Merge pull request #85 from PixelgenTechnologies/various-improvements

Small fixes before 1.1.0 release
nf-core · Mar 22, 2024 · d1a7731 · d1a7731
2 parents 548472f + f49632d
commit d1a7731
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Showing 4 changed files with 23 additions and 9 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,12 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [UNRELEASED] - YYYY-MM-DD
+## [[1.1.0](https://github.com/nf-core/pixelator/releases/tag/1.1.0)] - 2024-03-22
 
-### Changed
+### Enhancements & fixes
 
-- `collapse` and `graph` steps output parquet files
-- Update pixelator to 0.16.2
+- `collapse` and `graph` step now output parquet files
+- Update `process_medium` label to use 32 GiB of memory by default
+- Fix a warning from an unused parameter from the nf-core template
 
 ### Software dependencies
 

diff --git a/conf/base.config b/conf/base.config
@@ -36,7 +36,7 @@ process {
     }
     withLabel:process_medium {
         cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
+        memory = { check_max( 32.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 8.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_high {

diff --git a/nextflow.config b/nextflow.config
@@ -118,6 +118,13 @@ try {
 // } catch (Exception e) {
 //   System.err.println("WARNING: Could not load nf-core/config/pixelator profiles: ${params.custom_config_base}/pipeline/pixelator.config")
 // }
+
+
+def container_env_options = [
+    "MPLCONFIGDIR": '/tmp/.config/matplotlib',
+    "NUMBA_CACHE_DIR": "/tmp/.numba_cache",
+]
+
 profiles {
     debug {
         dumpHashes             = true
@@ -153,8 +160,8 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
-        // Disabled this to deal with libpysal temporary directory issue
-        // docker.runOptions      = '-u $(id -u):$(id -g)'
+        docker.runOptions      = '-u $(id -u):$(id -g)'
+        env                    = container_env_options
     }
     arm {
         docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
@@ -168,6 +175,7 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
+        env                    = container_env_options
     }
     podman {
         podman.enabled         = true
@@ -178,6 +186,7 @@ profiles {
         charliecloud.enabled   = false
         apptainer.enabled      = false
         podman.runOptions      = '--userns=keep-id'
+        env                    = container_env_options
     }
     shifter {
         shifter.enabled        = true
@@ -187,6 +196,7 @@ profiles {
         podman.enabled         = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
+        env                    = container_env_options
     }
     charliecloud {
         charliecloud.enabled   = true
@@ -196,6 +206,7 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
         apptainer.enabled      = false
+        env                    = container_env_options
     }
     apptainer {
         apptainer.enabled      = true
@@ -206,6 +217,7 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        env                    = container_env_options
     }
     gitpod {
         executor.name          = 'local'
@@ -271,7 +283,7 @@ manifest {
     description     = """Pipeline for analysis of Molecular Pixelation assays"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.0dev'
+    version         = '1.1.0'
     doi             = '10.1101/2023.06.05.543770'
 }
 

diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf
@@ -186,7 +186,8 @@ workflow PIPELINE_COMPLETION {
 // Check and validate pipeline parameters
 //
 def validateInputParameters() {
-    genomeExistsError()
+    // Keep this commented here to closely follow the template
+    // genomeExistsError()
 }
 
 //