diff --git a/bin/DTM/data_prepare.pl b/bin/DTM/data_prepare.pl
index 2b0776a03f59432d5d8d1643264c8c27229b3537..05d9b773e2e30bfbe1711681c28181c3ccfb565b 100644
--- a/bin/DTM/data_prepare.pl
+++ b/bin/DTM/data_prepare.pl
@@ -184,6 +184,7 @@ MAIN:
print ("\tFichier run NGL-Bi trouvé : $file_run_bi\n");
open (RUNBI, $file_run_bi);
my $ngl_bi_run_name = <RUNBI>;
+ chomp($ngl_bi_run_name);
close (RUNBI);
my $sq_xp_code = `grep 'Experiment Name' SampleSheet.csv | cut -d',' -f2`; $? and print STDERR("[Erreur]Récup du code experience NGL-SQ\n");
diff --git a/conf/base.config b/conf/base.config
index 0a6832f1daae4422ad7783c7ad2e5bc07d4af019..d330b07ab172b2b3015b9113d2ba5f7f26c29b5b 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -114,7 +114,7 @@ process {
// ----- WithName
// ----- CORE ----- //
- withName: illuminaFilter {
+ withName: ILLUMINA_FILTER {
publishDir = [
path: "${params.outdir}/IlluminaFilter",
mode: 'symlink',
diff --git a/modules/local/module_core.nf b/modules/local/module_core.nf
index 7d9c7c52f6f38c6b05f52c58d333cf7ad4cc7726..9b7f25c368e1b6f6d11f9be7494065d42731307a 100644
--- a/modules/local/module_core.nf
+++ b/modules/local/module_core.nf
@@ -2,7 +2,7 @@
* Module pour les analyses de base du pipeline
*/
-process extractInfoForDemuxStats {
+process PREP_DEMUXSTAT {
publishDir path: "${params.outdir}/Demux" , mode: 'copy'
input:
@@ -18,7 +18,7 @@ process extractInfoForDemuxStats {
"""
}
-process demultiplexStats {
+process DEMUX_STATS {
publishDir path: "${params.outdir}/Demux" , mode: 'copy'
//module 'system/R-4.0.4_gcc-9.3.0' // Ne fonctionne pas !
@@ -58,7 +58,7 @@ process FASTQC {
}
-process illuminaFilter {
+process ILLUMINA_FILTER {
tag " $name"
input:
diff --git a/nextflow.config b/nextflow.config
index 529dca9e170c4111b49e5fb19793412012357e57..157085f18b2fb84c07659ac2d27fbaebbe8e6577 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -33,6 +33,9 @@ params {
cluster_options = ''
+ // skip parameters
+ skip_core_illumina = false
+
monochrome_logs = true
help = false
diff --git a/sub-workflows/local/begin_nglbi.nf b/sub-workflows/local/begin_nglbi.nf
index 0473f635a5d8364db55e484e91a9c009b43d3aa4..0096dc4d87e515ad3cc6117f6cce8dac39b1139d 100644
--- a/sub-workflows/local/begin_nglbi.nf
+++ b/sub-workflows/local/begin_nglbi.nf
@@ -16,6 +16,7 @@ include { CREATE_RUN;
UPDATE_NGLBI_STATE_FROM_CODE as UPDATE_STATE_FS;
UPDATE_NGLBI_STATE_FROM_CODE as UPDATE_STATE_IPRG;
UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FRG;
+ UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_IPQC;
CREATE_READSETS;
} from "${params.shared_modules}/ngl_bi.nf"
@@ -32,7 +33,7 @@ include { CREATE_RUN;
workflow NGLBI {
main:
// Creation of the Run if needed
- if (params.insert_to_ngl && params.bi_run_code == '') {
+ if (params.bi_run_code == '') {
CREATE_RUN(params.sequencer, params.sqXpCode, '', 1)
@@ -57,9 +58,10 @@ workflow NGLBI {
// Update readset states
UPDATE_STATE_FRG(CREATE_READSETS.out.createdFile, 'F-RG', CREATE_READSETS.out.ready)
+ UPDATE_STATE_IPQC(CREATE_READSETS.out.createdFile, 'IP-QC', UPDATE_STATE_FRG.out.ready)
emit:
- ready = UPDATE_STATE_FRG.out.ready
+ ready = UPDATE_STATE_IPQC.out.ready
