Cleaned up workflow bits

AndersenLab · Jun 10, 2024 · 6a9908b · 6a9908b
1 parent 9db37fa
commit 6a9908b
Show file tree

Hide file tree

Showing 10 changed files with 267 additions and 211 deletions.
diff --git a/bin/pipeline.plotting.mod.R b/bin/pipeline.plotting.mod.R
@@ -93,7 +93,7 @@ for.plot <- combined.mappings %>%
         if(!("MtDNA" %in% mito_check$CHROM)) dplyr::filter(., CHROM != "MtDNA") else .
     }
 
-BF <- combined.mappings %>% 
+BF <- for.plot %>% 
     dplyr::group_by(trait) %>% 
     dplyr::filter(log10p != 0) %>% 
     dplyr::distinct(marker, log10p) %>%
@@ -160,7 +160,8 @@ man.plot <- ggplot() +
   facet_grid(. ~ CHROM, scales = "free_x", space = facet_scales) + 
   ggtitle(BF.frame$trait)
 
-ggsave(man.plot, filename = paste0(BF.frame$trait,"_manhattan_", args[3], ".plot.png"), width = 8, height = 4)
+
+  ggsave(man.plot, filename = paste0(BF.frame$trait,"_manhattan_", args[3], ".plot.png"), width = 8, height = 4)
 
 
 ## SWEPTNESS & EFFECTS SUMMARY ##

diff --git a/conf/rockfish.config b/conf/rockfish.config
@@ -70,4 +70,5 @@ singularity {
     autoMounts = true
     cacheDir = "${params.baseDir}/singularity"
     pullTimeout = '20 min'
+    envWhitelist = "SLURMD_HOSTNAME,SLURM_JOB_NODELIST,SLURM_NODELIST,SLURM_STEP_NODELIST,SLURM_TOPOLOGY_ADDR"
 }
diff --git a/env/conda.yml b/env/conda.yml
@@ -1,12 +1,11 @@
-name: nemascan
+name: base
 channels:
   - defaults
   - bioconda
   - r
   - biobuilds
   - conda-forge
 dependencies:
-  - bcftools=1.9
   - pandoc=2.12
   - plink=1.90b6.12
   - bedtools=2.29.2

diff --git a/input_data/all_species/rename_chromosomes b/input_data/all_species/rename_chromosomes
@@ -1,7 +1,7 @@
-I 1
-II 2
-III 3
-IV 4
-V 5
-X 6
-MtDNA 7
+I	1
+II	2
+III	3
+IV	4
+V	5
+X	6
+MtDNA	7
diff --git a/main.nf b/main.nf
@@ -175,13 +175,13 @@ if (params.matrix || params.mapping){
 
