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