diff --git a/cloudgene.yaml b/cloudgene.yaml index 9be428d9052067340f149755cfbecb28c16b698a..eb35fc8eca8919e0a7a25ef29c87f6cc8f5d6f28 100644 --- a/cloudgene.yaml +++ b/cloudgene.yaml @@ -16,8 +16,8 @@ workflow: script: main.nf params.project: ${job_id} - - name: Archieving results - cmd: /usr/bin/zip -0 -r ${zip_out}/impute_results_${job_id}.tar.xz -C ${outdir}/final . + - name: Archiving results + cmd: /usr/bin/zip -0 -r ${zip_out}/impute_results_${job_id}.zip ${outdir}/final stdout: true inputs: @@ -51,7 +51,7 @@ workflow: zip: false - id: zip_out - description: archieved imputation results + description: archived imputation results type: local_folder download: true zip: false diff --git a/main.nf b/main.nf index f089e5ff645d00aa7108960c491c61b2085be42f..2b7d39422fd3fcf23e1de4102306ceec73635671 100644 --- a/main.nf +++ b/main.nf @@ -84,7 +84,7 @@ process qc1 { //________modules__________ // module "bcftools/1.16" - publishDir "${params.out_dir}/proc_qc1", mode: 'copy', overwrite: true +// publishDir "${params.out_dir}/proc_qc1", mode: 'copy', overwrite: true //_____slurm_parameters_____ // executor = "slurm" @@ -114,7 +114,7 @@ process qc2 { //________modules__________ // module "bcftools/1.16" - publishDir "${params.out_dir}/proc_qc2", mode: 'copy', overwrite: true +// publishDir "${params.out_dir}/proc_qc2", mode: 'copy', overwrite: true //_____slurm_parameters_____ // executor = "slurm" @@ -144,7 +144,7 @@ process qc3 { //________modules__________ // module "bcftools/1.16" - publishDir "${params.out_dir}/proc_qc3", mode: 'copy', overwrite: true +// publishDir "${params.out_dir}/proc_qc3", mode: 'copy', overwrite: true //_____slurm_parameters_____ // executor = "slurm" @@ -179,7 +179,7 @@ process qc4 { //module "any/plink2/20211217" //module "bcftools/1.16" - publishDir "${params.out_dir}/proc_qc4", mode: 'copy', overwrite: true +// publishDir "${params.out_dir}/proc_qc4", mode: 'copy', overwrite: true input: tuple val(sample), path (bcf_qc3) @@ -209,7 +209,7 @@ process qc5 { // module "bcftools/1.16" // publishDir "${params.out_dir}/proc_qc5", mode: 'copy', overwrite: true - publishDir ( path: {"$params.out_dir/proc_qc5"} , pattern: "*.bcf*", mode: 'copy', overwrite: true ) +// publishDir ( path: {"$params.out_dir/proc_qc5"} , pattern: "*.bcf*", mode: 'copy', overwrite: true ) publishDir ( path: {"$params.out_dir/final"} , pattern: "*.log", mode: 'copy', overwrite: true ) input: @@ -239,7 +239,7 @@ process qc6 { //cpus 4 //memory '4 GB' - publishDir ( path: {"$params.out_dir/proc_qc6"} , pattern: "*.vcf*", mode: 'copy', overwrite: true ) +// publishDir ( path: {"$params.out_dir/proc_qc6"} , pattern: "*.vcf*", mode: 'copy', overwrite: true ) publishDir ( path: {"$params.out_dir/final"} , pattern: "*.log", mode: 'copy', overwrite: true ) // publishDir "${params.out_dir}/proc_qc6", mode: 'copy', overwrite: true @@ -274,7 +274,7 @@ process phasing { memory '4g' // // publishDir "${params.out_dir}/phasing", mode: 'copy', overwrite: true - publishDir ( path: {"$params.out_dir/phasing"}, pattern: "*.vcf*", mode: 'copy', overwrite: true ) +// publishDir ( path: {"$params.out_dir/phasing"}, pattern: "*.vcf*", mode: 'copy', overwrite: true ) publishDir ( path: {"$params.out_dir/final"}, pattern: "*.log", mode: 'copy', overwrite: true ) input: @@ -303,7 +303,7 @@ process split1 { // module "python/3.9.12" // module "py-numpy/1.22.4" - publishDir ( path: {"$params.out_dir/proc_split1"}, pattern: "*.bed", mode: 'copy', overwrite: true ) +// publishDir ( path: {"$params.out_dir/proc_split1"}, pattern: "*.bed", mode: 'copy', overwrite: true ) publishDir ( path: {"$params.out_dir/final"}, pattern: "*.log", mode: 'copy', overwrite: true ) // publishDir "${params.out_dir}/proc_split1", mode: 'copy', overwrite: true @@ -333,7 +333,7 @@ process split2 { //________modules__________ // module "bcftools/1.16" - publishDir "${params.out_dir}/proc_split2", mode: 'copy', overwrite: true +// publishDir "${params.out_dir}/proc_split2", mode: 'copy', overwrite: true input: tuple val(sample), path(indexed_vcf), path(bed) @@ -364,7 +364,7 @@ process impute { memory '8g' // publishDir "${params.out_dir}/imputation", mode: 'copy', overwrite: true - publishDir ( path: {"$params.out_dir/imputation"}, pattern: "*.vcf*" , mode: 'copy', overwrite: true ) +// publishDir ( path: {"$params.out_dir/imputation"}, pattern: "*.vcf*" , mode: 'copy', overwrite: true ) publishDir( path: {"$params.out_dir/final"}, pattern: "*_imputed.log", mode: 'copy', overwrite: true ) input: