diff --git a/assets/final_email_template.txt b/assets/final_email_template.txt
index fe40165f8cfdb69d0f1fe03d459c106171176194..4d0b8b66eb417522da383c29dcf91151056daf38 100644
--- a/assets/final_email_template.txt
+++ b/assets/final_email_template.txt
@@ -11,10 +11,13 @@ Project : $project
Run : $run
<% if (xpNGLSq){ out << "NGL-SQ Experiment : $xpNGLSq " } %>
<% if (runNGLBi){out << "NGL-Bi RunCode : $runNGLBi" } %>
+<% if (analysisNGLBi){out << "NGL-Bi AnalysisCode : $analysisNGLBi" } %>
<% if (success){
out << """## GeT-nextflow-NGL-Bi/wf-Illumina-nf execution completed successfully! ## \n"""
- if (runNGLBi){
+ if (analysisNGLBi){
+ out << """\tCheck your analyzes on NGL-Bi : https://ngl-bi.genomique.genotoul.fr/analyses/${analysisNGLBi} """
+ } else if (runNGLBi){
out << """\tCheck your analyzes on NGL-Bi : https://ngl-bi.genomique.genotoul.fr/runs/${runNGLBi} """
} else {
out << """\tYour analyzes are NOT on NGL-Bi : ask to a bioinfo team member for details."""
diff --git a/assets/get_plage_logo.jpg b/assets/get_plage_logo.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..ba357d5e88209733a2727b5bd198fa7d47470ecb
Binary files /dev/null and b/assets/get_plage_logo.jpg differ
diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
index 75a0989baa999e00600a60420d1c27afc1c065bf..d311a8713542ab769206d7d66b466ab8757aba78 100644
--- a/assets/multiqc_config.yaml
+++ b/assets/multiqc_config.yaml
@@ -94,7 +94,6 @@ sp:
fn: '*_screen.txt'
-custom_logo: "./get_logo.png"
custom_logo_url: "https://get.genotoul.fr/"
custom_logo_title: "GeT-GenoToul"
diff --git a/bin/demuxStatsElement.R b/bin/demuxStatsElement.R
index 2cf47cb82f6c43bcfb3afee08afba2d945757d93..4333cad720452ed0e4d93f950b154a2c657ee44e 100755
--- a/bin/demuxStatsElement.R
+++ b/bin/demuxStatsElement.R
@@ -88,6 +88,7 @@ for (i in 1:nrow(assigned_filtered)) {
sample <- assigned_filtered[i, 2]
bc1 <- assigned_filtered[i, 3]
bc2 <- assigned_filtered[i, 4]
+ barcode <- ifelse(is.na(bc2), bc1, paste(bc1, bc2, sep = "-"))
bcCount <- assigned_filtered[i, 5]*2
project <- run_manifest$Samples %>%
@@ -97,7 +98,7 @@ for (i in 1:nrow(assigned_filtered)) {
new_row <- data.frame(
Project = project,
Sample = sample,
- Barcode = paste(bc1, bc2, sep = "-"),
+ Barcode = barcode,
bcCount = bcCount,
percOfFrag = NA,
stringsAsFactors = FALSE
@@ -113,26 +114,31 @@ bcCount.threshold<-threshold*min(demultiplex_stat$bcCount)
# Parcourir les lignes du fichier unassigned
cat("\nExtraction des séquences non assignés\n")
-for (i in 1:nrow(unassigned_filtered)) {
- sample <- "Undetermined"
- bc1 <- unassigned_filtered[i, 1]
- bc2 <- unassigned_filtered[i, 2]
- bcCount <- unassigned_filtered[i, 4]*2
-
- project <- "DefaultProject"
-
- new_row <- data.frame(
- Project = project,
- Sample = sample,
- Barcode = paste(bc1, bc2, sep = "-"),
- bcCount = bcCount,
- percOfFrag = NA,
- stringsAsFactors = FALSE
- )
-
- cat("\tAjout de l'échantillon : ", project, "->" , sample, "\n")
-
- demultiplex_stat <- rbind(demultiplex_stat, new_row)
+if(nrow(unassigned_filtered) == 0){
+ cat("\tAucun index non assigné n'a été trouvé pour la lane ", lane, "\n")
+} else {
+ for (i in 1:nrow(unassigned_filtered)) {
+ sample <- "Undetermined"
+ bc1 <- unassigned_filtered[i, 1]
+ bc2 <- unassigned_filtered[i, 2]
+ barcode <- ifelse(is.na(bc2), bc1, paste(bc1, bc2, sep = "-"))
+ bcCount <- unassigned_filtered[i, 4]*2
+
+ project <- "DefaultProject"
+
+ new_row <- data.frame(
+ Project = project,
+ Sample = sample,
+ Barcode = barcode,
+ bcCount = bcCount,
