pgsc_calc

Web: https://pgsc-calc.readthedocs.io/en/latest/ (GitHub, ftp)

2.0.0

The ceuamdin/pgsc_calc/2.0.0 module is built as follows,

cd $CEUADMIN/pgsc_calc
mkdir 2.0.0
wget -qO- https://github.com/PGScatalog/pgsc_calc/archive/refs/tags/v2.0.0.tar.gz | \
tar xvz -C 2.0.0 --strip-components=1
cd 2.0.0
module load python/3.11.0-icl
virtualenv venv
source venv/bin/activate
pip install hypothesis pytest-workflow pandas requests
module load ceuadmin/singularity/4.0.3
module load ceuadmin/ncurses/6.3
module load curl/7.79.0/gcc/75dxv7ac
curl -s https://get.nextflow.io | bash
./nextflow pull pgscatalog/pgsc_calc
export NXF_SINGULARITY_CACHEDIR=work
./nextflow run pgscatalog/pgsc_calc -profile test,singularity
nextflow run pgscatalog/pgsc_calc -profile singularity --input samplesheet.csv --pgs_id PGS001229 --target_build GRCh37
deactivate

The source package has a Makefile which sets default to docker, but on CSD3 it is more straightforward with singularity pulled by nextflow via curl. Note that during setup, recent changes at CSD3 require the long-missed prefix ./ but it is unnecessary later.

Screen output form the test run (nextflow run pgscatalog/pgsc_calc -profile test,singularity) is again pasted here,

nextflow run pgscatalog/pgsc_calc -profile test,singularity

 N E X T F L O W   ~  version 24.10.1

Pulling pgscatalog/pgsc_calc ...
 downloaded from https://github.com/PGScatalog/pgsc_calc.git
Launching `https://github.com/pgscatalog/pgsc_calc` [mad_galileo] DSL2 - revision: 205cbfd1f5 [main]

Downloading plugin nf-schema@2.0.0
Downloading plugin nf-prov@1.2.2

INFO: The test profile is used to install the workflow and verify the software is working correctly on your system.
INFO: Test input data and results are are only useful as examples of outputs, and are not biologically meaningful.



------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-g205cbfd
------------------------------------------------------
Core Nextflow options
  revision       : main
  runName        : mad_galileo
  containerEngine: singularity
  launchDir      : /rds/user/jhz22/hpc-work/work
  workDir        : /rds/user/jhz22/hpc-work/work/work
  projectDir     : /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc
  userName       : jhz22
  profile        : test,singularity
  configFiles    :

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use pgscatalog/pgsc_calc for your analysis please cite:

* The Polygenic Score Catalog
  https://doi.org/10.1101/2024.05.29.24307783
  https://doi.org/10.1038/s41588-021-00783-5

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/pgscatalog/pgsc_calc/blob/main/CITATIONS.md

[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES     -
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM  -
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES     -
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM  -
executor >  local (1)
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                            -
executor >  local (1)
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES                            -
executor >  local (2)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                        [  0%] 0 of 1
executor >  local (3)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                        [100%] 1 of 1 ✔
executor >  local (3)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                        [100%] 1 of 1 ✔
executor >  local (3)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                        [100%] 1 of 1 ✔
executor >  local (4)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                        [100%] 1 of 1 ✔
executor >  local (5)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
executor >  local (6)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
executor >  local (6)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
executor >  local (7)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
executor >  local (7)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                 -
[ad/e17692] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22)         [100%] 1 of 1 ✔
executor >  local (8)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                 -
[ad/e17692] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22)         [100%] 1 of 1 ✔
executor >  local (8)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                 -
[ad/e17692] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22)         [100%] 1 of 1 ✔
executor >  local (9)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
executor >  local (9)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
executor >  local (9)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
executor >  local (9)
[ed/1ea035] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                [100%] 1 of 1 ✔
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                 -
[ad/e17692] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22)         [100%] 1 of 1 ✔
[-        ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF                                        -
[59/d4a83e] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22)                       [100%] 1 of 1 ✔
[e3/ec2a3c] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE (cineca)                                      [100%] 1 of 1 ✔
[d3/19be98] PGS…G_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE (cineca chromosome 22 effect type additive 0) [100%] 2 of 2 ✔
[ab/d57ff4] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE (cineca)                              [100%] 1 of 1 ✔
[ca/289259] PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT (cineca)                                      [100%] 1 of 1 ✔
[02/588836] PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS (1)                                          [100%] 1 of 1 ✔
Pulling Singularity image oras://ghcr.io/pgscatalog/report:2-beta-singularity [cache /rds/user/jhz22/hpc-work/work/ghcr.io-pgscatalog-report-2-beta-singularity.img]
Pulling Singularity image oras://ghcr.io/pgscatalog/pyyaml:6.0-singularity [cache /rds/user/jhz22/hpc-work/work/ghcr.io-pgscatalog-pyyaml-6.0-singularity.img]
-[pgscatalog/pgsc_calc] Pipeline completed successfully-
Completed at: 27-Nov-2024 08:04:14
Duration    : 1m 6s
CPU hours   : (a few seconds)
Succeeded   : 9

Note the working directory is /rds/user/CRSid/hpc-work/work. A copy of the report.html is also made available.

