PGScatalog · nebfield · Feb 22, 2024 · Feb 21, 2024 · Feb 22, 2024 · Feb 22, 2024
diff --git a/assets/report/renv.lock b/assets/report/renv.lock
@@ -190,6 +190,13 @@
       ],
       "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
     },
+    "commonmark": {
+      "Package": "commonmark",
+      "Version": "1.9.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "5d8225445acb167abf7797de48b2ee3c"
+    },
     "cpp11": {
       "Package": "cpp11",
       "Version": "0.4.7",
@@ -854,6 +861,50 @@
       ],
       "Hash": "c19df082ba346b0ffa6f833e92de34d1"
     },
+    "shiny": {
+      "Package": "shiny",
+      "Version": "1.8.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "bslib",
+        "cachem",
+        "commonmark",
+        "crayon",
+        "ellipsis",
+        "fastmap",
+        "fontawesome",
+        "glue",
+        "grDevices",
+        "htmltools",
+        "httpuv",
+        "jsonlite",
+        "later",
+        "lifecycle",
+        "methods",
+        "mime",
+        "promises",
+        "rlang",
+        "sourcetools",
+        "tools",
+        "utils",
+        "withr",
+        "xtable"
+      ],
+      "Hash": "3a1f41807d648a908e3c7f0334bf85e6"
+    },
+    "sourcetools": {
+      "Package": "sourcetools",
+      "Version": "0.1.7-1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "5f5a7629f956619d519205ec475fe647"
+    },
     "stringi": {
       "Package": "stringi",
       "Version": "1.8.3",
@@ -1047,6 +1098,18 @@
       ],
       "Hash": "fd1349170df31f7a10bd98b0189e85af"
     },
+    "xtable": {
+      "Package": "xtable",
+      "Version": "1.8-4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "stats",
+        "utils"
+      ],
+      "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
+    },
     "yaml": {
       "Package": "yaml",
       "Version": "2.3.8",

diff --git a/conf/base.config b/conf/base.config
@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    pgscatalog/pgsccalc Nextflow base config file
+    pgscatalog/pgsc_calc Nextflow base config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     A 'blank slate' config file, appropriate for general use on most high performance
     compute environments. Assumes that all software is installed and available on
@@ -9,8 +9,6 @@
 */
 
 process {
-    // defaults for unlabelled processes
-    // however all processes are labelled
     cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
@@ -19,15 +17,19 @@ process {
     maxRetries    = 1
     maxErrors     = '-1'
 
-    // reasonable resource limits for medium sized datasets
+    withLabel:process_single {
+        cpus   = { check_max( 1                  , 'cpus'    ) }
+        memory = { check_max( 4.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 2.h  * task.attempt, 'time'    ) }
+    }
     withLabel:process_low {
         cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
         memory = { check_max( 8.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {
         cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 16.GB * task.attempt, 'memory'   ) }
+        memory = { check_max( 16.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 8.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_high {
@@ -51,7 +53,4 @@ process {
     withName:DUMPSOFTWAREVERSIONS {
         cache = false
     }
-    withLabel:plink2{
-        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
@@ -63,7 +63,7 @@ process {
         ext.singularity = 'oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/report'
         ext.singularity_version = ':2.0'
         ext.docker = 'dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/report'
-        ext.docker_version = ':2.0'
+        ext.docker_version = ':dev'
     }
 
     withLabel: pyyaml {

diff --git a/conf/sequential.config b/conf/sequential.config
diff --git a/docs/how-to/bigjob.rst b/docs/how-to/bigjob.rst
@@ -57,12 +57,8 @@ pgsc_calc:
         -profile <docker/singularity/conda> \
         --input samplesheet.csv \
         --pgs_id PGS001229 \
-        --parallel \
         -c my_custom.config
 
-.. note:: Using the ``parallel`` parameter enables parallel score calculation,
-          which is a RAM and I/O intensive process. It's disabled by default to
-          prevent laptops with 16GB RAM crashing on smaller datasets.
 
