 - FastQC
+ */
+process fastqc {
+ tag "$name"
+ label 'process_medium'
+ publishDir "${params.outdir}/fastqc", mode: 'copy',
+ saveAs: { filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename" }
+
+ module 'bioinfo/FastQC_v0.11.7'
+
+ input:
+ tuple val(name), path(reads)
+
+ output:
+ path "*_fastqc.{zip,html}"
+
+ script:
+ """
+ fastqc --quiet --threads $task.cpus $reads
+ """
+}
+
+/*
+ * STEP 2 - Fake QC
+ */
+process qc1 {
+ module 'bioinfo/FastQC_v0.11.7'
+
+ input:
+ tuple val(replicate_id), path(reads)
+
+ output:
+ path("${replicate_id}.qc1")
+
+ script:
+ """
+ echo "mkdir ${replicate_id} ; fastqc --nogroup --quiet -o ${replicate_id} --threads ${task.cpus} ${reads[0]} ${reads[1]}" > ${replicate_id}.qc1
+ """
+}
+
+/*
+ * STEP 3 - Fake assembly
+ */
+process assembly {
+ input:
+ path(qc)
+ tuple val(replicate_id), path(reads)
+
+ output:
+ path("${replicate_id}.assembly")
+
+ script:
+ """
+ echo "ASSEMBLY ${replicate_id} ; " > ${replicate_id}.assembly
+ """
+}
diff --git a/nextflow.config b/nextflow.config
index 87e3584b4666dcd82ef1a565310727c0fdd45fae..562640c939616ac1fc729fce925a326e32dbf857 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,7 +10,7 @@ params {
// Workflow flags
// TODO nf-core: Specify your pipeline's command line flags
- inputdir = "./data"
+ inputdir = "./template/data"
samplesheet = "${params.inputdir}/samples.csv"
single_end = false
outdir = './results'
@@ -20,7 +20,7 @@ params {
name = false
multiqc_config = "$baseDir/assets/multiqc_config.yaml"
tracedir = "${params.outdir}/pipeline_info"
- email = false
+ email = 'claire.kuchly@inrae.fr'
email_on_fail = false
monochrome_logs = false
help = false
diff --git a/sub-workflows/local/core.nf b/sub-workflows/local/core.nf
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/sub-workflows/local/wf_report.nf b/sub-workflows/local/wf_report.nf
new file mode 100644
index 0000000000000000000000000000000000000000..28625d40aa36ddb69ff321028a2b00d07d3f9e18
--- /dev/null
+++ b/sub-workflows/local/wf_report.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+include { workflow_summary;
+ multiqc;
+ output_documentation; } from '../../modules/local/modules_report.nf'
+
+workflow report {
+ take:
+ ch_output_docs
+
+ main:
+
+ workflow_summary()
+ //multiqc(ch_multiqc_config, fastqc.out.collect().ifEmpty([]), workflow_summary.out.collect())
+ output_documentation(ch_output_docs)
+
+}
\ No newline at end of file
diff --git a/workflow/techno_qc.nf b/workflow/techno_qc.nf
new file mode 100644
index 0000000000000000000000000000000000000000..42f16cf3d05ee70b355a3d14b4597bb05ab14120
--- /dev/null
+++ b/workflow/techno_qc.nf
@@ -0,0 +1,224 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+def helpMessage() {
+ log.info"""
+
+ Usage:
+
+ The typical command for running the pipeline is as follows:
+
+ nextflow run get-nf/template --inputdir '/path/to/data' --samplesheet 'samples.csv' -profile docker
+
+ Mandatory arguments:
+ --inputdir Path to input directory
+ -profile Configuration profile to use. Can use multiple (comma separated)
+ Available: conda, docker, singularity, path, genotoul, test and more.
+
+ Options:
+ --samplesheet Default inputdir/samples.csv eg: SAMPLE_ID,SAMPLE_NAME,path/to/R1/fastq/file,path/to/R2/fastq/file (for paired-end only)
+ --contaminant Name of iGenomes // To be discussed ????
+ --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
+ --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.
+
+
+ =======================================================
+ Available profiles
+ -profile test Run the test dataset
+ -profile conda Build a new conda environment before running the pipeline. Use `--condaCacheDir` to define the conda cache path
+ -profile path Use the installation path defined for all tools. Use `--globalPath` to define the installation path
+ -profile docker Use the Docker images for each process
+ -profile singularity Use the singularity images for each process
+ -profile genologin Run the workflow on the cluster, instead of locally
+
+ """.stripIndent()
+}
+
+// Show help message
+if (params.help) {
+ helpMessage()
+ exit 0
+}
+
+
+
+
+// NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
+
+/*
+ * Create a channel for input read files
+ */
+// If you want to use the channel below in a process, define the following:
+// input:
+// file dir from inputDirCh
+//
+
+
+ch_inputdir = params.inputdir ? Channel.fromPath(params.inputdir, checkIfExists: true) : Channel.empty()
+
+// Create a channel for input read files
+if(params.samplesheet){
+ if(params.single_end){
+ ch_read_files=Channel
+ .from(file("${params.samplesheet}"))
+ .splitCsv(header: false)
+ .map{ row -> [ row[0], [file(row[2])]] }
+ }else{
+ ch_read_files=Channel
+ .from(file("${params.samplesheet}"))
+ .splitCsv(header: false)
+ .map{ row -> [ row[0], [file(row[2]), file(row[3])]] }
+ }
+ params.reads=false
+} else {
+ exit 1, "Expect a samplesheet and an input dir !"