 if (params.help) {
     log.info '''
-O~~~     O~~                                      O~~ ~~
+O~~~     O~~                                      O~ O~~
 O~ O~~   O~~                                    O~~    O~~
-O~~ O~~  O~~    O~~    O~~~ O~~ O~~     O~~       O~~          O~~~    O~~     O~~ O~~
-O~~  O~~ O~~  O~   O~~  O~~  O~  O~~  O~~  O~~      O~~      O~~     O~~  O~~   O~~  O~~
-O~~   O~ O~~ O~~~~~ O~~ O~~  O~  O~~ O~~   O~~         O~~  O~~     O~~   O~~   O~~  O~~
-O~~    O~ ~~ O~         O~~  O~  O~~ O~~   O~~   O~~    O~~  O~~    O~~   O~~   O~~  O~~
-O~~      O~~   O~~~~   O~~~  O~  O~~   O~~ O~~~    O~~ ~~      O~~~   O~~ O~~~ O~~~  O~~
+O~~ O~~  O~~    O~~   O~~~ O~~ O~~     O~~       O~~          O~~~    O~~     O~~ O~~
+O~~  O~~ O~~  O~   O~  O~~  O~  O~~  O~~  O~~      O~~      O~~     O~~  O~~   O~~  O~~
+O~~   O~ O~~ O~~~~~ O~ O~~  O~  O~~ O~~   O~~         O~~  O~~     O~~   O~~   O~~  O~~
+O~~    O~O~~ O~        O~~  O~  O~~ O~~   O~~   O~~    O~~  O~~    O~~   O~~   O~~  O~~
+O~~      O~~   O~~~~  O~~~  O~  O~~   O~~ O~~~    O~ O~~      O~~~   O~~ O~~~ O~~~  O~~
     '''
     log.info "----------------------------------------------------------------"
     log.info "                      USAGE                                     "
@@ -246,13 +246,13 @@ O~~      O~~   O~~~~   O~~~  O~  O~~   O~~ O~~~    O~~ ~~      O~~~   O~~ O~~~ O
     exit 1
 } else {
     log.info '''
-O~~~     O~~                                      O~~ ~~
+O~~~     O~~                                      O~ O~~
 O~ O~~   O~~                                    O~~    O~~
-O~~ O~~  O~~    O~~    O~~~ O~~ O~~     O~~       O~~          O~~~    O~~     O~~ O~~
-O~~  O~~ O~~  O~   O~~  O~~  O~  O~~  O~~  O~~      O~~      O~~     O~~  O~~   O~~  O~~
-O~~   O~ O~~ O~~~~~ O~~ O~~  O~  O~~ O~~   O~~         O~~  O~~     O~~   O~~   O~~  O~~
-O~~    O~ ~~ O~         O~~  O~  O~~ O~~   O~~   O~~    O~~  O~~    O~~   O~~   O~~  O~~
-O~~      O~~   O~~~~   O~~~  O~  O~~   O~~ O~~~    O~~ ~~      O~~~   O~~ O~~~ O~~~  O~~
+O~~ O~~  O~~    O~~   O~~~ O~~ O~~     O~~       O~~          O~~~    O~~     O~~ O~~
+O~~  O~~ O~~  O~   O~  O~~  O~  O~~  O~~  O~~      O~~      O~~     O~~  O~~   O~~  O~~
+O~~   O~ O~~ O~~~~~ O~ O~~  O~  O~~ O~~   O~~         O~~  O~~     O~~   O~~   O~~  O~~
+O~~    O~O~~ O~        O~~  O~  O~~ O~~   O~~   O~~    O~~  O~~    O~~   O~~   O~~  O~~
+O~~      O~~   O~~~~  O~~~  O~  O~~   O~~ O~~~    O~ O~~      O~~~   O~~ O~~~ O~~~  O~~
 '''
 log.info ""
 log.info "Trait File                              = ${params.traitfile}"
@@ -500,7 +500,7 @@ workflow {
                         .join(gcta_fine_maps.out.finemap_html_inbred, remainder: true) // fine mapping data
                         .join(gcta_fine_maps.out.finemap_html_loco, remainder: true)
                         .join(prep_ld_files.out.finemap_LD_inbred, remainder: true)
-                        .join(prep_ld_files.out.finemap_LD_loco, remainder: true)  | html_report_main
+                        .join(prep_ld_files.out.finemap_LD_loco, remainder: true).view { "$it" }  | html_report_main
                 }  
             } else {
                 // generate main html report
@@ -548,14 +548,15 @@ workflow {
     if(simulation) {
 
         // for simulations
-        Channel.fromPath("${params.data_dir}/${params.simulate_strains}").collect { it.tokenize( ' ' ) }
+        Channel.fromPath("${params.data_dir}/${params.simulate_strains}")
+            .splitCsv(sep:" ")
             .map { SM, STRAINS -> [SM, STRAINS] }
             .combine(vcf_file.combine(vcf_index))
             .combine(Channel.fromPath("${params.data_dir}/all_species/rename_chromosomes"))
             .combine(Channel.fromPath("${params.data_dir}/${params.simulate_maf}").splitCsv()) | prepare_simulation_files
 
         // eigen
-        contigs = Channel.from(["1", "2", "3", "4", "5", "6"])
+        contigs = Channel.from([1, 2, 3, 4, 5, 6])
         contigs.combine(prepare_simulation_files.out.sim_geno)
             .combine(Channel.fromPath("${params.bin_dir}/Get_GenoMatrix_Eigen.R")) | chrom_eigen_variants_sims
 
