From 5533b5b124d734311c004012e8a1151a3ae0737f Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 15 May 2024 11:04:02 +0200
Subject: [PATCH 1/4] Hot fix for ngl-bi run creation
- And create again the RunNGL-Bi.created file if needed
Ref: #93
---
sub-workflows/local/begin_nglbi.nf | 24 +++++++++++++++---------
workflow/illumina_qc.nf | 2 +-
2 files changed, 16 insertions(+), 10 deletions(-)
diff --git a/sub-workflows/local/begin_nglbi.nf b/sub-workflows/local/begin_nglbi.nf
index c565408..2e60dd9 100644
--- a/sub-workflows/local/begin_nglbi.nf
+++ b/sub-workflows/local/begin_nglbi.nf
@@ -13,8 +13,8 @@
// -------------------------------------------------
include { CREATE_RUN;
- UPDATE_NGLBI_STATE_FROM_CODE as UPDATE_STATE_FS;
- UPDATE_NGLBI_STATE_FROM_CODE as UPDATE_STATE_IPRG;
+ UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FS;
+ UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_IPRG;
UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FRG;
UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_IPQC;
CREATE_READSETS;
@@ -36,22 +36,27 @@ workflow NGLBI {
if (params.bi_run_code == '') {
CREATE_RUN(params.sequencer, params.sq_xp_code, '', 1)
-
- bi_run_code = CREATE_RUN.out.createdFile.splitText().map{it -> it.trim()}
+ createdFile = CREATE_RUN.out.createdFile
+ nglBiRunCode = CREATE_RUN.out.nglBiRunCode
ready_for_state = CREATE_RUN.out.ready
} else {
ready_for_state = Channel.value(1)
- bi_run_code = Channel.value(params.bi_run_code)
+ createdFile = Channel.of(params.bi_run_code).map { content ->
+ def file = file('RunNGL-Bi.created')
+ file.text = content
+ file
+ }
+ nglBiRunCode = params.bi_run_code
}
// Update run state
- UPDATE_STATE_FS(bi_run_code, 'F-S', ready_for_state)
- UPDATE_STATE_IPRG(bi_run_code, 'IP-RG', UPDATE_STATE_FS.out.ready)
+ UPDATE_STATE_FS(createdFile, 'F-S', ready_for_state)
+ UPDATE_STATE_IPRG(createdFile, 'IP-RG', UPDATE_STATE_FS.out.ready)
// Creation of ReadSets
CREATE_READSETS(
params.sq_xp_code,
- bi_run_code,
+ nglBiRunCode,
'',
'',
UPDATE_STATE_IPRG.out.ready
@@ -64,7 +69,8 @@ workflow NGLBI {
emit:
ready = UPDATE_STATE_IPQC.out.ready
readsetsFile = CREATE_READSETS.out.createdFile
- runFile = CREATE_RUN.out.createdFile
+ createdFile = createdFile
+ nglBiRunCode = nglBiRunCode
}
diff --git a/workflow/illumina_qc.nf b/workflow/illumina_qc.nf
index eb75e22..7500b06 100644
--- a/workflow/illumina_qc.nf
+++ b/workflow/illumina_qc.nf
@@ -103,7 +103,7 @@ workflow ILLUMINA_QC {
if (params.insert_to_ngl){
// Add demultiplexStat treatments
- TREATMENT_DEMUX_RUN(NGLBI.out.runFile, CORE_ILLUMINA.out.demuxStat)
+ TREATMENT_DEMUX_RUN(NGLBI.out.nglBiRunCode, CORE_ILLUMINA.out.demuxStat)
TREATMENT_DEMUX_READSETS(NGLBI.out.readsetsFile, CORE_ILLUMINA.out.demuxStat)
}
}
--
GitLab
From 6bbdee75ba0e318385b0815365f0a30a7521d2b6 Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 15 May 2024 11:08:10 +0200
Subject: [PATCH 2/4] Cast resource_factor to integer instead of decimal
Re: #94
---
conf/base.config | 5 +----
nextflow.config | 5 ++++-
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/conf/base.config b/conf/base.config
index f6ad4e7..5206416 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -130,10 +130,7 @@ process {
publishDir = [
path: "${params.outdir}/alignment/bwa",
- mode: {
- if (params.DTM_mode) 'symlink'
- else 'copy'
- }
+ mode: 'copy'
]
}
diff --git a/nextflow.config b/nextflow.config
index ea9a9d0..d4fa10e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -32,6 +32,9 @@ params {
miseq_subset_seq = "50000" // in reads must be a string
nova_subset_seq = "50000000" // in reads
large_indexing_nova_subset_seq = "500000" // in reads
+ coverage = 0 // coverage in X
+ len_r1 = 150
+ len_r2 = 150
// DNA / RNA params
reference_genome = ""
@@ -99,7 +102,7 @@ def n_read_files = Files.walk(Paths.get(params.inputdir.toString()))
// on retire les 2 fichiers undetermined
