From 6e74f10f7c04ed246976e1e9b1a1694e0be31e2e Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 27 Nov 2024 16:52:29 +0100
Subject: [PATCH 1/7] Little changes to add elembio demultiplexStat treatments
Ref: #126
---
bin/demuxStatsElement.R | 2 +-
workflow/short_reads_qc.nf | 15 ++++++---------
2 files changed, 7 insertions(+), 10 deletions(-)
diff --git a/bin/demuxStatsElement.R b/bin/demuxStatsElement.R
index c622209..2cf47cb 100755
--- a/bin/demuxStatsElement.R
+++ b/bin/demuxStatsElement.R
@@ -158,6 +158,6 @@ demultiplex_stat <- demultiplex_stat %>%
# Écriture du fichier de sortie
cat("\nEcriture du fichier de sortie :", demultiplexStat,"\n")
-write.csv(demultiplex_stat, demultiplexStat, row.names = FALSE, quote = FALSE)
+write.table(demultiplex_stat, demultiplexStat, sep="\t", row.names = FALSE, quote = FALSE)
cat("Fin normale du script.\n")
\ No newline at end of file
diff --git a/workflow/short_reads_qc.nf b/workflow/short_reads_qc.nf
index 3518b06..2a8bbca 100644
--- a/workflow/short_reads_qc.nf
+++ b/workflow/short_reads_qc.nf
@@ -103,16 +103,16 @@ workflow SHORT_READS_QC {
CORE_ILLUMINA(ch_ss, ch_DemuxStatXML, ch_DemuxSummary, ch_read)
fastq = CORE_ILLUMINA.out.fastq
ch_versions = ch_versions.mix(CORE_ILLUMINA.out.versions)
- illumina_demux_stats = CORE_ILLUMINA.out.demuxStat
+ demux_stats = CORE_ILLUMINA.out.demuxStat
} else {
fastq = ch_read
- illumina_demux_stats = channel.empty()
+ demux_stats = channel.empty()
}
if (! params.skip_core_element && params.sequencer =~ "AVITI") {
CORE_ELEMENT(ch_runManifestJSON, ch_indexAssigned, ch_indexUnassigned)
- elembio_demux_stats = CORE_ELEMENT.out.demuxStat
+ demux_stats = CORE_ELEMENT.out.demuxStat
} else {
- elembio_demux_stats = Channel.empty()
+ demux_stats = Channel.empty()
}
CORE(fastq)
@@ -199,11 +199,8 @@ workflow SHORT_READS_QC {
)
// Add demultiplexStat treatments
- ILLUMINA_TREATMENT_DEMUX_RUN(NGL.out.run_code, illumina_demux_stats, params.lane)
- ILLUMINA_TREATMENT_DEMUX_READSETS(NGL.out.readsets_file, illumina_demux_stats, '')
-
- // ELEMBIO_TREATMENT_DEMUX_RUN(NGL.out.run_code, elembio_demux_stats)
- // ELEMBIO_TREATMENT_DEMUX_READSETS(NGL.out.readsets_file, elembio_demux_stats)
+ TREATMENT_DEMUX_RUN(NGL.out.run_code, demux_stats, params.lane)
+ TREATMENT_DEMUX_READSETS(NGL.out.readsets_file, demux_stats, '')
}
}
--
GitLab
From 0990cb789466f67d562bc6aa7a26fab8ff6df173 Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 27 Nov 2024 16:54:51 +0100
Subject: [PATCH 2/7] Add cc email adress in dev mode
---
lib/pipeline.groovy | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/lib/pipeline.groovy b/lib/pipeline.groovy
index 37f5455..77af301 100644
--- a/lib/pipeline.groovy
+++ b/lib/pipeline.groovy
@@ -170,7 +170,7 @@ def endOfPipelineEvents(summary) {
}
if (params.is_dev_mode) {
email_address = emails_map.dev
- email = ''
+ email_cc = ''
}
workflow.onComplete {
--
GitLab
From a161c44e709ef2c9b777dad015f5252e0f5205ab Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 27 Nov 2024 16:57:33 +0100
Subject: [PATCH 3/7] Changes some email adresses
error -> bioinfo
labo -> labo
Ref: #127
---
lib/pipeline.groovy | 5 +++--
nextflow.config | 5 ++---
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/lib/pipeline.groovy b/lib/pipeline.groovy
index 77af301..d4de1f5 100644
--- a/lib/pipeline.groovy
+++ b/lib/pipeline.groovy
@@ -100,9 +100,9 @@ pipeline_options_map = [
is_dev_mode: [default: false, optional: false, help: 'Preset of some options'],
DTM_mode: [default: false, optional: false, help: 'Enable some process for DTM analysis'],
