From 93ae5c1edc57174dcb58f4403524a7ea76e67b04 Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Mon, 25 Nov 2024 14:37:57 +0100
Subject: [PATCH] Add ressources to create Illumina NGSRG readset treatment
Ref: #59
---
modules/local/module_NGL-Bi.nf | 24 ++++++++++++++++++++++++
sub-workflows/local/ngl.nf | 6 +++++-
workflow/short_reads_qc.nf | 7 +++++--
3 files changed, 34 insertions(+), 3 deletions(-)
diff --git a/modules/local/module_NGL-Bi.nf b/modules/local/module_NGL-Bi.nf
index 995ebf5..7fde2fa 100644
--- a/modules/local/module_NGL-Bi.nf
+++ b/modules/local/module_NGL-Bi.nf
@@ -70,4 +70,28 @@ process FILE_RENAME {
$args \\
1> ${fileType}_rename.log
"""
+}
+
+process NGSRG {
+ label 'ngl'
+
+ input:
+ path nglFile
+ path file
+ val level
+
+ output:
+ path("*.log"), emit: log
+
+ script:
+ def args = task.ext.args ?: ''
+ def statFileOpt = file.endsWith('Stats.json') ? "--demuxStatFile $file" : ''
+ """
+ perl ${params.ngl_bi_client}/GeT/perl/illumina/createNGL-BiTreatmentNGSRG.pl \\
+ --objectFile $nglFile \\
+ --level $level \\
+ $statFileOpt \\
+ 1> treatment_ngsrg_${level}.log
+
+ """
}
\ No newline at end of file
diff --git a/sub-workflows/local/ngl.nf b/sub-workflows/local/ngl.nf
index 968e899..a677806 100644
--- a/sub-workflows/local/ngl.nf
+++ b/sub-workflows/local/ngl.nf
@@ -20,7 +20,8 @@ include { UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FQC;
CREATE_ANALYSIS } from "${params.shared_modules}/ngl_bi.nf"
include { FILE_RENAME as RENAME_FASTQ;
- FILE_RENAME as RENAME_INDEX } from "$baseDir/modules/local/module_NGL-Bi.nf"
+ FILE_RENAME as RENAME_INDEX;
+ NGSRG as NGSRG_READSET; } from "$baseDir/modules/local/module_NGL-Bi.nf"
// -------------------------------------------------
// WORKFLOW
// -------------------------------------------------
@@ -36,6 +37,7 @@ workflow NGL {
project
project_hash
is_single_cell
+ demux_stat_json
main:
// First steps
@@ -45,6 +47,8 @@ workflow NGL {
readsets_created = BEGIN.out.readsets_created
ready = BEGIN.out.ready
+ NGSRG_READSET(readsets_created, demux_stat_json, 'readsets')
+
bi_run_code = nglBiRunCode.collect().map { it.toString() }
// Compute results
diff --git a/workflow/short_reads_qc.nf b/workflow/short_reads_qc.nf
index adac025..3518b06 100644
--- a/workflow/short_reads_qc.nf
+++ b/workflow/short_reads_qc.nf
@@ -62,6 +62,8 @@ ch_sortmerna_db = Channel.from(
params.sortmerna_db_path + '/silva-euk-28s-id98.fasta',
)
+ch_demux_stat_json = Channel.fromPath("${params.inputdir}/Stats/Stats.json")
+
mismatchNumber = params.sequencer == 'MiSeq'? 0 : 1
//banksForConta = params.addBankForConta ? params.genomesRefForConta << params.addBankForConta : params.genomesRefForConta
@@ -116,7 +118,7 @@ workflow SHORT_READS_QC {
CORE(fastq)
ch_versions = ch_versions.mix(CORE.out.versions)
- if (params.data_nature =~ 'DNA|GENOMIC') {
+ if (params.data_nature =~ 'DNA|GENOMIC|WGS') {
DNA_QC(CORE.out.subset_fastq
.collect{it[1]}
.flatten()
@@ -192,7 +194,8 @@ workflow SHORT_READS_QC {
MULTIQC.out.html,
params.project,
params.project_hash,
- params.single_cell
+ params.single_cell,
+ ch_demux_stat_json
)
// Add demultiplexStat treatments
--
GitLab