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Commit c332298c authored by Jules Sabban's avatar Jules Sabban
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FastQ namming using NGL api

	- Name of fastq with info from NGL databases
	- Uniformity with ng6 file names (new pipeline option)
	- Add files to readsets
	- Move MD5SUM process from CORE_PIPELINE to ILLUMINA_QC workflow

	ref: #91
parent 88e82a0d
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1 merge request!16FastQ namming using NGL api
......@@ -207,6 +207,13 @@ process {
}
withName: FILE_RENAME {
ext.args = [
params.run_date ? "--date " + params.run_date : '',
params.ng6_name ? "--ng6_like" : '',
].join(' ')
}
// ----- WithLabel
withLabel: littleJob {
executor = 'local'
......
......@@ -44,3 +44,28 @@ process TREATMENT_DEMUXSTAT {
1> treatment_demux_${lane}.log
"""
}
process FILE_RENAME {
label 'ngl'
input:
path(inputDirectory)
path(readsetsFile)
val(sqXpCode)
output:
path("outputs/*.fastq.gz"), emit: fastq
path("*.log"), emit: log
val 1, emit: ready
script:
def args = task.ext.args ?: ''
"""
perl ${params.ngl_bi_client}/GeT/perl/illumina/file_rename.pl \\
--input ./ \\
--readsets $readsetsFile \\
--sqExperimentCode $sqXpCode \\
$args \\
1> file_rename.log
"""
}
\ No newline at end of file
......@@ -58,6 +58,7 @@ params {
insert_to_ngl = true
bi_run_code = ''
sq_xp_code = ''
ng6_name = true
// Shared Modules
shared_modules = '/home/sbsuser/save/scripts-ngs/shared_modules_Current'
......
......@@ -13,8 +13,8 @@
// -------------------------------------------------
include { CREATE_RUN;
UPDATE_NGLBI_STATE_FROM_CODE as UPDATE_STATE_FS;
UPDATE_NGLBI_STATE_FROM_CODE as UPDATE_STATE_IPRG;
UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FS;
UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_IPRG;
UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FRG;
UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_IPQC;
CREATE_READSETS;
......@@ -35,22 +35,23 @@ workflow NGLBI {
// Creation of the Run if needed
if (params.bi_run_code == '') {
CREATE_RUN(params.sequencer, params.sqXpCode, '', 1)
CREATE_RUN(params.sequencer, params.sq_xp_code, '', 1)
params.bi_run_code = CREATE_RUN.out.createdFile.splitText().map{it -> it.trim()}
bi_run_code = CREATE_RUN.out.createdFile.splitText().map{it -> it.trim()}
ready_for_state = CREATE_RUN.out.ready
} else {
ready_for_state = Channel.value(1)
bi_run_code = params.bi_run_code
}
// Update run state
UPDATE_STATE_FS(params.bi_run_code, 'F-S', ready_for_state)
UPDATE_STATE_IPRG(params.bi_run_code, 'IP-RG', UPDATE_STATE_FS.out.ready)
UPDATE_STATE_FS(CREATE_RUN.out.createdFile, 'F-S', ready_for_state)
UPDATE_STATE_IPRG(CREATE_RUN.out.createdFile, 'IP-RG', UPDATE_STATE_FS.out.ready)
// Creation of ReadSets
CREATE_READSETS(
params.sq_xp_code,
params.bi_run_code,
bi_run_code,
'',
'',
UPDATE_STATE_IPRG.out.ready
......@@ -63,7 +64,7 @@ workflow NGLBI {
emit:
ready = UPDATE_STATE_IPQC.out.ready
readsetsFile = CREATE_READSETS.out.createdFile
runFile = CREATE_RUN.out.createdFile
}
......@@ -19,7 +19,6 @@ include {
} from "$baseDir/modules/local/module_core.nf"
include { GUNZIP } from "${params.shared_modules}/gzip.nf"
include { SEQTK_SAMPLE } from "${params.shared_modules}/seqtk.nf"
include { md5sum as MD5SUM } from "${params.shared_modules}/md5sum.nf"
//-------------------------------------------------
inNGL=true
......@@ -49,9 +48,6 @@ workflow CORE {
ch_read = ch_fastq
}
// ----------- md5sum
MD5SUM(ch_read.collect{it[1]}.flatten().collect(), params.run_name+'_fastq')
// ----------- FASTQC
FASTQC(ch_read)
......@@ -65,7 +61,16 @@ workflow CORE {
if (params.no_subset) {
unzipped_fastq = GUNZIP.out
} else {
SEQTK_SAMPLE(GUNZIP.out)
/*
if ( "$params.coverage" != 0 && ("$params.reference_genome" != '' || "$params.reference_transcriptome" != '')) {
reference = params.reference_genome ?: params.reference_transcriptome
GET_NB_SEQ_FROM_COV(reference, params.coverage, ch_read[0])
nb_seq = GET_NB_SEQ.out.value
} else {
nb_seq = params.subset_seq
}
*/
SEQTK_SAMPLE(GUNZIP.out/*, nb_seq*/)
unzipped_fastq = SEQTK_SAMPLE.out
}
......@@ -81,5 +86,4 @@ workflow CORE {
fastqscreen_report = FASTQSCREEN.out.report ?: Channel.empty()
fastp_report = DUPLICATED_READS.out.json
subset_fastq = unzipped_fastq
fastq_md5 = MD5SUM.out
}
......@@ -68,13 +68,15 @@ 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 "$baseDir/modules/local/module_DTM.nf"
include { TREATMENT_DEMUXSTAT as TREATMENT_DEMUX_RUN;
TREATMENT_DEMUXSTAT as TREATMENT_DEMUX_READSETS
TREATMENT_DEMUXSTAT as TREATMENT_DEMUX_READSETS;
FILE_RENAME as RENAME_FASTQ;
} from "$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 "${params.shared_modules}/workflow_summary.nf"
include { UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FQC } from "${params.shared_modules}/ngl_bi.nf"
include { READSET_FILE_FROM_FILE as ADD_RS_RAW_FILES } from "${params.shared_modules}/ngl_bi.nf" addParams(ext: 'RAW')
include { md5sum as MD5SUM } from "${params.shared_modules}/md5sum.nf"
// -------------------------------------------------
// EMAIL ON START
// -------------------------------------------------
......@@ -101,7 +103,7 @@ workflow ILLUMINA_QC {
if (params.insert_to_ngl){
// Add demultiplexStat treatments
TREATMENT_DEMUX_RUN(params.bi_run_code, CORE_ILLUMINA.out.demuxStat)
TREATMENT_DEMUX_RUN(NGLBI.out.runFile, CORE_ILLUMINA.out.demuxStat)
TREATMENT_DEMUX_READSETS(NGLBI.out.readsetsFile, CORE_ILLUMINA.out.demuxStat)
}
}
......@@ -162,7 +164,9 @@ workflow ILLUMINA_QC {
)
if (params.insert_to_ngl){
ADD_RS_RAW_FILES(NGLBI.out.readsetsFile, CORE.out.fastq_md5, 'RAW', NGLBI.out.ready)
RENAME_FASTQ(fastq.map{it[1]}.collect(), NGLBI.out.readsetsFile, params.sq_xp_code)
MD5SUM(RENAME_FASTQ.out.fastq.collect(), params.run_name+'_fastq')
ADD_RS_RAW_FILES(NGLBI.out.readsetsFile, MD5SUM.out, 'RAW', NGLBI.out.ready)
UPDATE_STATE_FQC(NGLBI.out.readsetsFile, 'F-QC', MULTIQC.out.html)
}
......
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