+ percOfFrag = NA,
+ stringsAsFactors = FALSE
+ )
+
+ cat("\tAjout de l'échantillon : ", project, "->" , sample, "\n")
+
+ demultiplex_stat <- rbind(demultiplex_stat, new_row)
+ }
}
cat("\n")
diff --git a/conf/base.config b/conf/base.config
index 0ce330ce58802443822a286121c938a9950f7678..4bc6650c6d84d233edb5dfd88c1910e5a009282f 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -345,8 +345,8 @@ process {
withName: MULTIQC {
ext.args = [
- "--config ${baseDir}/assets/multiqc_config.yaml",
- params.project ? "--title '${params.project} - ${params.run_name}'" : ''
+ params.project ? "--title '${params.project} - ${params.run_name}'" : '',
+ "--filename '${params.project}_${params.run_name}_${params.fc_id}_${params.lane}_multiqc.html'"
].join(' ')
beforeScript = "module purge"
diff --git a/conf/report.config b/conf/report.config
index 5a1322eade527ef37e10f0605f582577dd5323c6..42aef5472c129399343fd14a1a0d1f90bc62be06 100644
--- a/conf/report.config
+++ b/conf/report.config
@@ -29,5 +29,5 @@ manifest {
description = "Workflow for Illumina data quality control"
mainScript = 'main.nf'
nextflowVersion = '>=0.32.0'
- version = '1.25.0'
+ version = '1.26.5'
}
\ No newline at end of file
diff --git a/lib/pipeline.groovy b/lib/pipeline.groovy
index e785788b6bd2c848d8889fb7ecff8bd28998ca2c..4cc505efafaf00e69d28035acbd3791a6edfe6e9 100644
--- a/lib/pipeline.groovy
+++ b/lib/pipeline.groovy
@@ -120,6 +120,31 @@ begin_email_fields = get_workflow_info(
// ----------------------------------
// Functions Definition
// ----------------------------------
+def getPipelineInfo() {
+ def map = [:]
+ map['Analysis Name'] = params.run_name
+ File analysis_file = new File(params.outdir + '/ngl/NGL-BiAnalysis.created')
+ if (analysis_file.exists()) {
+ map['Analysis Code'] = analysis_file.getString()
+ } else {
+ map['Analysis Code'] = '###ANALYSIS_CODE###'
+ }
+ map['Library Type'] = params.data_nature ?: ''
+ map['Sequencing Type'] = params.is_multiplex ? 'Multiplex' : 'Simplex'
+ def ref = params.reference_genome ?: params.reference_transcriptome?: ''
+ File ref_source = new File(ref + '_source')
+ if (ref_source.exists()) {
+ map['Reference'] = ref_source.getText()
+ }
+ def seq = params.sequencer ?: ''
+ def sn = params.machine_id ?: ''
+ def platform = "$seq $sn"
+ map['Sequencing Platform'] = platform ?: ''
+ map['Contact E-mail'] = 'get-plage.contact@genotoul.fr'
+
+ return map
+}
+
def create_email_map() {
def hash = [:]
@@ -150,13 +175,33 @@ def create_email_map() {
}
def create_final_email_fields(formatted_date, summary) {
+ // Get AnalysisCode
+ def analysis_code = ''
+ File analysis_file = new File(params.outdir + '/ngl/NGL-BiAnalysis.created')
+ if (analysis_file.exists()) {
+ analysis_code = analysis_file.text
+ }
+
+ // Get RunCode
+ def run_code = ''
+ if (params.insert_to_ngl) {
+ if (params.bi_run_code) { run_code = params.bi_run_code }
+ else {
+ File run_file = new File(params.outdir + '/ngl/RunNGL-Bi.created')
+ if (run_file.exists()) {
+ run_code = run_file.text
+ }
+ }
+ }
+
return get_workflow_info(
[
subject_prefix: "[${params.sequencer}]",
subject_sufix: params.inputdir.split('/')[-1],
project: (params.project ?: ''),
run: (params.run_name ?: ''),
- runNGLBi: (params.bi_run_code ?: ''),
+ runNGLBi: run_code,
+ analysisNGLBi: analysis_code,
xpNGLSq: (params.sq_xp_code ?: ''),
dateComplete: formatted_date,
summary: (summary ?: [:])
diff --git a/workflow/short_reads_qc.nf b/workflow/short_reads_qc.nf
index 41bef8c9db65ddae0f10cc39985ade350f1b15a7..5dd432a5000a7b803d528d1e2df126a1dfd4a697 100644
