diff --git a/conf/report.config b/conf/report.config
index af1fc521f75faffe2351add15d2683ba3332edbe..cadd02f564850988e9780e14985924212ab313cc 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 = '1.17.0'
+ version = '1.18.0'
}
\ No newline at end of file
diff --git a/sub-workflows/local/begin_nglbi.nf b/sub-workflows/local/begin_nglbi.nf
deleted file mode 100644
index 2e60dd903a3a81db8c85bf74c2520d0b14bfad28..0000000000000000000000000000000000000000
--- a/sub-workflows/local/begin_nglbi.nf
+++ /dev/null
@@ -1,76 +0,0 @@
-// -------------------------------------------------
-// BEGIN NGL-BI
-// -------------------------------------------------
-/*
- * Subworkflow to prepare NGL-Bi process
- * creation of the Run if needed
- * creation of readsets
- * change of status
-*/
-
-// -------------------------------------------------
-// MODULES
-// -------------------------------------------------
-
-include { CREATE_RUN;
- 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;
-} from "${params.shared_modules}/ngl_bi.nf"
-
-
-// -------------------------------------------------
-// LOCAL PARAMS
-// -------------------------------------------------
-
-
-// -------------------------------------------------
-// WORKFLOW
-// -------------------------------------------------
-
-workflow NGLBI {
- main:
- // Creation of the Run if needed
- if (params.bi_run_code == '') {
-
- CREATE_RUN(params.sequencer, params.sq_xp_code, '', 1)
- createdFile = CREATE_RUN.out.createdFile
- nglBiRunCode = CREATE_RUN.out.nglBiRunCode
- ready_for_state = CREATE_RUN.out.ready
- } else {
- ready_for_state = Channel.value(1)
- createdFile = Channel.of(params.bi_run_code).map { content ->
- def file = file('RunNGL-Bi.created')
- file.text = content
- file
- }
- nglBiRunCode = params.bi_run_code
- }
-
- // Update run state
- UPDATE_STATE_FS(createdFile, 'F-S', ready_for_state)
- UPDATE_STATE_IPRG(createdFile, 'IP-RG', UPDATE_STATE_FS.out.ready)
-
- // Creation of ReadSets
- CREATE_READSETS(
- params.sq_xp_code,
- nglBiRunCode,
- '',
- '',
- UPDATE_STATE_IPRG.out.ready
- )
-
- // Update readset states
- UPDATE_STATE_FRG(CREATE_READSETS.out.createdFile, 'F-RG', CREATE_READSETS.out.ready)
- UPDATE_STATE_IPQC(CREATE_READSETS.out.createdFile, 'IP-QC', UPDATE_STATE_FRG.out.ready)
-
- emit:
- ready = UPDATE_STATE_IPQC.out.ready
- readsetsFile = CREATE_READSETS.out.createdFile
- createdFile = createdFile
- nglBiRunCode = nglBiRunCode
-}
-
-
diff --git a/workflow/illumina_qc.nf b/workflow/illumina_qc.nf
index 7500b068c9e68a9fb42dc4eb52af06111018b99f..6f8d1ebe4497eae1584e861217d4ad2d1d452806 100644
--- a/workflow/illumina_qc.nf
+++ b/workflow/illumina_qc.nf
@@ -60,7 +60,6 @@ createDir = file(params.outdir).mkdir()
// -------------------------------------------------
// INCLUDES
// -------------------------------------------------
-include { NGLBI } from "$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 "$baseDir/sub-workflows/local/dna_qc.nf"
@@ -74,9 +73,12 @@ include { TREATMENT_DEMUXSTAT as TREATMENT_DEMUX_RUN;
include { MULTIQC } from "${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 "${params.shared_modules}/ngl_bi.nf"
+include { UPDATE_NGLBI_STATE_FROM_FILE as UPDATE_STATE_FQC;
+ CREATE_ANALYSIS; } from "${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"
+include { BEGIN_NGLBI as NGLBI } from "${params.shared_modules}/workflows/begin_nglbi.nf"
+
// -------------------------------------------------
// EMAIL ON START
// -------------------------------------------------
@@ -92,7 +94,7 @@ workflow ILLUMINA_QC {
WORKFLOW_SUMMARY()
if (params.insert_to_ngl){
- NGLBI()
+ NGLBI(params.bi_run_code, params.sq_xp_code, '', params.sequencer)
}
if ( params.skip_core_illumina ) {
@@ -104,7 +106,7 @@ workflow ILLUMINA_QC {
if (params.insert_to_ngl){
// Add demultiplexStat treatments
TREATMENT_DEMUX_RUN(NGLBI.out.nglBiRunCode, CORE_ILLUMINA.out.demuxStat)
- TREATMENT_DEMUX_READSETS(NGLBI.out.readsetsFile, CORE_ILLUMINA.out.demuxStat)
+ TREATMENT_DEMUX_READSETS(NGLBI.out.readsets_created, CORE_ILLUMINA.out.demuxStat)
}
}
@@ -164,10 +166,11 @@ workflow ILLUMINA_QC {
)
if (params.insert_to_ngl){
- RENAME_FASTQ(fastq.map{it[1]}.collect(), NGLBI.out.readsetsFile, params.sq_xp_code)
+ RENAME_FASTQ(fastq.map{it[1]}.collect(), NGLBI.out.readsets_created, 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)
+ ADD_RS_RAW_FILES(NGLBI.out.readsets_created, MD5SUM.out, 'RAW', NGLBI.out.ready)
+ UPDATE_STATE_FQC(NGLBI.out.readsets_created, 'F-QC', MULTIQC.out.html)
+ CREATE_ANALYSIS(NGLBI.out.nglBiRunCode, NGLBI.out.readsets_created, 1)
}
/*