Merge pull request #11 from Sage-Bionetworks-Workflows/bwmac/orca-256…

…/failure_prototyping

New Full Test Config

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @Sage-Bionetworks-Workflows/dpe

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -44,7 +44,8 @@ body:
 
         * Executor _(eg. slurm, local, awsbatch)_
 
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
 
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
 

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'sage-bionetworks-workflows/nf-dcqc'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == sage-bionetworks-workflows/nf-dcqc ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == sage-bionetworks-workflows/nf-dcqc ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.8"
           architecture: "x64"
 
       - name: Install dependencies

conf/test_full.config

@@ -16,6 +16,5 @@ params {
 
     // Input data for full size test
     input = "${projectDir}/testdata/input_full.csv"
-    required_tests = "LibTiffInfoTest,BioFormatsInfoTest,OmeXmlSchemaTest"
-    skipped_tests = "FileExtensionTest,Md5ChecksumTest"
+    required_tests = "LibTiffInfoTest,BioFormatsInfoTest,OmeXmlSchemaTest,JsonLoadTest,JsonLdLoadTest,PairedFastqParityTest,TiffDateTimeTest,TiffTag306DateTimeTest"
 }

lib/NfcoreSchema.groovy

@@ -2,6 +2,7 @@
 // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
 //
 
+import nextflow.Nextflow
 import org.everit.json.schema.Schema
 import org.everit.json.schema.loader.SchemaLoader
 import org.everit.json.schema.ValidationException
@@ -83,6 +84,7 @@ class NfcoreSchema {
             'stub-run',
             'test',
             'w',
+            'with-apptainer',
             'with-charliecloud',
             'with-conda',
             'with-dag',
@@ -177,7 +179,7 @@ class NfcoreSchema {
         }
 
         if (has_error) {
-            System.exit(1)
+            Nextflow.error('Exiting!')
         }
     }
 

testdata/input_full.csv

@@ -1,12 +1,15 @@
-url,file_type,md5_checksum
-syn://syn41864974,TXT,38b86a456d1f441008986c6f798d5ef9
-syn://syn41864977,TXT,a542e9b744bedcfd874129ab0f98c4ff
-syn://syn43716055,TIFF,38b86a456d1f441008986c6f798d5ef9
-syn://syn43716711,TIFF,a542e9b744bedcfd874129ab0f98c4ff
-syn://syn26644414,TIFF,0a3d8f1d2d69f15aeccedea0d54efa6c
-syn://syn26644414,OME-TIFF,0a3d8f1d2d69f15aeccedea0d54efa6c
-syn://syn26644421,OME-TIFF,313257a6822ff5b52e7e35a626b6c33f
-syn://syn50944309,TIFF,7408a1bb12e39228ad096a95c2a839ac
-syn://syn50944267,OME-TIFF,a2550a887091d51351d547c8beae8f0c
-syn://syn50944248,OME-TIFF,64bbfe1d1c9c171cad17b11e666b31b4
-syn://syn50944306,TIFF,dcca48d86b2e1d97677e8de533b4d74b
+url,file_type,md5_checksum,test
+syn://syn58937898,TXT,1d6155b60405bab055527913efd734a7,good_txt
+syn://syn59069842,TXT,not_the_right_md5,bad_md5_extension_txt
+syn://syn59095050,TIFF,c7b08f6decb5e7572efbe6074926a843,good_tiff
+syn://syn59094930,TIFF,d817d0c76ce47b4ddc75368cfc7996ff,bad_date_tag_tiff
+syn://syn59094943,TIFF,28a9ee7d0e994d494068ce8d6cda0268,bad_date_time_tiff
+syn://syn59094934,OME-TIFF,64bbfe1d1c9c171cad17b11e666b31b4,good_ome_tiff
+syn://syn59094932,OME-TIFF,a2550a887091d51351d547c8beae8f0c,bad_xml_ome_tiff
+syn://syn59094945,HDF5,93d78663da24b6a708f6c81207e4410a,good_hd5
+syn://syn59094941,TSV,2ff237d635d9eb35e09aacda22f0417f,good_tsv
+syn://syn59095211,CSV,72c61a50b286ff6fd3d038211426b910,good_csv
+syn://syn59095268,JSON,9e7f473ccbc055ef7ac800ce861a88af,good_json
+syn://syn59094940,JSON-LD,56bb5f34da6d6df2ade3ac37e25586b7,good_json_ld
+syn://syn59094935,BAM,14758f1afd44c09b7992073ccf00b43d,good_bam
+syn://syn59094937,FASTQ,14758f1afd44c09b7992073ccf00b43d,good_fastq