2.0.0-alpha.4

Prerequistes

This is furnished by a number of modules,

module load ceuadmin/Anaconda3/2023.09-0
module load ceuadmin/fraposa_pgsc/0.1.0
module load ceuadmin/go/1.21.6
module load ceuadmin/nextflow/23.10.1
module load ceuadmin/openjdk/11.0.20+8
module load ceuadmin/plink/2.00a3.3
module load ceuadmin/quarto/1.4.549
module load ceuadmin/R/latest
module load ceuadmin/singularity/4.0.3

Under icelake, one can use ceuadmin/quarto/1.3.450-icelake1 and R/4.3.1-icelake. Handling of specific modules is documented on the ceuadmin section when appropriate.

pgsc_calc

As of 31 January 2024, 2.0.0-alpha.4 is the latest.

mkdir -p $CEUADMIN/pgsc_calc && cd $CEUADMIN/pgsc_calc
wget -qO- https://github.com/PGScatalog/pgsc_calc/archive/refs/tags/v2.0.0-alpha.4.tar.gz | \
tar xvfz -
mv pgsc_calc-2.0.0-alpha.4/ 2.0.0-alpha.4/

CSD3 (ceuadmin) modules

These are pgsc_calc/2.0.0-alpha.4 and pgsc_calc/2.0.0-alpha.4-icelake (experimental) built from the two steps above; the icelake version allows for the possibility to use an indepeendent collection of R packages via $R_LIBS, say vctrs2.

Usage: benchmark

This is done as follows,

module load ceuadmin/pgsc_calc
export NXF_HOME=/rds/user/$USER/hpc-work/work
export DENO_HOME=/home/$USER/.cache/deno/gen
export QUARTO_HOME=/home/$USER/.cache/quarto
cd $NXF_HOME
nextflow run pgscatalog/pgsc_calc -profile test,singularity
nextflow run pgscatalog/pgsc_calc -profile test,singularity -c b.config

NXF_HOME=/home/$USER/.nextflow3 without the -c option, which allows for additional configurations, e.g.:

singularity {
  enabled = true
  autoMounts = true
  runOptions = '-B $NXF_HOME -B $DENO_HOME -B $QUARTO_HOME'
}

For convenience, the three environmental variables have been defined with the module.

Directed acyclic graph (DAG)

Shown here is from left to right instead – refresh screen to fit if necessary,

flowchart LR subgraph " " v0["Channel.fromPath"] v3["Channel.fromPath"] v8["Channel.fromPath"] v43["Channel.fromPath"] v44["Channel.fromPath"] v45["Channel.of"] v105["Channel.fromPath"] v112["reference_panel_name"] end subgraph PGSCATALOG_PGSCALC subgraph PGSCALC subgraph INPUT_CHECK v10([SAMPLESHEET_JSON]) v18([COMBINE_SCOREFILES]) v4(( )) v12(( )) end subgraph MAKE_COMPATIBLE v28([PLINK2_RELABELBIM]) v31([PLINK2_RELABELPVAR]) v34([PLINK2_VCF]) v40(( )) end subgraph MATCH v51([MATCH_VARIANTS]) v65([MATCH_COMBINE]) v68(( )) end subgraph APPLY_SCORE v83([PLINK2_SCORE]) v90([SCORE_AGGREGATE]) v37(( )) v88(( )) v92(( )) end subgraph REPORT v113([SCORE_REPORT]) v103(( )) v117(( )) v119(( )) end v122([DUMPSOFTWAREVERSIONS]) v11(( )) end end subgraph " " v41["vmiss"] v57[" "] v66[" "] v75[" "] v84[" "] v85[" "] v114[" "] v115[" "] v116[" "] v118["versions"] v123[" "] v124[" "] v125[" "] end v0 --> v10 v3 --> v4 v8 --> v18 v10 --> v11 v10 --> v12 v4 --> v18 v18 --> v11 v18 --> v37 v18 --> v103 v12 --> v28 v28 --> v11 v28 --> v37 v28 --> v40 v12 --> v31 v31 --> v11 v31 --> v37 v31 --> v40 v12 --> v34 v34 --> v11 v34 --> v37 v34 --> v40 v40 --> v41 v43 --> v37 v44 --> v113 v45 --> v37 v37 --> v51 v51 --> v11 v51 --> v37 v37 --> v57 v37 --> v65 v65 --> v66 v65 --> v11 v65 --> v37 v65 --> v68 v65 --> v103 v37 --> v75 v37 --> v83 v83 --> v85 v83 --> v84 v83 --> v11 v83 --> v88 v88 --> v90 v90 --> v11 v90 --> v92 v90 --> v103 v105 --> v103 v112 --> v113 v103 --> v113 v113 --> v116 v113 --> v115 v113 --> v114 v113 --> v117 v113 --> v119 v117 --> v118 v11 --> v122 v122 --> v125 v122 --> v124 v122 --> v123