@@ -645,7 +646,6 @@ workflow.onComplete {
     Mapping                                 = ${params.mapping}
     Simulation                              = ${params.simulate}
     Simulate QTL effects                    = ${params.simulate_qtlloc}
-    Annotation                              = ${params.annotate}
     Result Directory                        = ${params.out}
     """
 

diff --git a/modules/mapping.nf b/modules/mapping.nf
@@ -58,28 +58,31 @@ process gcta_grm {
     label "lg"
 
     input:
-        tuple val(TRAIT), file(traits), file(bed), file(bim), file(fam), file(map), file(nosex), file(ped), file(log)
+        tuple val(TRAIT), file(traits), file(bed), file(bim), file(fam), file(map), file(nosex), \
+              file(ped), file(log), val(algorithm)
 
     output:
         tuple val(TRAIT), file(traits), file(bed), file(bim), file(fam), file(map), file(nosex), \
-        file(ped), file(log), file("${TRAIT}_gcta_grm.grm.bin"), file("${TRAIT}_gcta_grm.grm.id"), \
-        file("${TRAIT}_gcta_grm.grm.N.bin"), file("${TRAIT}_gcta_grm_inbred.grm.bin"), file("${TRAIT}_gcta_grm_inbred.grm.id")
+              file(ped), file(log), file("${TRAIT}_gcta_grm_${algorithm}.grm.bin"), \
+              file("${TRAIT}_gcta_grm_${algorithm}.grm.id"), \
+              file("${TRAIT}_gcta_grm_${algorithm}.grm.N.bin"), val(algorithm)
 
     when:
-        params.maps
+        params.mapping
 
     """
+    if [[ ${algorithm} == "inbred" ]];
+    then
+        option="--make-grm-inbred"
+    else
+        options="--make-grm"
+    fi
+
     gcta64 --bfile ${TRAIT} \\
            --autosome \\
            --maf ${params.maf} \\
-           --make-grm \\
-           --out ${TRAIT}_gcta_grm \\
-           --thread-num 5
-    gcta64 --bfile ${TRAIT} \\
-           --autosome \\
-           --maf ${params.maf} \\
-           --make-grm-inbred \\
-           --out ${TRAIT}_gcta_grm_inbred \\
+           \${option} \\
+           --out ${TRAIT}_gcta_grm_${algorithm} \\
            --thread-num 5
     """
 }
@@ -89,63 +92,44 @@ process gcta_lmm_exact_mapping {
 
     label "lg"
 
-    publishDir "${params.out}/INBRED/Mapping/Raw", pattern: "*pca.fastGWA", overwrite: true
-    publishDir "${params.out}/LOCO/Mapping/Raw", pattern: "*pca.loco.mlma", overwrite: true
+    publishDir "${params.out}/INBRED/Mapping/Raw", pattern: "*inbred_pca.fastGWA", overwrite: true
+    publishDir "${params.out}/LOCO/Mapping/Raw", pattern: "*loco_pca.mlma", overwrite: true
 
     input:
     tuple val(TRAIT), file(traits), file(bed), file(bim), file(fam), file(map), \
-    file(nosex), file(ped), file(log), file(grm_bin), file(grm_id), file(grm_nbin), \
-    file(grm_bin_inbred), file(grm_id_inbred)
+          file(nosex), file(ped), file(log), file(grm_bin), file(grm_id), file(grm_nbin),
+          val(algorithm)
 
     output:
-    tuple val(TRAIT), file("${TRAIT}_lmm-exact_inbred_pca.fastGWA"), file("${TRAIT}_lmm-exact_pca.loco.mlma")
+    tuple val(TRAIT), file("${TRAIT}_lmm-exact_${algorithm}_pca.*", arity=1)
 
