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( -- GitLab