Screen output

N E X T F L O W  ~  version 23.10.1
Pulling pgscatalog/pgsc_calc ...
 downloaded from https://github.com/PGScatalog/pgsc_calc.git
Launching `https://github.com/pgscatalog/pgsc_calc` [stupefied_cray] DSL2 - revision: 83326a1e60 [main]

WARN: Found unexpected parameters:
* --config_profile_description: Minimal test dataset to check pipeline function
* --config_profile_name: Test profile
* --ref_format_version: v0.1
* --ancestry_checksums: /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt
- Ignore this warning: params.schema_ignore_params = "config_profile_description,config_profile_name,ref_format_version,ancestry_checksums"



------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-alpha.4
------------------------------------------------------
Core Nextflow options
  revision          : main
  runName           : stupefied_cray
  containerEngine   : singularity
  launchDir         : /rds/user/jhz22/hpc-work/work
  workDir           : /rds/user/jhz22/hpc-work/work/work
  projectDir        : /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc
  userName          : jhz22
  profile           : test,singularity
  configFiles       : /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc/nextflow.config, /usr/local/Cluster-Apps/ceuadmin/pgsc_calc/tests/b.config

Input/output options
  input             : /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc/assets/examples/samplesheet.csv
  scorefile         : /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc/assets/examples/scorefiles/PGS001229_22.txt
  genotypes_cache   : null
  outdir            : /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc/results

Reference options
  run_ancestry      : null
  ref_samplesheet   : /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37         : /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38         : /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt

Compatibility options
  target_build      : GRCh37

Max job request options
  max_cpus          : 2
  max_memory        : 6.GB
  max_time          : 6.h

Generic options
  tracedir          : ./results/pipeline_info

Other parameters
  ancestry_checksums: /rds/user/jhz22/hpc-work/work/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use pgscatalog/pgsc_calc for your analysis please cite:

* The Polygenic Score Catalog
  https://doi.org/10.1038/s41588-021-00783-5

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/pgscatalog/pgsc_calc/blob/master/CITATIONS.md
------------------------------------------------------
[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON       -
executor >  local (1)
executor >  local (2)
executor >  local (2)
executor >  local (3)
executor >  local (4)
executor >  local (4)
executor >  local (5)
executor >  local (6)
executor >  local (7)
executor >  local (7)
[c6/45eaa6] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv)                         [100%] 1 of 1 ✔
executor >  local (7)
[c6/45eaa6] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv)                         [100%] 1 of 1 ✔
executor >  local (8)
[c6/45eaa6] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv)                         [100%] 1 of 1 ✔
executor >  local (8)
[c6/45eaa6] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv)                         [100%] 1 of 1 ✔
executor >  local (9)
[c6/45eaa6] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv)                         [100%] 1 of 1 ✔
executor >  local (9)
[c6/45eaa6] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv)                         [100%] 1 of 1 ✔
executor >  local (9)
[c6/45eaa6] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv)                         [100%] 1 of 1 ✔
executor >  local (9)
[c6/45eaa6] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv)                         [100%] 1 of 1 ✔
[25/1dbd87] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                                     [100%] 1 of 1 ✔
[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                                      -
[5d/8952b5] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22)              [100%] 1 of 1 ✔
[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF                                             -
[0b/b2699f] process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22)                            [100%] 1 of 1 ✔
[12/113b82] process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (cineca)                                           [100%] 1 of 1 ✔
[e2/e5866c] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE (cineca chromosome 22 effect type additive 0) [100%] 1 of 1 ✔
[58/28ad9d] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:SCORE_AGGREGATE (cineca)                                   [100%] 1 of 1 ✔
[4c/32e9ee] process > PGSCATALOG_PGSCALC:PGSCALC:REPORT:SCORE_REPORT (cineca)                                           [100%] 1 of 1 ✔
[38/951766] process > PGSCATALOG_PGSCALC:PGSCALC:DUMPSOFTWAREVERSIONS (1)                                               [100%] 1 of 1 ✔
Pulling Singularity image oras://ghcr.io/pgscatalog/pgscatalog_utils:v0.4.3-singularity [cache /rds/user/jhz22/hpc-work/work/ghcr.io-pgscatalog-pgscatalog_utils-v0.4.3-singularity.img]
Pulling Singularity image oras://ghcr.io/pgscatalog/plink2:2.00a3.3-singularity [cache /rds/user/jhz22/hpc-work/work/ghcr.io-pgscatalog-plink2-2.00a3.3-singularity.img]
Pulling Singularity image oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/report:2.0 [cache /rds/user/jhz22/hpc-work/work/dockerhub.ebi.ac.uk-gdp-public-pgsc_calc-singularity-report-2.0.img]
Pulling Singularity image oras://ghcr.io/pgscatalog/pyyaml:6.0-singularity [cache /rds/user/jhz22/hpc-work/work/ghcr.io-pgscatalog-pyyaml-6.0-singularity.img]
-[pgscatalog/pgsc_calc] Pipeline completed successfully-
Please remember to cite polygenic score authors if you publish with them!
Check the output report for citation details