 High performance computing cluster
 ----------------------------------
@@ -125,7 +121,6 @@ instead:
         -profile singularity \
         --input samplesheet.csv \
         --pgs_id PGS001229 \
-        --parallel \
         -c my_custom.config
 
 .. note:: The name of the nextflow and singularity modules will be different in

diff --git a/environments/report/Dockerfile b/environments/report/Dockerfile
@@ -1,13 +1,11 @@
-ARG QUARTO_VERSION=1.3.433
-
 FROM continuumio/miniconda3 AS build
 
-ARG QUARTO_VERSION
+ARG QUARTO_VERSION=1.4.550
 ARG TARGETARCH
 
-RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.deb && \
-    dpkg -i quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.deb && \
-    rm quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.deb
+RUN apt-get update \
+    && apt-get install -y procps zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
 
 RUN conda install -c conda-forge r-renv
 
@@ -19,7 +17,6 @@ RUN R -e "renv::restore(clean=TRUE, prompt=FALSE)"
 
 # RUN conda env export > environment.yml
 
-RUN apt-get update \
-    && apt-get install -y procps \
-    && rm -rf /var/lib/apt/lists/*
-
+RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.deb && \
+    dpkg -i quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.deb && \
+    rm quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.deb
diff --git a/environments/report/environment.yml b/environments/report/environment.yml
@@ -1,17 +1,146 @@
+# generated from docker image
 name: report
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - r-dplyr
-  - r-dt
-  - r-tidyr
-  - r-ggplot2
-  - r-forcats
-  - r-readr
-  - r-purrr
-  - r-jsonlite
-  - r-data.table
-  - quarto=1.3.433
-  - r-rmarkdown
-  - r-r.utils
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=51_gnu
+  - _r-mutex=1.0.1=anacondar_1
+  - _sysroot_linux-aarch64_curr_repodata_hack=4=h57d6b7b_14
+  - archspec=0.2.1=pyhd3eb1b0_0
+  - binutils_impl_linux-aarch64=2.38=h0c9fd12_1
+  - boltons=23.0.0=py311hd43f75c_0
+  - brotli-python=1.0.9=py311h419075a_7
+  - bwidget=1.9.14=h8af1aa0_1
+  - bzip2=1.0.8=hfd63f10_2
+  - c-ares=1.19.1=h998d150_0
+  - ca-certificates=2024.2.2=hcefe29a_0
+  - cairo=1.18.0=ha13f110_0
+  - certifi=2024.2.2=pyhd8ed1ab_0
+  - cffi=1.15.1=py311h998d150_3
+  - charset-normalizer=2.0.4=pyhd3eb1b0_0
+  - conda=24.1.1=py311hec3470c_0
+  - conda-content-trust=0.2.0=py311hd43f75c_0
+  - conda-libmamba-solver=23.11.1=py311hd43f75c_0
+  - conda-package-handling=2.2.0=py311hd43f75c_0
+  - conda-package-streaming=0.9.0=py311hd43f75c_0
+  - cryptography=41.0.3=py311h5077475_0
+  - curl=8.4.0=h6ac735f_0
+  - distro=1.9.0=pyhd8ed1ab_0
+  - expat=2.5.0=hd600fc2_1
+  - fmt=9.1.0=hb8fdbf2_0
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=h77eed37_1
+  - fontconfig=2.14.2=ha9a116f_0
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - freetype=2.12.1=hf0a5ef3_2
+  - fribidi=1.0.10=hb9de7d4_0
+  - gcc_impl_linux-aarch64=12.1.0=h9c21524_17
+  - gettext=0.21.1=ha18d298_0
+  - gfortran_impl_linux-aarch64=12.1.0=hd36f8f4_17
+  - graphite2=1.3.13=h7fd3ca4_1001
+  - gxx_impl_linux-aarch64=12.1.0=h9c21524_17
+  - harfbuzz=8.3.0=hebeb849_0
+  - icu=73.2=h787c7f5_0
+  - idna=3.4=py311hd43f75c_0
+  - jsonpatch=1.32=pyhd3eb1b0_0