email: [default: '', optional: false, help: 'Main email adress for execution pipeline notifications'],
- email_on_fail: [default: 'jules.sabban@inrae.fr', optional: false, help: 'Email adress to notify execution pipeline errors'],
+ email_on_fail: [default: 'get-plage.bioinfo@genotoul.fr', optional: false, help: 'Email adress to notify execution pipeline errors'],
email_bioinfo: [default: 'get-plage.bioinfo@genotoul.fr', optional: true, help: 'Bioinformatics team email adress for execution pipeline notifications'],
- email_labo: [default: '', optional: true, help: 'Biologists team email adress for execution pipeline notifications'],
+ email_labo: [default: 'get-plage.labo@genotoul.fr', optional: true, help: 'Biologists team email adress for execution pipeline notifications'],
host: [default: 'genobioinfo', optional: false, help: 'Name of the HPC where the pipeline is executed. Must have special config file in conf folder'],
skip_core_illumina: [default: false, optional: false, help: 'To skip Illumina subworkflow'],
skip_core_element: [default: false, optional: false, help: 'To skip Elembio subworkflow'],
@@ -168,6 +168,7 @@ def endOfPipelineEvents(summary) {
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 = ''
diff --git a/nextflow.config b/nextflow.config
index e557d19..be101c7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -85,10 +85,9 @@ params {
host = 'genobioinfo'
email=""
email_dev="jules.sabban@inrae.fr"
- email_on_fail="jules.sabban@inrae.fr"
+ email_on_fail="get-plage.bioinfo@genotoul.fr"
email_bioinfo="get-plage.bioinfo@genotoul.fr"
- //email_labo="get-plage.labo@genotoul.fr"
- email_labo=""
+ email_labo="get-plage.labo@genotoul.fr"
// skip parameters
skip_core_illumina = false
--
GitLab
From 2ccb885ebc4e4f24a22d52315df79340c6c1ee8d Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Wed, 27 Nov 2024 17:00:19 +0100
Subject: [PATCH 4/7] Rename demultiplexStat process
Remove illumina tag
Ref: #126
---
modules/local/module_NGL-Bi.nf | 4 ++--
workflow/short_reads_qc.nf | 8 +++-----
2 files changed, 5 insertions(+), 7 deletions(-)
diff --git a/modules/local/module_NGL-Bi.nf b/modules/local/module_NGL-Bi.nf
index 7fde2fa..dd2aeb8 100644
--- a/modules/local/module_NGL-Bi.nf
+++ b/modules/local/module_NGL-Bi.nf
@@ -20,7 +20,7 @@ process prepareReadSetCreation {
"""
}
-process TREATMENT_DEMUXSTAT_ILLUMINA {
+process TREATMENT_DEMUXSTAT {
label 'ngl'
input:
@@ -42,7 +42,7 @@ process TREATMENT_DEMUXSTAT_ILLUMINA {
--stat $csvFile \\
${forceOption} \\
$args \\
- 1> treatment_demux_${lane}.log
+ 1> treatment_demux_${level}.log
"""
}
diff --git a/workflow/short_reads_qc.nf b/workflow/short_reads_qc.nf
index 2a8bbca..042c1d3 100644
--- a/workflow/short_reads_qc.nf
+++ b/workflow/short_reads_qc.nf
@@ -81,11 +81,9 @@ include { RNA_QC } from "$baseDir/sub-workflows/local/rna_qc.nf"
include { DIVERSITY_QC } from "$baseDir/sub-workflows/local/diversity_qc.nf"
include { PARSE_REPORTS } from "$baseDir/modules/local/module_DTM.nf"
include { NGL } from "$baseDir/sub-workflows/local/ngl.nf"
-include { TREATMENT_DEMUXSTAT_ILLUMINA as ILLUMINA_TREATMENT_DEMUX_RUN;
- TREATMENT_DEMUXSTAT_ILLUMINA as ILLUMINA_TREATMENT_DEMUX_READSETS;
- // TREATMENT_DEMUXSTAT_ELEMENT as ELEMBIO_TREATMENT_DEMUX_RUN;
- // TREATMENT_DEMUXSTAT_ELEMENT as ELEMBIO_TREATMENT_DEMUX_READSETS;
- } from "$baseDir/modules/local/module_NGL-Bi.nf"
+include { TREATMENT_DEMUXSTAT as ILLUMINA_TREATMENT_DEMUX_RUN;
+ TREATMENT_DEMUXSTAT as ILLUMINA_TREATMENT_DEMUX_READSETS;