readsetsFile = CREATE_READSETS.out.createdFile
}
diff --git a/sub-workflows/local/core_illumina.nf b/sub-workflows/local/core_illumina.nf
new file mode 100644
index 0000000000000000000000000000000000000000..6a79fdff11ca9db5709b0aceb77675f0a74d68e6
--- /dev/null
+++ b/sub-workflows/local/core_illumina.nf
@@ -0,0 +1,51 @@
+// -------------------------------------------------
+// CORE ILLUMINA
+// -------------------------------------------------
+/*
+ * Statistiques de démultiplexage
+ * IlluminaFilter
+*/
+
+// -------------------------------------------------
+// MODULES
+// -------------------------------------------------
+include {
+ PREP_DEMUXSTAT;
+ DEMUX_STATS;
+ ILLUMINA_FILTER;
+} from "$baseDir/modules/local/module_core.nf"
+
+// -------------------------------------------------
+// LOCAL PARAMS
+// -------------------------------------------------
+
+
+// -------------------------------------------------
+// WORKFLOW
+// -------------------------------------------------
+
+workflow CORE_ILLUMINA {
+ take:
+ sampleSheet
+ demuxStatXML
+ demuxSummary
+ fastq
+
+ main:
+ // ----------- DemultiplexStat
+ PREP_DEMUXSTAT(sampleSheet)
+ DEMUX_STATS(demuxStatXML, PREP_DEMUXSTAT.out, demuxSummary)
+
+ // ----------- Illumina Filter // ou SubsetSeqFiles : dans quel cas on fait l'un ou l'autre ????
+ if ("$params.sequencer" =~ /NovaSeq.*/ && params.is_multiplex) {
+ System.out.println "Les données ne nécessite pas de passer par IlluminaFilter"
+ fastq_good = fastq
+ } else { // Si MiSeq ou Nova + noIndex
+ ILLUMINA_FILTER(fastq)
+ fastq_good = ILLUMINA_FILTER.out.reads
+ }
+
+ emit:
+ fastq = fastq_good
+}
+
diff --git a/sub-workflows/local/core_pipeline.nf b/sub-workflows/local/core_pipeline.nf
index 25787334c1fc27fae2db6bb1ee42d6120bc886e7..96b89a8ed5bd27aa6098cd79993a9e927262d613 100644
--- a/sub-workflows/local/core_pipeline.nf
+++ b/sub-workflows/local/core_pipeline.nf
@@ -3,8 +3,6 @@
// CORE PIPELINE
// -------------------------------------------------
/*
- * Creation readsets NGL-Bi -> plus tard
- * Statistiques de démultiplexage
* QC des reads
* Recherche contaminations
* Recherche duplicats
@@ -14,15 +12,12 @@
// MODULES
// -------------------------------------------------
include {
- extractInfoForDemuxStats;
- demultiplexStats;
FASTQC;
- illuminaFilter;
FASTQSCREEN;
DUPLICATED_READS;
} from "$baseDir/modules/local/module_core.nf"
-include { GUNZIP } from "${params.shared_modules}/gzip.nf"
-include { SEQTK_SAMPLE } from "${params.shared_modules}/seqtk.nf"
+include { GUNZIP } from "${params.shared_modules}/gzip.nf"
+include { SEQTK_SAMPLE } from "${params.shared_modules}/seqtk.nf"
include { md5sum as MD5SUM } from "${params.shared_modules}/md5sum.nf"
//-------------------------------------------------
@@ -33,36 +28,20 @@ isResume=workflow.resume
//-------------------------------------------------
workflow CORE {
take:
- ch_sampleSheet
- ch_DemuxStatXML
- ch_DemuxSummary
ch_read
- main:
- // ----------- DemultiplexStat
- extractInfoForDemuxStats(ch_sampleSheet)
- demultiplexStats(ch_DemuxStatXML, extractInfoForDemuxStats.out, ch_DemuxSummary)
-
- // ----------- Illumina Filter // ou SubsetSeqFiles : dans quel cas on fait l'un ou l'autre ????
