diff --git a/assets/final_email_template.txt b/assets/final_email_template.txt
index 1edfcc2321bd49588901b58e248d88d167f88a78..fe40165f8cfdb69d0f1fe03d459c106171176194 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."""
}
diff --git a/bin/demuxStatsElement.R b/bin/demuxStatsElement.R
index c6222094abc730a0561fd575b6ab0a8f7593ffe0..2cf47cb82f6c43bcfb3afee08afba2d945757d93 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/conf/base.config b/conf/base.config
index 385975b616f208c48079768e1d49b4d5f6ba9016..74e388bfce93c960054042899129714706f92abd 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/lib/pipeline.groovy b/lib/pipeline.groovy
index 37f5455a681a33ad13ec40bb53c04c58319a1a8e..d4de1f5d809492fc4e06294b24aeaff341bda0c1 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'],
@@ -168,9 +168,10 @@ 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 = ''
+ email_cc = ''
}
workflow.onComplete {
diff --git a/modules/local/module_NGL-Bi.nf b/modules/local/module_NGL-Bi.nf
index 7fde2fa1fa93352fbfe8b06af5367517d84a2532..dd2aeb8a17eaee88f4dc282821d4c7c1fe61deb0 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_${level}.log
"""
}
diff --git a/nextflow.config b/nextflow.config
index e557d19f050fc5dd97c3165ebdd5dbeb226e7488..be101c7a03f203bd9e80907e5a1ee31da550b204 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -85,10 +85,9 @@ params {
host = 'genobioinfo'
email=""
email_dev="jules.sabban@inrae.fr"
- email_on_fail="jules.sabban@inrae.fr"
+ email_on_fail="get-plage.bioinfo@genotoul.fr"
email_bioinfo="get-plage.bioinfo@genotoul.fr"
- //email_labo="get-plage.labo@genotoul.fr"
- email_labo=""
+ email_labo="get-plage.labo@genotoul.fr"
// skip parameters
skip_core_illumina = false
diff --git a/sub-workflows/local/ngl.nf b/sub-workflows/local/ngl.nf
index a6778060f8767806572df50ddd2a6021def7c946..6a22fbffbe5a52e45e369283fa2791cc1a7776be 100644
--- a/sub-workflows/local/ngl.nf
+++ b/sub-workflows/local/ngl.nf
@@ -47,7 +47,9 @@ workflow NGL {
readsets_created = BEGIN.out.readsets_created
ready = BEGIN.out.ready
- NGSRG_READSET(readsets_created, demux_stat_json, 'readsets')
+ if(sequencer_name =~ "NovaSeq|MiSeq") {
+ NGSRG_READSET(readsets_created, demux_stat_json, 'readsets')
+ }
bi_run_code = nglBiRunCode.collect().map { it.toString() }
diff --git a/workflow/short_reads_qc.nf b/workflow/short_reads_qc.nf
index 3518b0610144681054728161335065692d936b37..41bef8c9db65ddae0f10cc39985ade350f1b15a7 100644
--- a/workflow/short_reads_qc.nf
+++ b/workflow/short_reads_qc.nf
@@ -81,11 +81,9 @@ include { RNA_QC } from "$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 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 "${params.shared_modules}/gcbias.nf"
include { workflow_summary as WORKFLOW_SUMMARY } from "${params.shared_modules}/workflow_summary.nf"
@@ -103,16 +101,16 @@ 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 +197,8 @@ 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, '')
}
}