Updated readme and dockerfiles

AndersenLab · Jul 19, 2024 · 3513894 · 3513894
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commit 3513894
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Showing 10 changed files with 172 additions and 158 deletions.
diff --git a/.github/workflows/build_docker.yml → .github/workflows/build_nemascan_docker.yml b/.github/workflows/build_docker.yml → .github/workflows/build_nemascan_docker.yml
diff --git a/bin/plot_genes.R b/bin/plot_genes.R
@@ -201,7 +201,7 @@ tidy_genes_in_region <- if(ann_type == "bcsq") {
  #         path = glue::glue("{analysis_trait}_{cq}_{sq}-{eq}_{ann_type}_genes_{args[5]}.tsv"))
 
 write_tsv(tidy_genes_in_region,
-          file = glue::glue("{analysis_trait}_{cq}_{output_sq}-{output_eq}_{ann_type}_genes_{args[5]}.tsv"))
+          path = glue::glue("{analysis_trait}_{cq}_{output_sq}-{output_eq}_{ann_type}_genes_{args[5]}.tsv"))
 
 
 for(r in 1:length(unique(ugly_genes_in_region$start_pos))){

diff --git a/env/gcta.Dockerfile b/env/gcta.Dockerfile
@@ -0,0 +1,18 @@
+FROM mambaorg/micromamba:1.5.0
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER gcta_conda.yml .
+
+RUN micromamba install -n base -f gcta_conda.yml -y \
+	&& micromamba clean -a -y
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+USER root
+
+RUN apt-get --allow-releaseinfo-change update && apt-get install -y procps && \
+    apt-get clean && \
+	rm -rf /var/lib/apt/lists/*
+
+USER $MAMBA_USER
+
+ENTRYPOINT source /usr/local/bin/_entrypoint.sh
diff --git a/env/gcta_conda.yml b/env/gcta_conda.yml
@@ -0,0 +1,13 @@
+name: base
+channels:
+  - defaults
+  - bioconda
+  - r
+  - biobuilds
+  - conda-forge
+dependencies:
+  - plink=1.90b6.12
+  - gcta
+  - bcftools
+  - tabix
+  - gsl==2.5
diff --git a/env/nemascan.Dockerfile b/env/nemascan.Dockerfile
@@ -1,9 +1,9 @@
 FROM continuumio/miniconda
 MAINTAINER Katie Evans <[email protected]>
 
-COPY conda.yml .
+COPY nemascan_conda.yml .
 RUN \
-   conda env update -n root -f conda.yml \
+   conda env update -n root -f nemascan_conda.yml \
 && conda clean -a
 
 RUN Rscript -e "install.packages('valr', dependencies=TRUE, repos='http://cran.us.r-project.org')"

diff --git a/env/conda.yml → env/nemascan_conda.yml b/env/conda.yml → env/nemascan_conda.yml
diff --git a/env/nemascan_new.Dockerfile b/env/nemascan_new.Dockerfile
diff --git a/main.nf b/main.nf
diff --git a/modules/mapping.nf b/modules/mapping.nf
@@ -112,14 +112,7 @@ process gcta_lmm_exact_mapping {
     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}
+           --thread-num ${task.cpus}\
     gcta64 --mlma-loco \\
            --grm ${TRAIT}_sparse_grm \\
            --bfile ${TRAIT} \\
@@ -137,13 +130,6 @@ process gcta_lmm_exact_mapping {
            --pca 1 \\
            --out ${TRAIT}_sparse_grm_inbred \\
            --thread-num ${task.cpus}
-    gcta64 --fastGWA-lmm-exact \\
-           --grm-sparse ${TRAIT}_sparse_grm_inbred \\
-           --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_inbred \\
            --bfile ${TRAIT} \\
@@ -184,13 +170,6 @@ process gcta_lmm_exact_mapping_nopca {
            --pheno ${traits} \\
            --maf ${params.maf} \\
            --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 --grm ${TRAIT}_gcta_grm_inbred \\
            --make-bK-sparse ${params.sparse_cut} \\
@@ -203,13 +182,6 @@ process gcta_lmm_exact_mapping_nopca {
            --pheno ${traits} \\
            --maf ${params.maf} \\
            --thread-num ${task.cpus}
-    gcta64 --fastGWA-lmm-exact \\
-           --grm-sparse ${TRAIT}_sparse_grm_inbred \\
-           --bfile ${TRAIT} \\
-           --out ${TRAIT}_lmm-exact_inbred \\
-           --pheno ${traits} \\
-           --maf ${params.maf} \\
-           --thread-num ${task.cpus}
     """
 }
 
@@ -222,7 +194,7 @@ process gcta_intervals_maps {
     publishDir "${params.out}/LOCO/Mapping/Processed", mode: 'copy', pattern: "*_loco.tsv" 
 
     input:
-        tuple val(TRAIT), file(pheno), file(tests), file(geno), val(P3D), val(sig_thresh), \
+        tuple val(TRAIT), file(pheno), file(tests), file(geno), val(sig_thresh), \
               val(qtl_grouping_size), val(qtl_ci_size), file(lmmexact_inbred), file(lmmexact_loco), \
               file(find_aggregate_intervals_maps)
 

diff --git a/nextflow.config b/nextflow.config
@@ -14,16 +14,15 @@ params {
     debug = false
     download_vcf = false
     finemap = true
-    fix = "fix"
+    fix = true
     maf = 0.05
     sparse_cut = 0.05
     group_qtl = 1000
     ci_size = 150
-    p3d = "TRUE"
     pca = false
-    mapping = false
+    mapping = true
     matrix = false
-    simulate = true
+    simulation = false
     species = "c_elegans"
     mediation = false
 
@@ -72,7 +71,7 @@ process {
     }
 
     withLabel: gcta {
-        container = 'msauria/gcta:060624'
+        container = 'andersenlab/gcta:060624'
     }
 
     withLabel: assess_sims {