From 19eb9d3eef10d71d80ee67776e2e983670c5e7da Mon Sep 17 00:00:00 2001 From: Benjamin Wingfield Date: Tue, 3 Oct 2023 11:25:59 +0100 Subject: [PATCH 1/2] version reference db separately --- modules/local/ancestry/bootstrap/make_database.nf | 2 +- modules/local/ancestry/extract_database.nf | 2 +- nextflow.config | 7 +++---- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/modules/local/ancestry/bootstrap/make_database.nf b/modules/local/ancestry/bootstrap/make_database.nf index 51a3da3c..e6d2aa16 100644 --- a/modules/local/ancestry/bootstrap/make_database.nf +++ b/modules/local/ancestry/bootstrap/make_database.nf @@ -26,7 +26,7 @@ process MAKE_DATABASE { """ md5sum -c $checksums - echo $workflow.manifest.version > meta.txt + echo ${params.ref_format_version} > meta.txt # can't use meta variables in stageAs # don't want to use renameTo because it's destructive for the input diff --git a/modules/local/ancestry/extract_database.nf b/modules/local/ancestry/extract_database.nf index 90b17e82..b7c2fc1b 100644 --- a/modules/local/ancestry/extract_database.nf +++ b/modules/local/ancestry/extract_database.nf @@ -31,7 +31,7 @@ process EXTRACT_DATABASE { DB_VERSION=\$(cat meta.txt) - if [ "\$DB_VERSION" != "2.0.0-alpha.3" ]; then + if [ "\$DB_VERSION" != "${params.ref_format_version}" ]; then echo "Old reference database version detected, please redownload the latest version and try again" echo "See https://pgsc-calc.readthedocs.io/en/latest/how-to/ancestry.html" exit 1 diff --git a/nextflow.config b/nextflow.config index 279c6779..5892f786 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,7 +22,7 @@ params { efo_direct = false // reference params - run_ancestry = null // path to reference database + run_ancestry = null // path to reference database TODO: replace with NO_FILE ancestry_checksums = "$projectDir/assets/ancestry/checksums.txt" // if you want to liftover --scorefiles, set the chain files hg19_chain = null // "https://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz" @@ -37,7 +37,7 @@ params { ld_grch38 = "$projectDir/assets/ancestry/high-LD-regions-hg38-GRCh38.txt" // ancestry params - ancestry_params_file = null + ref_format_version = "v0.1" ref_samplesheet = "$projectDir/assets/ancestry/reference.csv" projection_method = "oadp" ancestry_method = "RandomForest" @@ -47,7 +47,6 @@ params { n_normalization = 4 // compatibility params - compat_params_file = null liftover = false target_build = null min_lift = 0.95 @@ -80,7 +79,7 @@ params { help = false validate_params = true show_hidden_params = false - schema_ignore_params = 'only_bootstrap,only_input,only_compatible,only_match,only_projection,only_score,skip_ancestry,igenomes_ignore' + schema_ignore_params = 'only_bootstrap,only_input,only_compatible,only_match,only_projection,only_score,skip_ancestry' // Max resource options // Defaults only, expecting to be overwritten From da4ef3c6fd6400d526851bc11f4fee74c1352424 Mon Sep 17 00:00:00 2001 From: Sam Lambert Date: Tue, 3 Oct 2023 11:36:45 +0100 Subject: [PATCH 2/2] Update RELEASE-CHECKLIST.md Information about the ancestry version --- RELEASE-CHECKLIST.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/RELEASE-CHECKLIST.md b/RELEASE-CHECKLIST.md index 2abc6f5b..b12a8d27 100644 --- a/RELEASE-CHECKLIST.md +++ b/RELEASE-CHECKLIST.md @@ -31,6 +31,10 @@ - [ ] Has the changelog been updated? - [ ] Update the nextflow schema +# Reference panels +- [ ] Did anything change to the modules for creating the reference panel? Bump ref_format_version in nextflow.config + - [ ] Publish new reference panels to FTP, update any documentation. + # Tests - [ ] Make sure unit tests pass on singularity, docker, and conda (CI)