+ } from "$baseDir/modules/local/module_NGL-Bi.nf"
include { MULTIQC } from "${params.shared_modules}/multiqc.nf"
include { GCBIAS as GC_BIAS } from "${params.shared_modules}/gcbias.nf"
include { workflow_summary as WORKFLOW_SUMMARY } from "${params.shared_modules}/workflow_summary.nf"
--
GitLab
From 88c8674d44d8468ee09155b1876f9249f6b371d7 Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Thu, 28 Nov 2024 16:31:38 +0100
Subject: [PATCH 5/7] Rename some treatment modules
- remove dependency to illumina
These modules will be use for AVITI to
Ref: #126
---
conf/base.config | 2 +-
workflow/short_reads_qc.nf | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/conf/base.config b/conf/base.config
index 385975b..74e388b 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -268,7 +268,7 @@ process {
].join(' ')
}
- withName: ILLUMINA_TREATMENT_DEMUX_RUN {
+ withName: TREATMENT_DEMUX_RUN {
ext.args = [
"--lane '${params.lane}'",
].join(' ')
diff --git a/workflow/short_reads_qc.nf b/workflow/short_reads_qc.nf
index 042c1d3..41bef8c 100644
--- a/workflow/short_reads_qc.nf
+++ b/workflow/short_reads_qc.nf
@@ -81,8 +81,8 @@ include { RNA_QC } from "$baseDir/sub-workflows/local/rna_qc.nf"
include { DIVERSITY_QC } from "$baseDir/sub-workflows/local/diversity_qc.nf"
include { PARSE_REPORTS } from "$baseDir/modules/local/module_DTM.nf"
include { NGL } from "$baseDir/sub-workflows/local/ngl.nf"
-include { TREATMENT_DEMUXSTAT as ILLUMINA_TREATMENT_DEMUX_RUN;
- TREATMENT_DEMUXSTAT as ILLUMINA_TREATMENT_DEMUX_READSETS;
+include { TREATMENT_DEMUXSTAT as TREATMENT_DEMUX_RUN;
+ TREATMENT_DEMUXSTAT as TREATMENT_DEMUX_READSETS;
} from "$baseDir/modules/local/module_NGL-Bi.nf"
include { MULTIQC } from "${params.shared_modules}/multiqc.nf"
include { GCBIAS as GC_BIAS } from "${params.shared_modules}/gcbias.nf"
--
GitLab
From 9bd58cf7a29a043ae934e42b4cdef983ac795765 Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Thu, 28 Nov 2024 16:36:54 +0100
Subject: [PATCH 6/7] NGSRG treatment at RS only for illumina
---
sub-workflows/local/ngl.nf | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/sub-workflows/local/ngl.nf b/sub-workflows/local/ngl.nf
index a677806..6a22fbf 100644
--- a/sub-workflows/local/ngl.nf
+++ b/sub-workflows/local/ngl.nf
@@ -47,7 +47,9 @@ workflow NGL {
readsets_created = BEGIN.out.readsets_created
ready = BEGIN.out.ready
- NGSRG_READSET(readsets_created, demux_stat_json, 'readsets')
+ if(sequencer_name =~ "NovaSeq|MiSeq") {
+ NGSRG_READSET(readsets_created, demux_stat_json, 'readsets')
+ }
bi_run_code = nglBiRunCode.collect().map { it.toString() }
--
GitLab
From 47785ab792d50f28e50e47d05c1c23e8882fa46a Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Thu, 28 Nov 2024 16:43:03 +0100
Subject: [PATCH 7/7] Change NGL-bi URL
Use the new one
Ref: #128
---
assets/final_email_template.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/assets/final_email_template.txt b/assets/final_email_template.txt
index 1edfcc2..fe40165 100644
--- a/assets/final_email_template.txt
+++ b/assets/final_email_template.txt
@@ -15,7 +15,7 @@ Run : $run
<% if (success){
out << """## GeT-nextflow-NGL-Bi/wf-Illumina-nf execution completed successfully! ## \n"""
if (runNGLBi){
- out << """\tCheck your analyzes on NGL-Bi : http://esitoul-rocky-${instance}.toulouse.inra.fr:9096/runs/${runNGLBi} """
+ out << """\tCheck your analyzes on NGL-Bi : https://ngl-bi.genomique.genotoul.fr/runs/${runNGLBi} """
} else {
out << """\tYour analyzes are NOT on NGL-Bi : ask to a bioinfo team member for details."""
}
--
GitLab