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, '') } }