Report

This is report.html4, which is rendered from report.qmd at assets/pgscatalog/pgsc_calc/assets/report/*.

quarto render report.qmd -M "self-contained:true" -P score_path:aggregated_scores.txt.gz -P sampleset:cineca -P run_ancestry:false -P reference_panel_name:NO_PANEL

It is handy to have all options of quarto render listed here,

  Usage:   quarto render [input] [args...]
  Version: 1.4.549

  Description:

    Render files or projects to various document types.

  Options:

    -h, --help                          - Show this help.
    -t, --to                            - Specify output format(s).
    -o, --output                        - Write output to FILE (use '--output -' for stdout).
    --output-dir                        - Write output to DIR (path is input/project relative)
    -M, --metadata                      - Metadata value (KEY:VALUE).
    --site-url                          - Override site-url for website or book output
    --execute                           - Execute code (--no-execute to skip execution).
    -P, --execute-param                 - Execution parameter (KEY:VALUE).
    --execute-params                    - YAML file with execution parameters.
    --execute-dir                       - Working directory for code execution.
    --execute-daemon                    - Keep Jupyter kernel alive (defaults to 300 seconds).
    --execute-daemon-restart            - Restart keepalive Jupyter kernel before render.
    --execute-debug                     - Show debug output when executing computations.
    --use-freezer                       - Force use of frozen computations for an incremental file render.
    --cache                             - Cache execution output (--no-cache to prevent cache).
    --cache-refresh                     - Force refresh of execution cache.
    --no-clean                          - Do not clean project output-dir prior to render
    --debug                             - Leave intermediate files in place after render.
    pandoc-args...                      - Additional pandoc command line arguments.
    --log                     <file>    - Path to log file
    --log-level               <level>   - Log level (info, warning, error, critical)
    --log-format              <format>  - Log format (plain, json-stream)
    --quiet                             - Suppress console output.
    --profile                           - Active project profile(s)

  Commands:

    help  [command]  - Show this help or the help of a sub-command.

  Examples:

    Render Markdown:    quarto render document.qmd
                        quarto render document.qmd --to html
                        quarto render document.qmd --to pdf --toc
    Render Notebook:    quarto render notebook.ipynb
                        quarto render notebook.ipynb --to docx
                        quarto render notebook.ipynb --to pdf --toc
    Render Project:     quarto render
                        quarto render projdir
    Render w/ Metadata: quarto render document.qmd -M echo:false
                        quarto render document.qmd -M code-fold:true
    Render to Stdout:   quarto render document.qmd --output -

References

Lambert, S. A., et al. (2021). "The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation." Nature Genetics 53(4): 420-425, https://doi.org/10.1038/s41588-021-00783-5

  1. issues

    It appears problematic with the Internet under icelake and with GLIBC_2.18 due to deno as in ceuadmin/deno/1.40.2-icelake, but now fixed as ceuadmin/deno/1.40.2.

    An attempt was made for ceuadmin/glibc/2.18|2.55, but this could be very complex.

    export version=2.18
wget -qO- https://ftp.gnu.org/gnu/glibc/glibc-${version}.tar.gz | \
tar xvfz -
mkdir ${version}
mv glibc-${version}/ src
mv src ${version}
cd ${version}/src
module load texinfo-6.5-gcc-5.4.0-vxuomb7 binutils/2.25 texlive/2015 gcc/6
mkdir build && cd build
../configure --prefix=${CEUADMIN}/glibc/${version}
make install

    The usual prepend-path for modules somehow will purge modules, so append-path is used instead (effectively dysfunctional but providing the information) in definition of the module file. ↩

  2. vctrs

    Vector Helpers: https://vctrs.r-lib.org/ (CRAN) ↩

  3. config

    By default, NXF_HOME=/home/$USER/.nextflow but works well with NXF_SINGULARITY_CACHEDIR=/rds/user/$USER/hpc-work/work (could be used as NXF_HOME as well). ↩

  4. report

    At least vctrs 0.6.4 is required. ↩