+}
+/*
+ * SET UP CONFIGURATION VARIABLES
+ */
+// Has the run name been specified by the user?
+// this has the bonus effect of catching both -name and --name
+params.custom_runName = params.name
+if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
+ params.custom_runName = workflow.runName
+}
+// Stage config files
+ch_multiqc_config = Channel.fromPath("${params.multiqc_config}", checkIfExists: true)
+ch_output_docs = Channel.fromPath("$projectDir/docs/output.md", checkIfExists: true)
+
+
+params.summary = [:]
+if (workflow.revision) params.summary['Pipeline Release'] = workflow.revision
+params.summary['Run Name'] = params.custom_runName ?: workflow.runName
+// TODO nf-core: Report custom parameters here
+params.summary['Input dir'] = params.inputdir
+params.summary['Sample sheet'] = params.samplesheet
+params.summary['Data Type'] = params.single_end ? 'Single-End' : 'Paired-End'
+params.summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
+if (workflow.containerEngine) params.summary['Container'] = "$workflow.containerEngine - $workflow.container"
+params.summary['Output dir'] = params.outdir
+params.summary['Launch dir'] = workflow.launchDir
+params.summary['Working dir'] = workflow.workDir
+params.summary['Script dir'] = workflow.projectDir
+params.summary['User'] = workflow.userName
+if (workflow.profile == 'awsbatch') {
+ params.summary['AWS Region'] = params.awsregion
+ params.summary['AWS Queue'] = params.awsqueue
+}
+params.summary['Config Profile'] = workflow.profile
+if (params.email || params.email_on_fail) {
+ params.summary['E-mail Address'] = params.email
+ params.summary['E-mail on failure'] = params.email_on_fail
+}
+log.info "-\033[2m--------------------------------------------------\033[0m-"
+log.info "-\033[2m----------------"+ workflow.manifest.name +" --\033[0m-"
+log.info "-\033[2m--------------------------------------------------\033[0m-"
+log.info params.summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
+log.info "-\033[2m--------------------------------------------------\033[0m-"
+
+
+
+// -------------------------------------------------
+// INCLUDES
+// -------------------------------------------------
+
+include { report } from '../sub-workflows/local/wf_report.nf'
+
+
+
+workflow techno_qc {
+ report(ch_output_docs)
+
+}
+
+
+/*
+ * Completion e-mail notification
+ */
+workflow.onComplete {
+
+ // Set up the e-mail variables
+ def name_wf = workflow.manifest.name
+ def subject = "[$name_wf] Successful: $workflow.runName"
+ if (!workflow.success) {
+ subject = "[$name_wf] FAILED: $workflow.runName"
+ }
+ def email_fields = [:]
+ email_fields['version'] = workflow.manifest.version
+ email_fields['runName'] = params.custom_runName ?: workflow.runName
+ email_fields['success'] = workflow.success
+ email_fields['dateComplete'] = workflow.complete
+ email_fields['duration'] = workflow.duration
+ email_fields['exitStatus'] = workflow.exitStatus
+ email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+ email_fields['errorReport'] = (workflow.errorReport ?: 'None')
+ email_fields['commandLine'] = workflow.commandLine
+ email_fields['projectDir'] = workflow.projectDir
+ email_fields['summary'] = params.summary
+ println(workflow)
+
+ email_fields['summary']['Date Started'] = 11 // workflow.start
+ email_fields['summary']['Date Completed'] = 11 // workflow.complete
+ email_fields['summary']['Pipeline script file path'] = 'aaa' //workflow.scriptFile
+ email_fields['summary']['Pipeline script hash ID'] = 'aaa' //workflow.scriptId
+ if (workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
+ if (workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
+ if (workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
+ if (workflow.container) email_fields['summary']['Docker image'] = workflow.container
+ email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
+ email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
+ email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+ // Check if we are only sending emails on failure
+ email_address = params.email
+ if (!params.email && params.email_on_fail && !workflow.success) {
+ email_address = params.email_on_fail
+ }
+
+ // Render the TXT template
+ def engine = new groovy.text.GStringTemplateEngine()
+ def tf = new File("$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
+ try {
+ def sending = [ 'echo', '-e' , email_txt ].execute() | [ 'mail', '-s', subject, email_address ].execute()
+ log.debug "[$name_wf] Sent summary e-mail to $email_address (mail)"
+ } catch (all) {
+ log.error "[$name_wf] ERROR ON EMAIL SENDING TO $email_address !!"
+ }
+ log.info "$email_txt"
+ }
+
+ // Write summary e-mail HTML to a file
+ def output_d = new File( "${params.outdir}/pipeline_info/" )
+ if (!output_d.exists()) {
+ output_d.mkdirs()
+ }
+ def output_tf = new File( output_d, "pipeline_report.txt" )
+ output_tf.withWriter { w -> w << email_txt }
+ c_green = params.monochrome_logs ? '' : "\033[0;32m";
+ c_purple = params.monochrome_logs ? '' : "\033[0;35m";
+ c_red = params.monochrome_logs ? '' : "\033[0;31m";
+ c_reset = params.monochrome_logs ? '' : "\033[0m";
+
+ if (workflow.stats.ignoredCount > 0 && workflow.success) {
+ log.info "-${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}[${name_wf}]${c_green} Pipeline completed successfully${c_reset}"
+ } else {
+ log.info "-${c_purple}[${name_wf}]${c_red} Pipeline completed with errors${c_reset}"
+ }
+
+}