diff --git a/conf/report.config b/conf/report.config index ba4a99dfa11bd13af624b050ae439b23d71db8ab..11866bf09cdaf7e4f794fef7b6bca1971c9b7668 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 e8ba1ef1e4d8d9e9da44c8afd30bafdcceb80d08..c6d32e95fb4ecfc733270922967d165564088c1e 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 2a50f520261de972e9de16728c5b98f566b3093b..c5654082a307b4502264cdafbb6cd3b7d019261f 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(