v2.0.0-alpha.4 (#217)

* add mount docs * mount tmpdir in test * move env * how did tabs get in here!! * fix reference link (#214) * Update FTP links * Additional docs re: panel * -profile test + --run_ancestry = bad * fix trait parameter (#196) * fix reference link * update ref paths --------- Co-authored-by: smlmbrt <[email protected]> * bump workflow version * Bump pgscatalog utils (#219) * bump pgscatalog_utils * bump pgscatalog-utils --------- Co-authored-by: smlmbrt <[email protected]>
PGScatalog · Dec 5, 2023 · 83326a1 · 83326a1
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commit 83326a1
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diff --git a/.github/workflows/ancestry.yml b/.github/workflows/ancestry.yml
@@ -17,7 +17,7 @@ on:
 env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/singularity
   SINGULARITY_VERSION: 3.8.3
-  
+
 jobs:
   docker:
     if: ${{ inputs.docker }}
@@ -135,6 +135,8 @@ jobs:
 
       - name: Run ancestry test
         run: TMPDIR=~ PROFILE=singularity pytest --kwdof --symlink --git-aware --wt 2 --tag "ancestry" --ignore tests/bin
+        env:
+          TMPDIR: ${{ runner.temp }}
 
       - name: Upload logs on failure
         if: failure()

diff --git a/conf/modules.config b/conf/modules.config
@@ -38,8 +38,8 @@ process {
         ext.conda = "$projectDir/environments/pgscatalog_utils/environment.yml"
         ext.docker = 'ghcr.io/pgscatalog/pgscatalog_utils'
         ext.singularity = 'oras://ghcr.io/pgscatalog/pgscatalog_utils'
-        ext.docker_version = ':v0.4.2'
-        ext.singularity_version = ':v0.4.2-singularity'
+        ext.docker_version = ':v0.4.3'
+        ext.singularity_version = ':v0.4.3-singularity'
     }
 
     withLabel: plink2 {

diff --git a/docs/getting-started.rst b/docs/getting-started.rst
@@ -129,11 +129,17 @@ for more information). If your custom PGS was in GRCh37 an example would look li
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 To enable genetic ancestry similarity calculations and PGS normalisation,
-download our pre-built reference database:
+download one of our pre-built reference databases:
 
 .. code-block:: console
 
-    $ wget https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/pgsc_calc.tar.zst
+    $ wget https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/pgsc_HGDP+1kGP_v1.tar.zst
+
+This database contains a merged 1000 Genomes and Human Genome Diversity Project reference panel, and is the recommended default panel. 
+
+You may prefer to use 1000 Genomes only:
+
+    $ wget https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/pgsc_1000G_v1.tar.zst
 
 See :ref:`ancestry` for more details.
 
@@ -149,7 +155,7 @@ they match the scoring file genome build.
         -profile <docker/singularity/conda> \
         --input samplesheet.csv --target_build GRCh37 \
         --pgs_id PGS001229 \
-        --run_ancestry pgsc_calc.tar.zst 
+        --run_ancestry pgsc_HGDP+1kGP_v1.tar.zst
 
 Congratulations, you've now (`hopefully`) calculated some scores!
 |:partying_face:|

diff --git a/docs/how-to/ancestry.rst b/docs/how-to/ancestry.rst
@@ -46,6 +46,6 @@ To enable genetic similarity analysis and score normalisation, just include the
 .. code-block:: console
 
     $ nextflow run pgscatalog/pgsc_calc -profile test,docker \
-        --run_ancestry path/to/reference/pgsc_calc.tar.zst
+        --run_ancestry path/to/reference/pgsc_HGDP+1kGP_v1.tar.zst
 
 The ``--run_ancestry`` parameter requires the path to the reference database.
diff --git a/docs/how-to/index.rst b/docs/how-to/index.rst
@@ -42,6 +42,7 @@ Working in different environments
    bigjob
    arm
    offline
+   mount
 
 Working with complex datasets
 -----------------------------

diff --git a/docs/how-to/mount.rst b/docs/how-to/mount.rst
@@ -0,0 +1,33 @@
+
+.. _mount:
+
+How do I mount non-standard directories in singularity?
+=======================================================
+
+In some situations you may get ``FileNotFound`` errors with the singularity profile even if the file definitely exists.
+
+If your sensitive genomic data are stored in a non-standard Linux directory, then containers may need extra configuration to mount the directory correctly
+
+This problem probably affects you if:
+
+- you can run the test profile OK on singularity
+- you get ``FileNotFound`` errors when working with your own data
+- you are certain the file path reported in the error does exist and is accessible to you
+
+Create a new nextflow configuration file `as described here`_:
+
+.. code-block:: text
+
+    singularity {
+      enabled = true
+      autoMounts = true
+      runOptions = '-B /path/to/genomes'
+    }
+
+.. _`as described here`:  https://github.com/PGScatalog/pgsc_calc/issues/158#issuecomment-1713783129
+
+You will need to edit ``runOptions`` to match the path to your local directory containing sensitive data.
+
+And run the calculator with the extra parameter ``-c mount.config``.
+
+Another possible solution is to test your own data with the ``conda`` profile, which doesn't require extra configuration to work with non-standard directories. 
diff --git a/environments/pgscatalog_utils/environment.yml b/environments/pgscatalog_utils/environment.yml
@@ -3,4 +3,4 @@ dependencies:
 - python=3.10
 - pip
 - pip:
-    - pgscatalog_utils==0.4.2
+    - pgscatalog_utils==0.4.3
diff --git a/nextflow.config b/nextflow.config
@@ -208,7 +208,7 @@ manifest {
     description     = 'The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation'
     mainScript      = 'main.nf'
     nextflowVersion = '>=22.10.0'
-    version         = '2.0.0-alpha.2'
+    version         = '2.0.0-alpha.4'
 }
 
 // Load modules.config for DSL2 module specific options

diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
@@ -30,6 +30,7 @@ def mount_home = "-v $HOME:$HOME -v /private/var/folders/"
 if ("$PROFILE" == "singularity") {
     singularity.enabled = true
     singularity.autoMounts = true
+    singularity.runOptions = "--bind $TMPDIR:$TMPDIR"
 } else if ("$PROFILE" == "conda") {
     conda.enabled = true
 } else if ("$PROFILE" == "mamba") {