 
     """
-    gcta64 --grm ${TRAIT}_gcta_grm \\
-           --make-bK-sparse ${params.sparse_cut} \\
-           --out ${TRAIT}_sparse_grm \\
-           --thread-num ${task.cpus}
-    gcta64 --grm ${TRAIT}_gcta_grm \\
-           --pca 1 \\
-           --out ${TRAIT}_sparse_grm \\
-           --thread-num ${task.cpus}
-    gcta64 --mlma-loco \\
-           --grm ${TRAIT}_sparse_grm \\
-           --bfile ${TRAIT} \\
-           --out ${TRAIT}_lmm-exact \\
-           --pheno ${traits} \\
-           --maf ${params.maf} \\
-           --thread-num ${task.cpus}
-    gcta64 --mlma-loco \\
-           --grm ${TRAIT}_sparse_grm \\
-           --bfile ${TRAIT} \\
-           --qcovar ${TRAIT}_sparse_grm.eigenvec \\
-           --out ${TRAIT}_lmm-exact_pca \\
-           --pheno ${traits} \\
-           --maf ${params.maf} \\
-           --thread-num ${task.cpus}
-
-    gcta64 --grm ${TRAIT}_gcta_grm_inbred \\
+    if [[ ${algorithm} == "inbred" ]];
+    then
+        options="--fastqGWA-lmm-exact --grm-sparse"
+    else
+        options="--mlma-loco --grm"
+    fi
+    
+    gcta64 --grm ${TRAIT}_gcta_grm_${algorithm} \\
            --make-bK-sparse ${params.sparse_cut} \\
-           --out ${TRAIT}_sparse_grm_inbred \\
+           --out ${TRAIT}_sparse_grm_${algorithm} \\
            --thread-num ${task.cpus}
-    gcta64 --grm ${TRAIT}_gcta_grm_inbred \\
+    gcta64 --grm ${TRAIT}_gcta_grm_${algorithm} \\
            --pca 1 \\
-           --out ${TRAIT}_sparse_grm_inbred \\
+           --out ${TRAIT}_sparse_grm_${algorithm} \\
            --thread-num ${task.cpus}
-    gcta64 --fastGWA-lmm-exact \\
-           --grm-sparse ${TRAIT}_sparse_grm \\
+    gcta64 \${options} ${TRAIT}_sparse_grm \\
            --bfile ${TRAIT} \\
-           --out ${TRAIT}_lmm-exact_inbred \\
+           --out ${TRAIT}_lmm-exact_${algorithm} \\
            --pheno ${traits} \\
            --maf ${params.maf} \\
            --thread-num ${task.cpus}
-    gcta64 --fastGWA-lmm-exact \\
-           --grm-sparse ${TRAIT}_sparse_grm \\
+    gcta64 \${options} ${TRAIT}_sparse_grm \\
            --bfile ${TRAIT} \\
-           --qcovar ${TRAIT}_sparse_grm_inbred.eigenvec \\
-           --out ${TRAIT}_lmm-exact_inbred_pca \\
+           --qcovar ${TRAIT}_sparse_grm_${algorithm}.eigenvec \\
+           --out ${TRAIT}_lmm-exact_${algorithm}_pca \\
            --pheno ${traits} \\
            --maf ${params.maf} \\
            --thread-num ${task.cpus}
@@ -163,57 +147,38 @@ process gcta_lmm_exact_mapping_nopca {
     input:
     tuple val(TRAIT), file(traits), file(bed), file(bim), file(fam), file(map), \
     file(nosex), file(ped), file(log), file(grm_bin), file(grm_id), file(grm_nbin), \
-    file(grm_bin_inbred), file(grm_id_inbred)
+    val(algorithm)
 
     output:
-    tuple val(TRAIT), file("${TRAIT}_lmm-exact_inbred.fastGWA"), file("${TRAIT}_lmm-exact.loco.mlma")
+    tuple val(TRAIT), file("${TRAIT}_lmm-exact_${algorithm}.*", arity=1)
 
 
     """
-    gcta64 --grm ${TRAIT}_gcta_grm \\
+    if [[ ${algorithm} == "inbred" ]];
+    then
+        options="--fastqGWA-lmm-exact --grm-sparse"
+    else
+        options="--mlma-loco --grm"
+    fi
+    
+    gcta64 --grm ${TRAIT}_gcta_grm_${algorithm} \\
            --make-bK-sparse ${params.sparse_cut} \\
-           --out ${TRAIT}_sparse_grm \\
+           --out ${TRAIT}_sparse_grm_${algorithm} \\
            --thread-num ${task.cpus}
-    gcta64 --grm ${TRAIT}_gcta_grm \\
+    gcta64 --grm ${TRAIT}_gcta_grm_${algorithm} \\
            --pca 1 \\
-           --out ${TRAIT}_sparse_grm \\
+           --out ${TRAIT}_sparse_grm_${algorithm} \\
            --thread-num ${task.cpus}
-    gcta64 --mlma-loco \\
-           --grm ${TRAIT}_sparse_grm \\
+    gcta64 \${options} ${TRAIT}_sparse_grm \\
            --bfile ${TRAIT} \\
-           --out ${TRAIT}_lmm-exact \\
+           --out ${TRAIT}_lmm-exact_${algorithm} \\
            --pheno ${traits} \\
            --maf ${params.maf} \\
            --thread-num ${task.cpus}
-    gcta64 --mlma-loco \\
-           --grm ${TRAIT}_sparse_grm \\
+    gcta64 \${options} ${TRAIT}_sparse_grm \\
            --bfile ${TRAIT} \\
-           --qcovar ${TRAIT}_sparse_grm.eigenvec \\
-           --out ${TRAIT}_lmm-exact_pca \\
-           --pheno ${traits} \\
-           --maf ${params.maf} \\
-           --thread-num ${task.cpus}
-
-    gcta64 --grm ${TRAIT}_gcta_grm_inbred \\
-           --make-bK-sparse ${params.sparse_cut} \\
-           --out ${TRAIT}_sparse_grm_inbred \\
-           --thread-num ${task.cpus}
-    gcta64 --grm ${TRAIT}_gcta_grm_inbred \\
-           --pca 1 \\
-           --out ${TRAIT}_sparse_grm_inbred \\
-           --thread-num ${task.cpus}
-    gcta64 --fastGWA-lmm-exact \\
-           --grm-sparse ${TRAIT}_sparse_grm \\
-           --bfile ${TRAIT} \\
-           --out ${TRAIT}_lmm-exact_inbred \\
-           --pheno ${traits} \\
-           --maf ${params.maf} \\
-           --thread-num ${task.cpus}
-    gcta64 --fastGWA-lmm-exact \\
-           --grm-sparse ${TRAIT}_sparse_grm \\
-           --bfile ${TRAIT} \\
-           --qcovar ${TRAIT}_sparse_grm_inbred.eigenvec \\
-           --out ${TRAIT}_lmm-exact_inbred_pca \\
+           --qcovar ${TRAIT}_sparse_grm_${algorithm}.eigenvec \\
+           --out ${TRAIT}_lmm-exact_${algorithm}_pca \\
            --pheno ${traits} \\
            --maf ${params.maf} \\
            --thread-num ${task.cpus}
@@ -230,19 +195,18 @@ process gcta_intervals_maps {
 
