diff --git a/workflow/main.nf b/workflow/main.nf index 345011b1c15209c74664a4790fd6ee2da2e34ade..34d6e792a35c21f9b67866669a4676c5730c4165 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -7,6 +7,7 @@ params.bcl = "$baseDir/../test_data/*.tar.gz" params.designFile = "$baseDir/../test_data/design.csv" params.outDir = "$baseDir/output" +params.references = "$baseDir/../docs/references.md" // Define List of Files tarList = Channel.fromPath( params.bcl ) @@ -16,6 +17,7 @@ designLocation = Channel .fromPath(params.designFile) .ifEmpty { exit 1, "design file not found: ${params.designFile}" } outDir = params.outDir +references = params.references process checkDesignFile { @@ -140,6 +142,7 @@ process versions { ulimit -a module load python/3.6.1-2-anaconda echo $workflow.nextflow.version > version_nextflow.txt + python3 $baseDir/scripts/generate_references.py -r $references -o references python3 $baseDir/scripts/generate_versions.py -f version_*.txt -o versions """ } @@ -164,6 +167,6 @@ process multiqc { hostname ulimit -a module load multiqc/1.7 - multiqc . + multiqc . -c $baseDir/scripts/.multiqc_config.yaml """ } diff --git a/workflow/scripts/.multiqc_config.yaml b/workflow/scripts/.multiqc_config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a729f7477725fb9656a1b4c5c5a727cc4aa4761b --- /dev/null +++ b/workflow/scripts/.multiqc_config.yaml @@ -0,0 +1,6 @@ +top_modules: + - 'Software Versions' + +module_order: + - bcl2fastq + - fastqc