updated allowable parameters

h3abionet · May 30, 2019 · 1adb787 · 1adb787
1 parent 29a3eb1
commit 1adb787
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/assoc.nf b/assoc.nf
@@ -27,7 +27,9 @@ import java.nio.file.Paths
 
 def helps = [ 'help' : 'help' ]
 
-allowed_params = ["input_dir","input_pat","output","output_dir","data","plink_mem_req","covariates","gemma_num_cores","gemma_mem_req","gemma","linear","logistic","assoc","fisher", "work_dir", "scripts", "max_forks", "high_ld_regions_fname", "sexinfo_available", "cut_het_high", "cut_het_low", "cut_diff_miss", "cut_maf", "cut_mind", "cut_geno", "cut_hwe", "pi_hat", "super_pi_hat", "f_lo_male", "f_hi_female", "case_control", "case_control_col", "phenotype", "pheno_col", "batch", "batch_col", "samplesize", "strandreport", "manifest", "idpat", "accessKey", "access-key", "secretKey", "secret-key", "region", "other_mem_req", "max_plink_cores", "pheno","big_time","thin", "gemma_mat_rel","print_pca", "file_rs_buildrelat","genetic_map_file", "rs_list","adjust"]
+
+
+allowed_params = ["mperm","sharedStorageMount","shared-storage-mount","max-instances","maxInstances","AMI","gc10","input_dir","instanceType","input_pat","output","output_dir","data","plink_mem_req","covariates","gemma_num_cores","gemma_mem_req","gemma","linear","logistic","assoc","fisher", "work_dir", "scripts", "max_forks", "high_ld_regions_fname", "sexinfo_available", "cut_het_high", "cut_het_low", "cut_diff_miss", "cut_maf", "cut_mind", "cut_geno", "cut_hwe", "pi_hat", "super_pi_hat", "f_lo_male", "f_hi_female", "case_control", "case_control_col", "phenotype", "pheno_col", "batch", "batch_col", "samplesize", "strandreport", "manifest", "idpat", "accessKey", "access-key", "secretKey", "secret-key", "region", "other_mem_req", "max_plink_cores", "pheno","big_time","thin", "gemma_mat_rel","print_pca", "file_rs_buildrelat","genetic_map_file", "rs_list","adjust","bootStorageSize","instance-type","boot-storage-size"]
 
 
 /*JT : append argume boltlmm, bolt_covariates_type */
@@ -1007,7 +1009,6 @@ if (params.assoc+params.fisher+params.logistic+params.linear > 0) {
        perm = (params.mperm == 0 ? "" : "mperm=${params.mperm}")
        adjust = (params.adjust ? "--adjust" : "")
        outfname = "${pheno_name}"
-       test = test_choice 
        if (params.data == "") {
            pheno_cmd = ""
            out = base