diff --git a/hello-nextflow/hello-modules/nextflow.config b/hello-nextflow/hello-modules/nextflow.config index 46bc2d83..2efec7cb 100644 --- a/hello-nextflow/hello-modules/nextflow.config +++ b/hello-nextflow/hello-modules/nextflow.config @@ -1,5 +1,26 @@ docker.fixOwnership = true +/* + * Pipeline parameters + */ + +params { + // Primary input (file of input files, one per line) + reads_bam = null + + // Output directory + params.outdir = "results_genomics" + + // Accessory files + reference = null + reference_index = null + reference_dict = null + intervals = null + + // Base name for final output file + cohort_name = "my_cohort" +} + profiles { docker_on { docker.enabled = true @@ -47,21 +68,3 @@ process { cpus = 4 } } - -/* - * Pipeline parameters - */ - -params { - // Primary input (file of input files, one per line) - reads_bam = null - - // Accessory files - reference = null - reference_index = null - reference_dict = null - intervals = null - - // Base name for final output file - cohort_name = "my_cohort" -} diff --git a/hello-nextflow/hello-nf-test/nextflow.config b/hello-nextflow/hello-nf-test/nextflow.config index 58a16e19..2efec7cb 100644 --- a/hello-nextflow/hello-nf-test/nextflow.config +++ b/hello-nextflow/hello-nf-test/nextflow.config @@ -1,7 +1,25 @@ docker.fixOwnership = true -// Default output directory -params.outdir = 'results_genomics' +/* + * Pipeline parameters + */ + +params { + // Primary input (file of input files, one per line) + reads_bam = null + + // Output directory + params.outdir = "results_genomics" + + // Accessory files + reference = null + reference_index = null + reference_dict = null + intervals = null + + // Base name for final output file + cohort_name = "my_cohort" +} profiles { docker_on { @@ -50,21 +68,3 @@ process { cpus = 4 } } - -/* - * Pipeline parameters - */ - -params { - // Primary input (file of input files, one per line) - reads_bam = null - - // Accessory files - reference = null - reference_index = null - reference_dict = null - intervals = null - - // Base name for final output file - cohort_name = "my_cohort" -} diff --git a/hello-nextflow/solutions/hello-config/5-nextflow.config b/hello-nextflow/solutions/hello-config/5-nextflow.config index 150bff59..24d06833 100644 --- a/hello-nextflow/solutions/hello-config/5-nextflow.config +++ b/hello-nextflow/solutions/hello-config/5-nextflow.config @@ -1,5 +1,28 @@ docker.fixOwnership = true + +/* + * Pipeline parameters + */ + +params { + // Primary input (file of input files, one per line) + reads_bam = null + + // Output directory + params.outdir = "results_genomics" + + // Accessory files + reference = null + reference_index = null + reference_dict = null + intervals = null + + // Base name for final output file + cohort_name = "my_cohort" +} + + profiles { docker_on { docker.enabled = true @@ -44,21 +67,3 @@ process { cpus = 4 } } - -/* - * Pipeline parameters - */ - -params { - // Primary input (file of input files, one per line) - reads_bam = null - - // Accessory files - reference = null - reference_index = null - reference_dict = null - intervals = null - - // Base name for final output file - cohort_name = "my_cohort" -}