From 745f499cfa4d2e688edef8f10e967fd0c7fa480d Mon Sep 17 00:00:00 2001
From: jsabban <jules.sabban@inrae.fr>
Date: Mon, 29 Apr 2024 12:22:19 +0200
Subject: [PATCH] Hot fix to get ngl-biRunCode from file
Ref: #93
---
conf/report.config | 2 +-
conf/test.config | 6 ++++++
sub-workflows/local/begin_nglbi.nf | 10 +++++-----
3 files changed, 12 insertions(+), 6 deletions(-)
diff --git a/conf/report.config b/conf/report.config
index ba4a99d..11866bf 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 = '1.16.0'
+ version = '1.16.1'
}
\ No newline at end of file
diff --git a/conf/test.config b/conf/test.config
index e8ba1ef..c6d32e9 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -17,4 +17,10 @@ process {
pattern: "*.{log,created}"
]
}
+
+ withName: CREATE_READSETS {
+ ext.args = [
+ params.lane ? "--laneNumberToWorkOn '${params.lane}'" : '',
+ ].join(' ')
+ }
}
diff --git a/sub-workflows/local/begin_nglbi.nf b/sub-workflows/local/begin_nglbi.nf
index 2a50f52..c565408 100644
--- a/sub-workflows/local/begin_nglbi.nf
+++ b/sub-workflows/local/begin_nglbi.nf
@@ -13,8 +13,8 @@
// -------------------------------------------------
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_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;
@@ -41,12 +41,12 @@ workflow NGLBI {
ready_for_state = CREATE_RUN.out.ready
} else {
ready_for_state = Channel.value(1)
- bi_run_code = params.bi_run_code
+ bi_run_code = Channel.value(params.bi_run_code)
}
// Update run state
- 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)
+ UPDATE_STATE_FS(bi_run_code, 'F-S', ready_for_state)
+ UPDATE_STATE_IPRG(bi_run_code, 'IP-RG', UPDATE_STATE_FS.out.ready)
// Creation of ReadSets
CREATE_READSETS(
--
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