From aa7d2c97e8afb8d5abbecae782f4ec2d00e00ca1 Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 4 Dec 2024 10:10:39 +0100
Subject: [PATCH 1/5] Remove techno arg in Analysis creation
Ref: #133
---
conf/base.config | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/conf/base.config b/conf/base.config
index 74e388b..0ce330c 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -256,9 +256,7 @@ process {
//=========================================
process {
withName: CREATE_ANALYSIS {
- def techno = params.sequencer =~ "MiSeq|NovaSeq" ? 'illumina' : params.sequencer =~ "AVITI" ? 'elembio' : 'other'
- ext.args = "--techno $techno "
- ext.args += params.project_hash ? "--projectDir '${params.project}-${params.project_hash}'" : ''
+ ext.args = params.project_hash ? "--projectDir '${params.project}-${params.project_hash}'" : ''
}
withName: CREATE_READSETS {
--
GitLab
From df85a4b431f405aeeb4e5d11a0300e9faeca3b7f Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 4 Dec 2024 10:11:16 +0100
Subject: [PATCH 2/5] Little changes in shared_modules/lib/utils.groovy
Ref: #132
---
lib/pipeline.groovy | 80 ++++++++++++++++++++++++++-------------------
1 file changed, 47 insertions(+), 33 deletions(-)
diff --git a/lib/pipeline.groovy b/lib/pipeline.groovy
index d4de1f5..caaf64c 100644
--- a/lib/pipeline.groovy
+++ b/lib/pipeline.groovy
@@ -28,19 +28,7 @@ pipeline_group = pipeline_info[0]
pipeline_project = pipeline_info[1]
pipeline_techno = pipeline_project.split('-')[1]
-if (params.email == null) {
- email_main = params.email_bioinfo
-} else {
- email_main = params.email
-}
-
-emails_map = [
- main: email_main,
- bioinfo: params.email_bioinfo,
- labo: params.email_labo,
- failure: params.email_on_fail,
- dev: params.email_dev
-]
+emails_map = create_email_map()
pipeline_options_map = [
inputdir: [default: '', optional: false, help: 'Path to the input directory [demultiplexing output directory]'],
@@ -132,6 +120,35 @@ begin_email_fields = get_workflow_info(
// ----------------------------------
// Functions Definition
// ----------------------------------
+def create_email_map() {
+ def hash = [:]
+
+ def email_main = ''
+ def email_bioinfo = ''
+ def email_labo = ''
+ def email_failure = ''
+
+ email_main = params.email ?: params.email_bioinfo?: ''
+ email_bioinfo = params.email_bioinfo ?: ''
+ email_labo = params.email_labo ?: ''
+ email_failure = params.email_on_fail ?: ''
+
+ if (params.is_dev_mode) {
+ email_main = params.email_dev
+ email_bioinfo = email_main
+ email_labo = email_main
+ email_failure = email_main
+ log.info "DEV mode activated : overwriting every email adresses to $email_main"
+ }
+
+ hash.main = email_main
+ hash.bioinfo = email_bioinfo
+ hash.labo = email_labo
+ hash.failure = email_failure
+
+ return hash
+}
+
def create_final_email_fields(formatted_date, summary) {
return get_workflow_info(
[
@@ -160,28 +177,19 @@ def create_error_email_fields(formatted_date) {
def endOfPipelineEvents(summary) {
SimpleDateFormat format = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss")
end_mail_sent = false
-
- def email_address = emails_map.main
- def email_cc = emails_map.bioinfo
-
- if (emails_map.main && emails_map.failure && !workflow.success) {
- email_address = emails_map.failure
- email_cc = ''
- }
- log.debug "IS DEV MODE ? $params.is_dev_mode"
- if (params.is_dev_mode) {
- email_address = emails_map.dev
- email_cc = ''
- }
-
+
workflow.onComplete {
+ emails_map = create_email_map()
+ if (emails_map.main && emails_map.failure && !workflow.success) {
+ emails_map.main = emails_map.failure
+ }
log.info "Sending final e-mail"
template_final = "$baseDir/assets/final_email_template.txt"
final_email_fields = create_final_email_fields(format.format(new Date()), summary)
- end_mail_sent = sendFinalMail(template_final, final_email_fields, email_address, email_cc, end_mail_sent)
+ end_mail_sent = sendFinalMail(template_final, final_email_fields, emails_map, end_mail_sent) //email_address, email_cc
// remove work directory if pipeline is successful
- if (workflow.success) {
+ if (workflow.success && !params.sequencer.equalsIgnoreCase('AVITI')) {
if (!workflow.profile.contains('dev') ) {
println "Pipeline terminé avec succès => suppression du workdir : $workflow.workDir"
exec:
@@ -202,16 +210,23 @@ def endOfPipelineEvents(summary) {
}
workflow.onError {
+ emails_map = create_email_map()
+ if (emails_map.main && emails_map.failure && !workflow.success) {
+ emails_map.main = emails_map.failure
+ }
error_email_fields = create_error_email_fields(format.format(new Date()))
template_error = "$baseDir/assets/error_email_template.txt"
log.info "Sending error e-mail"
- end_mail_sent = sendFinalMail(template_error, error_email_fields, email_address, email_cc, end_mail_sent)