- if ("$params.sequencer" =~ /NovaSeq.*/ && params.is_multiplex) {
- System.out.println "Les données ne nécessite pas de passer par IlluminaFilter"
- ch_read_good = ch_read
- } else { // Si MiSeq ou Nova + noIndex
- illuminaFilter(ch_read)
- ch_read_good = illuminaFilter.out.reads
- }
-
+ main:
// ----------- md5sum
- MD5SUM(ch_read_good.collect{it[1]}.flatten().collect(), params.run_name+'_fastq')
+ MD5SUM(ch_read.collect{it[1]}.flatten().collect(), params.run_name+'_fastq')
// ----------- FASTQC
- FASTQC(ch_read_good)
+ FASTQC(ch_read)
// ----------- ContaminationSearch
- FASTQSCREEN(ch_read_good)
+ FASTQSCREEN(ch_read)
// ----------- Recherche Duplicats
- GUNZIP(ch_read_good)
+ GUNZIP(ch_read)
GUNZIP.out.branch{
large : it[1].size() >= params.bytes_subset_seq
diff --git a/workflow/illumina_qc.nf b/workflow/illumina_qc.nf
index 1c3ba605d3d64d9d2d44dc3afca33d1d25c7fef9..8bdf8f68b1b3cd406308a846338560c2a9078682 100644
--- a/workflow/illumina_qc.nf
+++ b/workflow/illumina_qc.nf
@@ -58,14 +58,13 @@ createDir = file(params.outdir).mkdir()
// INCLUDES
// -------------------------------------------------
include { NGLBI } from "$baseDir/sub-workflows/local/begin_nglbi.nf"
+include { CORE_ILLUMINA } from "$baseDir/sub-workflows/local/core_illumina.nf"
include { CORE } from "$baseDir/sub-workflows/local/core_pipeline.nf"
include { DNA_QC } from "$baseDir/sub-workflows/local/dna_qc.nf"
include { RNA_QC } from "$baseDir/sub-workflows/local/rna_qc.nf"
include { MULTIQC } from "${params.shared_modules}/multiqc.nf"
include { workflow_summary as WORKFLOW_SUMMARY } from "${params.shared_modules}/workflow_summary.nf"
-include { UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_IPQC;
- UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FQC
- } from "${params.shared_modules}/ngl_bi.nf"
+include { UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FQC } from "${params.shared_modules}/ngl_bi.nf"
// -------------------------------------------------
// EMAIL ON START
@@ -80,13 +79,19 @@ sendBeginMail(format.format(new Date()))
workflow ILLUMINA_QC {
ch_mqc = Channel.empty()
WORKFLOW_SUMMARY()
- NGLBI()
if (params.insert_to_ngl){
- UPDATE_STATE_IPQC(NGLBI.out.readsetsFile, 'IP-QC', NGLBI.out.ready)
+ NGLBI()
}
- CORE(ch_ss, ch_DemuxStatXML, ch_DemuxSummary, ch_read) /*ch_ngl, ch_runInfo, mismatchNumber, params.raw_data*/
+ if ( ! params.skip_core_illumina ) {
+ CORE_ILLUMINA(ch_ss, ch_DemuxStatXML, ch_DemuxSummary, ch_read)
+ fastq = CORE_ILLUMINA.out.fastq
+ } else {
+ fastq = ch_read
+ }
+
+ CORE(fastq)
if (params.data_nature == 'DNA') {
DNA_QC(CORE.out.subset_fastq)