Merge branch 'CW-5371-empty-fastq' into 'dev'

Update fastcat and add empty test cases [CW-5371] Closes CW-5371 See merge request epi2melabs/workflows/wf-template!244
epi2me-labs · Dec 6, 2024 · 49f9cd9 · 49f9cd9
2 parents 259d7c0 + ee6e1ae
commit 49f9cd9
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Showing 8 changed files with 40 additions and 4 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -58,6 +58,7 @@ docker-run:
                 "case21",
                 "case22",
                 "case22-allow_multiple_basecall_models",
+                "case23-empty_fastq", "case24-empty_fastq_gz",
                 "mutateParams",
                 "xam-single-file", "xam-single-file-s3",
                 "xam-case01", "xam-case01-s3",
@@ -89,6 +90,7 @@ docker-run:
                 "xam-case17", "xam-case17-s3",
                 "xam-case18", "xam-case18-s3",
                 "xam-case19", "xam-case19-s3",
+                "xam-case20",
               ]
     rules:
         # NOTE As we're overriding the rules block for the included docker-run
@@ -298,7 +300,7 @@ docker-run:
               AFTER_NEXTFLOW_CMD: >
                 $TEST_CMD test_data/fastq_ingress/case16 fastq $$PWD/$$CI_PROJECT_NAME
                 && grep "Dwight" $$PWD/$$CI_PROJECT_NAME/wf-template-report.html
-        
+
         - if: $MATRIX_NAME == "case16-nonexisting-client-fields"
           variables:
               NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case16 --sample_sheet test_data/fastq_ingress/case16/sample_sheet.csv --client_fields test_data/fastq_ingress/case16/client_fields_not_there.json"
@@ -353,6 +355,16 @@ docker-run:
             AFTER_NEXTFLOW_CMD: >
               set -ex; $TEST_CMD test_data/fastq_ingress/case22 fastq $$PWD/$$CI_PROJECT_NAME
               && ! grep "Found multiple basecall models for sample 'case22':" .nextflow.log
+        - if: $MATRIX_NAME == "case23-empty_fastq"
+          variables:
+            NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case23/"
+            AFTER_NEXTFLOW_CMD: >
+              $TEST_CMD test_data/fastq_ingress/case23 fastq $$PWD/$$CI_PROJECT_NAME
+        - if: $MATRIX_NAME == "case24-empty_fastq_gz"
+          variables:
+            NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case24/"
+            AFTER_NEXTFLOW_CMD: >
+              $TEST_CMD test_data/fastq_ingress/case24 fastq $$PWD/$$CI_PROJECT_NAME
 
         - if: $MATRIX_NAME == "mutateParams"
           variables:
@@ -611,3 +623,9 @@ docker-run:
           variables:
               NF_WORKFLOW_OPTS: "--bam ${S3_TEST_DATA}/xam_ingress/case19"
               AFTER_NEXTFLOW_CMD: $TEST_CMD ${S3_TEST_DATA}/xam_ingress/case19/ bam $$PWD/$$CI_PROJECT_NAME; grep -v "sortBam" $$PWD/$$CI_PROJECT_NAME/execution/trace.txt;
+
+        - if: $MATRIX_NAME == "xam-case20"
+          variables:
+              NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case20"
+              AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case20/ bam $$PWD/$$CI_PROJECT_NAME;
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+
+## [v5.3.3]
+### Fixed
+- Fixed regression in handling empty FASTQ files by updating wf-common to shabadd33adae761be6f2d59c6ecfb44b19cf472cfc to use fastcat v0.20.0
+
 ## [v5.3.2]
 ### Changed
 - Corrected permissions for non-executable workflow_glue files in bin/.

diff --git a/nextflow.config b/nextflow.config
@@ -43,7 +43,7 @@ params {
         example_cmd = [
             "--fastq 'wf-template-demo/test_data/reads.fastq.gz'",
         ]
-        common_sha = "shaf15f9d80aba72c20e3e71f84869619873a56b8af"
+        common_sha = "shabadd33adae761be6f2d59c6ecfb44b19cf472cfc"
         agent = null
         epi2me_instance = null
         epi2me_user = null
@@ -57,7 +57,7 @@ manifest {
     description     = 'Template workflow'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v5.3.2'
+    version         = 'v5.3.3'
 }
 
 

diff --git a/test_data/fastq_ingress/README b/test_data/fastq_ingress/README
@@ -245,4 +245,12 @@
 # Two basecall models in the same sample
 ├── case22
 │   ├── reads0.fastq
-│   └── reads1.fastq
+│   └── reads1.fastq
+
+# take empty fastq
+├── case23
+│   ├── empty.fq
+
+# take empty fastq
+├── case24
+│   ├── empty.fq.gz  # (gzip)
diff --git a/test_data/fastq_ingress/case23/empty.fq b/test_data/fastq_ingress/case23/empty.fq
diff --git a/test_data/fastq_ingress/case24/empty.fq.gz b/test_data/fastq_ingress/case24/empty.fq.gz
diff --git a/test_data/xam_ingress/README b/test_data/xam_ingress/README
@@ -143,3 +143,8 @@
 │   ├── reads0.bam
 │   ├── reads1.bam
 │   └── reads2.bam
+
+
+# Case20: BAM from SAM with just a header
+├── case20
+│   ├── just_header.bam
diff --git a/test_data/xam_ingress/case20/just_header.bam b/test_data/xam_ingress/case20/just_header.bam