     input:
         tuple val(TRAIT), file(pheno), file(tests), file(geno), val(P3D), val(sig_thresh), \
-        val(qtl_grouping_size), val(qtl_ci_size), file(lmmexact_inbred), file(lmmexact_loco), file(find_aggregate_intervals_maps)
+              val(qtl_grouping_size), val(qtl_ci_size), file(lmmexact), \
+              file(find_aggregate_intervals_maps), val(algorithm)
 
     output:
-        tuple file(geno), file(pheno), val(TRAIT), file(tests), file("*AGGREGATE_mapping_inbred.tsv"), file("*AGGREGATE_mapping_loco.tsv"), emit: maps_to_plot
-        path "*AGGREGATE_qtl_region_inbred.tsv", emit: qtl_peaks_inbred
-        tuple file("*AGGREGATE_mapping_inbred.tsv"), file("*AGGREGATE_mapping_loco.tsv"), val(TRAIT), emit: for_html
-
-        path "*AGGREGATE_qtl_region_loco.tsv", emit: qtl_peaks_loco
-       //  tuple val('loco'), file("*AGGREGATE_mapping_loco.tsv"), val(TRAIT), emit: for_html_loco
+        tuple file(geno), file(pheno), val(TRAIT), file(tests), file("*AGGREGATE_mapping_${algorithm}.tsv"), emit: maps_to_plot
+        path "*AGGREGATE_qtl_region${algorithm}.tsv", emit: qtl_peaks
+        tuple file("*AGGREGATE_mapping_${algorithm}.tsv"), val(TRAIT), val(algorithm), emit: for_html
 
     """
-    Rscript --vanilla ${find_aggregate_intervals_maps} ${geno} ${pheno} ${lmmexact_inbred} ${tests} ${qtl_grouping_size} ${qtl_ci_size} ${sig_thresh} ${TRAIT}_AGGREGATE inbred
-    Rscript --vanilla ${find_aggregate_intervals_maps} ${geno} ${pheno} ${lmmexact_loco} ${tests} ${qtl_grouping_size} ${qtl_ci_size} ${sig_thresh} ${TRAIT}_AGGREGATE loco
+    Rscript --vanilla ${find_aggregate_intervals_maps} ${geno} ${pheno} ${lmmexact} \\
+                      ${tests} ${qtl_grouping_size} ${qtl_ci_size} ${sig_thresh} \\
+                      ${TRAIT}_AGGREGATE ${algorithm}
     """
 }
-Original file line number
+Diff line change
@@ -1,7 +1,7 @@
-    I 1
-    II 2
-    III 3
-    IV 4
-    V 5
-    X 6
-    MtDNA 7
+    I	1
+    II	2
+    III	3
+    IV	4
+    V	5
+    X	6
+    MtDNA	7