+  - jsonpointer=2.1=pyhd3eb1b0_0
+  - kernel-headers_linux-aarch64=4.18.0=h5b4a56d_14
+  - krb5=1.20.1=h2e2fba8_1
+  - ld_impl_linux-aarch64=2.38=h8131f2d_1
+  - lerc=4.0.0=h4de3ea5_0
+  - libarchive=3.6.2=h654c02d_2
+  - libblas=3.9.0=21_linuxaarch64_openblas
+  - libcurl=8.4.0=hfa2bbb0_0
+  - libdeflate=1.19=h31becfc_0
+  - libedit=3.1.20221030=h998d150_0
+  - libev=4.33=hfd63f10_1
+  - libexpat=2.5.0=hd600fc2_1
+  - libffi=3.4.4=h419075a_0
+  - libgcc-devel_linux-aarch64=12.1.0=hf2ffb8d_17
+  - libgcc-ng=13.2.0=hf8544c7_5
+  - libgfortran-ng=13.2.0=he9431aa_5
+  - libgfortran5=13.2.0=h582850c_5
+  - libglib=2.78.4=h311d5f7_0
+  - libgomp=13.2.0=hf8544c7_5
+  - libiconv=1.17=h31becfc_2
+  - libjpeg-turbo=3.0.0=h31becfc_1
+  - liblapack=3.9.0=21_linuxaarch64_openblas
+  - libmamba=1.5.3=h78dbd8a_0
+  - libmambapy=1.5.3=py311hd82f176_0
+  - libnghttp2=1.57.0=hb788212_0
+  - libnsl=2.0.1=h31becfc_0
+  - libopenblas=0.3.26=pthreads_h5a5ec62_0
+  - libpng=1.6.42=h194ca79_0
+  - libsanitizer=12.1.0=hd01590b_17
+  - libsolv=0.7.24=h94b7715_0
+  - libsqlite=3.45.1=h194ca79_0
+  - libssh2=1.10.0=h6ac735f_2
+  - libstdcxx-devel_linux-aarch64=12.1.0=hf2ffb8d_17
+  - libstdcxx-ng=13.2.0=h9a76618_5
+  - libtiff=4.6.0=h1708d11_2
+  - libuuid=2.38.1=hb4cce97_0
+  - libwebp-base=1.3.2=h31becfc_0
+  - libxcb=1.15=h2a766a3_0
+  - libxcrypt=4.4.36=h31becfc_1
+  - libxml2=2.10.4=h045d036_1
+  - libzlib=1.2.13=h31becfc_5
+  - lz4-c=1.9.4=h419075a_0
+  - make=4.3=h309ac5b_1
+  - menuinst=2.0.2=py311hec3470c_0
+  - ncurses=6.4=h419075a_0
+  - openssl=3.2.1=h31becfc_0
+  - packaging=23.1=py311hd43f75c_0
+  - pango=1.50.14=h11ef544_2
+  - pcre2=10.42=hcfaa891_0
+  - pip=23.3=py311hd43f75c_0
+  - pixman=0.43.2=h2f0025b_0
+  - platformdirs=4.2.0=pyhd8ed1ab_0
+  - pluggy=1.0.0=py311hd43f75c_1
+  - pthread-stubs=0.4=hb9de7d4_1001
+  - pybind11-abi=4=hd3eb1b0_1
+  - pycosat=0.6.6=py311h998d150_0
+  - pycparser=2.21=pyhd3eb1b0_0
+  - pyopenssl=23.2.0=py311hd43f75c_0
+  - pysocks=1.7.1=py311hd43f75c_0
+  - python=3.11.8=h43d1f9e_0_cpython
+  - python_abi=3.11=4_cp311
+  - r-base=4.3.2=h7dc8e12_1
+  - r-renv=1.0.4=r43hc72bb7e_0
+  - readline=8.2=h998d150_0
+  - reproc=14.2.4=h22f4aa5_1
+  - reproc-cpp=14.2.4=h22f4aa5_1
+  - requests=2.31.0=py311hd43f75c_0
+  - ruamel.yaml=0.17.21=py311h998d150_0
+  - sed=4.8=ha0d5d3d_0
+  - setuptools=68.0.0=py311hd43f75c_0
+  - sqlite=3.41.2=h998d150_0
+  - sysroot_linux-aarch64=2.17=h5b4a56d_14
+  - tk=8.6.13=h194ca79_0
+  - tktable=2.10=h4f9ca69_5
+  - tqdm=4.65.0=py311h2163289_0
+  - truststore=0.8.0=py311hd43f75c_0
+  - tzdata=2023c=h04d1e81_0
+  - urllib3=1.26.18=py311hd43f75c_0
+  - wheel=0.41.2=py311hd43f75c_0
+  - xorg-kbproto=1.0.7=h3557bc0_1002
+  - xorg-libice=1.1.1=h7935292_0
+  - xorg-libsm=1.2.4=h5a01bc2_0
+  - xorg-libx11=1.8.7=h055a233_0
+  - xorg-libxau=1.0.11=h31becfc_0
+  - xorg-libxdmcp=1.1.3=h3557bc0_0
+  - xorg-libxext=1.3.4=h2a766a3_2
+  - xorg-libxrender=0.9.11=h7935292_0
+  - xorg-libxt=1.3.0=h7935292_1
+  - xorg-renderproto=0.11.1=h3557bc0_1002
+  - xorg-xextproto=7.3.0=h2a766a3_1003
+  - xorg-xproto=7.0.31=h3557bc0_1007
+  - xz=5.4.2=h998d150_0
+  - yaml-cpp=0.8.0=h419075a_0
+  - zlib=1.2.13=h31becfc_5
+  - zstandard=0.19.0=py311h998d150_0
+  - zstd=1.5.5=h6a09583_0