+ end_mail_sent = sendFinalMail(template_error, error_email_fields, emails_map, end_mail_sent)
}
}
def getSummary() {
SimpleDateFormat format = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss")
- return createSummary(format.format(new Date()))
+ def summary = createSummary(format.format(new Date()))
+ summary['Sequencing Type'] = params.is_multiplex ? 'Multiplex' : 'Simplex'
+ summary['Reference'] = params.reference_genome ?: params.reference_transcriptome?: ''
+ return summary
}
// ----------------------------------
@@ -236,8 +251,7 @@ if (paramsValidation(pipeline_options_map)) { // true s'il manque 1 param
customMailSend(
"$baseDir/assets/begin_template.txt",
begin_email_fields,
- emails_map.main,
- "${emails_map.labo},${emails_map.bioinfo}",
+ emails_map,
!workflow.resume,
false
)
--
GitLab
From bd50ec1fbe5c1f2836680f8f01e33d85075a62c2 Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 4 Dec 2024 15:03:31 +0100
Subject: [PATCH 3/5] bad if on workflow.success in lib/pipepline.groovy
---
lib/pipeline.groovy | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/lib/pipeline.groovy b/lib/pipeline.groovy
index caaf64c..e785788 100644
--- a/lib/pipeline.groovy
+++ b/lib/pipeline.groovy
@@ -189,11 +189,11 @@ def endOfPipelineEvents(summary) {
end_mail_sent = sendFinalMail(template_final, final_email_fields, emails_map, end_mail_sent) //email_address, email_cc
// remove work directory if pipeline is successful
- if (workflow.success && !params.sequencer.equalsIgnoreCase('AVITI')) {
- if (!workflow.profile.contains('dev') ) {
- println "Pipeline terminé avec succès => suppression du workdir : $workflow.workDir"
- exec:
- workflow.workDir.deleteDir()
+ if (workflow.success) {
+ if (!workflow.profile.contains('dev') && !params.sequencer.equalsIgnoreCase('AVITI')) {
+ println "Pipeline terminé avec succès => suppression du workdir : $workflow.workDir"
+ exec:
+ workflow.workDir.deleteDir()
}
if (workflow.stats.ignoredCount > 0) {
--
GitLab
From 28d173e996c7a6bd9f10096355550e248c796259 Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 4 Dec 2024 15:05:10 +0100
Subject: [PATCH 4/5] Add NGSRG treatment for elembio
Ref: #130
---
modules/local/module_NGL-Bi.nf | 28 +++++++++++++++++++++++++++-
sub-workflows/local/ngl.nf | 7 +++++--
2 files changed, 32 insertions(+), 3 deletions(-)
diff --git a/modules/local/module_NGL-Bi.nf b/modules/local/module_NGL-Bi.nf
index dd2aeb8..59f2360 100644
--- a/modules/local/module_NGL-Bi.nf
+++ b/modules/local/module_NGL-Bi.nf
@@ -72,7 +72,7 @@ process FILE_RENAME {
"""
}
-process NGSRG {
+process NGSRG_ILLUMINA {
label 'ngl'
input:
@@ -94,4 +94,30 @@ process NGSRG {
1> treatment_ngsrg_${level}.log
"""
+}
+
+process NGSRG_ELEMBIO {
+ label 'ngl'
+
+ input:
+ path nglFile
+ path demuxDirectory
+ val lane
+ val level
+
+ output:
+ path("*.log"), emit: log
+
+ script:
+ def args = task.ext.args ?: ''
+ """
+ perl ${params.ngl_bi_client}/GeT/perl/elemBio/createNGL-BiTreatmentNGSRG.pl \\
+ --objectFile $nglFile \\
+ --pathdemuxRunStatsFile $demuxDirectory/RunStats.json \\
+ --pathdemuxRunParametersFile $demuxDirectory/RunParameters.json \\
+ --laneNumberToWorkOn $lane \\
+ --level $level \\
+ $args \\
+ 1> treatment_ngsrg_${level}_${lane}.log
+ """
}
\ No newline at end of file
diff --git a/sub-workflows/local/ngl.nf b/sub-workflows/local/ngl.nf
index 6a22fbf..20ebc14 100644
--- a/sub-workflows/local/ngl.nf
+++ b/sub-workflows/local/ngl.nf
@@ -21,7 +21,8 @@ include { UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FQC;
include { FILE_RENAME as RENAME_FASTQ;
FILE_RENAME as RENAME_INDEX;
- NGSRG as NGSRG_READSET; } from "$baseDir/modules/local/module_NGL-Bi.nf"
+ NGSRG_ILLUMINA;
+ NGSRG_ELEMBIO; } from "$baseDir/modules/local/module_NGL-Bi.nf"
// -------------------------------------------------
// WORKFLOW
// -------------------------------------------------
@@ -48,7 +49,9 @@ workflow NGL {
ready = BEGIN.out.ready
if(sequencer_name =~ "NovaSeq|MiSeq") {
- NGSRG_READSET(readsets_created, demux_stat_json, 'readsets')
+ NGSRG_ILLUMINA(readsets_created, demux_stat_json, 'readsets')
+ } else if (sequencer_name =~ "AVITI") {
+ NGSRG_ELEMBIO(readsets_created, params.inputdir, params.lane, 'readsets')
}
bi_run_code = nglBiRunCode.collect().map { it.toString() }
--
GitLab
From 8c1ba5df616a22a667b68bc4daac8ec52a95f0ef Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 4 Dec 2024 15:16:20 +0100
Subject: [PATCH 5/5] Add analysis name
Ref: #134
---
sub-workflows/local/ngl.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sub-workflows/local/ngl.nf b/sub-workflows/local/ngl.nf
index 20ebc14..34a1f01 100644
--- a/sub-workflows/local/ngl.nf
+++ b/sub-workflows/local/ngl.nf
@@ -80,7 +80,7 @@ workflow NGL {
project_hash,
fq,
MD5SUM_FASTQ.out.md5sum,
- techno
+ params.run_name
)
emit:
--
GitLab