--- a/workflow/short_reads_qc.nf
+++ b/workflow/short_reads_qc.nf
@@ -3,7 +3,8 @@
nextflow.enable.dsl = 2
include { getSummary;
- endOfPipelineEvents } from "${baseDir}/lib/pipeline.groovy"
+ endOfPipelineEvents;
+ getPipelineInfo } from "${baseDir}/lib/pipeline.groovy"
include { softwareVersionsToYAML } from "${params.shared_modules}/lib/utils.groovy"
// -------------------------------------------------
// CHANNELS
@@ -67,6 +68,9 @@ ch_demux_stat_json = Channel.fromPath("${params.inputdir}/Stats/Stats.json")
mismatchNumber = params.sequencer == 'MiSeq'? 0 : 1
//banksForConta = params.addBankForConta ? params.genomesRefForConta << params.addBankForConta : params.genomesRefForConta
+ch_mqc_config = Channel.fromPath("${baseDir}/assets/multiqc_config.yaml")
+ch_mqc_logo = Channel.from("${baseDir}/assets/get_logo.png")
+
createDir = file(params.outdir).mkdir()
params.summary = getSummary()
params.summary.collect{k,v -> println "$k : $v"}
@@ -85,6 +89,7 @@ include { TREATMENT_DEMUXSTAT as TREATMENT_DEMUX_RUN;
TREATMENT_DEMUXSTAT as TREATMENT_DEMUX_READSETS;
} from "$baseDir/modules/local/module_NGL-Bi.nf"
include { MULTIQC } from "${params.shared_modules}/multiqc.nf"
+include { MQC_HEADER } from "${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"
@@ -97,24 +102,36 @@ workflow SHORT_READS_QC {
WORKFLOW_SUMMARY()
- if (! params.skip_core_illumina && params.sequencer =~ "NovaSeq|MiSeq" ) {
- CORE_ILLUMINA(ch_ss, ch_DemuxStatXML, ch_DemuxSummary, ch_read)
- fastq = CORE_ILLUMINA.out.fastq
- ch_versions = ch_versions.mix(CORE_ILLUMINA.out.versions)
- demux_stats = CORE_ILLUMINA.out.demuxStat
- } else {
- fastq = ch_read
- demux_stats = channel.empty()
+ if ( params.sequencer =~ "NovaSeq|MiSeq" ) {
+ if (params.skip_core_illumina) {
+ log.info "Illumina's sequencer but skipping CORE_ILLUMINA"
+ fastq = ch_read
+ demux_stats = channel.empty()
+ } else {
+ CORE_ILLUMINA(ch_ss, ch_DemuxStatXML, ch_DemuxSummary, ch_read)
+ fastq = CORE_ILLUMINA.out.fastq
+ ch_versions = ch_versions.mix(CORE_ILLUMINA.out.versions)
+ demux_stats = CORE_ILLUMINA.out.demuxStat
+ }
}
- if (! params.skip_core_element && params.sequencer =~ "AVITI") {
- CORE_ELEMENT(ch_runManifestJSON, ch_indexAssigned, ch_indexUnassigned)
- demux_stats = CORE_ELEMENT.out.demuxStat
- } else {
- demux_stats = Channel.empty()
+
+ if ( params.sequencer =~ "AVITI") {
+ if (params.skip_core_element) {
+ log.info "Elembio's sequencer but skipping CORE_ELEMENT"
+ demux_stats = Channel.empty()
+ } else {
+ CORE_ELEMENT(ch_runManifestJSON, ch_indexAssigned, ch_indexUnassigned)
+ demux_stats = CORE_ELEMENT.out.demuxStat
+ }
}
CORE(fastq)
ch_versions = ch_versions.mix(CORE.out.versions)
+ ch_mqc = ch_mqc.mix(
+ CORE.out.fastqc_report.collect{it[1]}.ifEmpty([]),
+ CORE.out.fastqscreen_report.collect{it[1]}.ifEmpty([]),
+ CORE.out.fastp_report.collect{it[1]}.ifEmpty([])
+ )
if (params.data_nature =~ 'DNA|GENOMIC|WGS') {
DNA_QC(CORE.out.subset_fastq
@@ -171,14 +188,14 @@ workflow SHORT_READS_QC {
newLine: true
)
- MULTIQC(WORKFLOW_SUMMARY.out.ifEmpty([])
- .mix(
- CORE.out.fastqc_report.collect{it[1]}.ifEmpty([]),
- CORE.out.fastqscreen_report.collect{it[1]}.ifEmpty([]),
- CORE.out.fastp_report.collect{it[1]}.ifEmpty([]),
- ch_mqc.collect().ifEmpty([]),
- version_yaml
- ).collect()
+ MQC_HEADER(getPipelineInfo())
+ ch_mqc_config = ch_mqc_config.mix(MQC_HEADER.out.yaml)
+ ch_mqc = ch_mqc.mix(version_yaml)
+
+ MULTIQC(
+ ch_mqc.collect(),
+ ch_mqc_config.collect(),
+ ch_mqc_logo
)
if (params.insert_to_ngl){