def n_samples = ( n_read_files - 2 ) / 2
System.out.println "\nNombre d'échantillons trouvés sur cette lane : $n_samples"
-params.resource_factor = 0.1 * n_samples
+params.resource_factor = java.lang.Math.round(0.1 * n_samples)
import java.text.SimpleDateFormat
SimpleDateFormat uniqueness_format = new SimpleDateFormat("yyyyMMddHHmmss")
--
GitLab
From 0abfd1079cc042dc41580c19f116d4f247703d8e Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 15 May 2024 11:12:20 +0200
Subject: [PATCH 3/4] Add NGL codes in emails and MultiQC
- Only if exists, of course
Ref: #95
---
assets/begin_template.txt | 3 ++-
assets/final_email_template.txt | 2 ++
conf/functions.config | 4 ++++
3 files changed, 8 insertions(+), 1 deletion(-)
diff --git a/assets/begin_template.txt b/assets/begin_template.txt
index 1dd968d..69415f3 100644
--- a/assets/begin_template.txt
+++ b/assets/begin_template.txt
@@ -18,7 +18,8 @@ The analysis of the following sequencing is running :
- FlowCell : $flowcell
- Lane : $lane
- Directory : $directory
-
+<% if (xpNGLSq){ out << "- NGL-SQ Experiment : $xpNGLSq " } %>
+<% if (runNGLBi){ out << "- NGL-Bi RunCode : $runNGLBi " } %>
The command used to launch the workflow was as follows :
diff --git a/assets/final_email_template.txt b/assets/final_email_template.txt
index 5221db8..64f89de 100644
--- a/assets/final_email_template.txt
+++ b/assets/final_email_template.txt
@@ -9,6 +9,8 @@
NextFlow Run Name : $runName
Project : $project
Run : $run
+<% if (xpNGLSq){ out << "NGL-SQ Experiment : $xpNGLSq " } %>
+<% if (runNGLBi){out << "NGL-Bi RunCode : $runNGLBi" } %>
<% if (success){
out << """## GeT-nextflow-NGL-Bi/wf-Illumina-nf execution completed successfully! ##
diff --git a/conf/functions.config b/conf/functions.config
index 2099a7a..9be15ad 100644
--- a/conf/functions.config
+++ b/conf/functions.config
@@ -106,6 +106,8 @@ def sendBeginMail(formatted_date) {
begin_email_fields['version'] = workflow.manifest.version
begin_email_fields['wfRunName'] = workflow.runName
begin_email_fields['run_name'] = params.run_name
+ begin_email_fields['runNGLBi'] = (params.bi_run_code ?: '')
+ begin_email_fields['xpNGLSq'] = (params.sq_xp_code ?: '')
begin_email_fields['project'] = params.project
begin_email_fields['sequencer'] = params.sequencer
begin_email_fields['flowcell'] = params.fc_id
@@ -148,6 +150,8 @@ def sendFinalMail(formatted_date, summary) {
email_fields['runName'] = workflow.runName
email_fields['project'] = params.project
email_fields['run'] = params.run_name
+ email_fields['runNGLBi'] = (params.bi_run_code ?: '')
+ email_fields['xpNGLSq'] = (params.sq_xp_code ?: '')
email_fields['success'] = workflow.success
email_fields['dateComplete'] = formatted_date
email_fields['duration'] = workflow.duration
--
GitLab
From 46d9a035248c3d167636ae4e81fbf6df5e7f21cc Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 15 May 2024 11:16:31 +0200
Subject: [PATCH 4/4] Update shared_modules path in dev mode
---
conf/report.config | 2 +-
conf/test.config | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/conf/report.config b/conf/report.config
index 11866bf..af1fc52 100644
--- a/conf/report.config
+++ b/conf/report.config
@@ -29,5 +29,5 @@ manifest {
description = "Workflow for Illumina data quality control"
mainScript = 'main.nf'
nextflowVersion = '>=0.32.0'
- version = '1.16.1'
+ version = '1.17.0'
}
\ No newline at end of file
diff --git a/conf/test.config b/conf/test.config
index c6d32e9..4294ca1 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -4,7 +4,7 @@
System.out.println "Profil dev => on ajuste les paramètres..."
params {
ngl_bi_client = '/work/project/PlaGe/test/jules/VisualStudioSources/ngl-bi_client/'
- shared_modules = '/save/user/sbsuser/scripts-ngs/shared_modules_Current/'
+ shared_modules = '/work/project/PlaGe/test/jules/VisualStudioSources/shared_modules/'
is_dev_mode = true
}
--
GitLab