Fixed test_full issues

Plant-Food-Research-Open · Oct 9, 2024 · 7afc159 · 7afc159
1 parent 1404b29
commit 7afc159
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Showing 8 changed files with 24 additions and 15 deletions.
diff --git a/assets/schema_xref_assemblies.json b/assets/schema_xref_assemblies.json
@@ -1,11 +1,12 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/assets/schema_xref_assemblies.json",
     "title": "plant-food-research-open/assemblyqc pipeline - params.synteny_xref_assemblies schema",
     "description": "Schema for the file provided with params.synteny_xref_assemblies",
     "type": "array",
     "items": {
         "type": "object",
+        "uniqueEntries": ["tag"],
         "properties": {
             "tag": {
                 "type": "string",

diff --git a/conf/base.config b/conf/base.config
@@ -57,23 +57,23 @@ process {
         maxRetries    = 2
     }
     withName:NCBI_FCS_GX_SCREEN_SAMPLES {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
-        memory = { check_max( 512.GB * task.attempt, 'memory' ) }
+        time   = { 20.h  * task.attempt }
+        memory = { 512.GB * task.attempt }
     }
     withName:KRAKEN2 {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withName:BWA_MEM {
-        time   = { check_max( 2.day  * task.attempt, 'time'    ) }
+        time   = { 2.day  * task.attempt }
     }
     withName:SAMBLASTER {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withName:DNADIFF {
-        time   = { check_max( 7.day  * task.attempt, 'time'    ) }
+        time   = { 7.day  * task.attempt }
     }
     withName:MERQURY_HAPMERS {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withName:CREATEREPORT {
         cache   = false

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -10,6 +10,14 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 10,
+        memory: '32.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name         = 'Full test profile'
     config_profile_description  = 'Full test dataset to check pipeline function'

diff --git a/docs/usage.md b/docs/usage.md
@@ -126,7 +126,7 @@ The data for these examples comes from: [umd.edu](https://obj.umiacs.umd.edu/mar
 
 ## Minimum System Requirements
 
-All the modules have been tested to work on a single machine with 10 CPUs + 30 GBs of memory, except NCBI FCS GX and Kraken2. Their minimum requirements are:
+All the modules have been tested to work on a single machine with 10 CPUs + 32 GBs of memory, except NCBI FCS GX and Kraken2. Their minimum requirements are:
 
 - NCBI FCS GX: 1 CPU + 512 GBs memory
 - Kraken2: 1 CPU + 200 GBs memory

diff --git a/local_assemblyqc b/local_assemblyqc
@@ -17,10 +17,9 @@ nextflow run \
     -profile docker,test_full \
     -resume \
     $stub \
-    --max_cpus 8 \
-    --max_memory '32.GB' \
     --ncbi_fcs_gx_skip false \
     --ncbi_fcs_gx_db_path ../dbs/gxdb/test \
     --busco_download_path ../dbs/busco \
     --kraken2_skip false \
-    --kraken2_db_path ../dbs/kraken2db/k2_minusb
+    --kraken2_db_path ../dbs/kraken2db/k2_minusb \
+    --outdir results
diff --git a/nextflow.config b/nextflow.config
@@ -96,7 +96,7 @@ params {
 
 }
 
-// // Max resources
+// Max resources
 process {
     resourceLimits = [
         cpus: 16,

diff --git a/pfr_assemblyqc b/pfr_assemblyqc
@@ -41,7 +41,8 @@ if [ $full_test_flag -eq 1 ]; then
         --ncbi_fcs_gx_db_path "/workspace/ComparativeDataSources/NCBI/FCS/GX/r2023-01-24" \
         --kraken2_skip false \
         --kraken2_db_path "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314" \
-        -resume
+        -resume \
+        --outdir results
 else
     nextflow \
         main.nf \

diff --git a/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf b/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf
@@ -101,7 +101,7 @@ workflow PIPELINE_INITIALISATION {
 
     ch_xref_assembly                        = params.synteny_skip || ! params.synteny_xref_assemblies
                                             ? Channel.empty()
-                                            : Channel.fromSamplesheet('synteny_xref_assemblies')
+                                            : Channel.fromList(samplesheetToList(params.synteny_xref_assemblies, "assets/schema_xref_assemblies.json"))
 
     ch_xref_assembly_validated              = ch_xref_assembly
                                             | map { row -> row[0] }