Bump wipertools to 1.1.4 (#7328)

* Refactor fastq and report variable names for consistency across wipertools modules * Refactor variable names for consistency in fastq and report processing modules * Update test assertions to reflect changes in output variable names in fastqwiper module * Update test assertions to match changes in report output structure in fastqwiper tests * pypgx/runngspipeline (#6823) * pypgx/runngspipeline * update PR comments --------- Co-authored-by: Jorisvansteenbrugge <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * Update actions/upload-artifact digest to 65c4c4a (#7293) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * fixed typo that produces "unknown recognition error type: groovyjarja… (#7295) fixed typo that produces "unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException" in pipelines * Update Galah & add nf-tests (#7291) * Update Galah & add nf-tests * Fix linting * Update main.nf * Update inputs in meta.yml * Fix missing snapshot output from broken test * Added nftests to gseagsea (#7266) * Added nftests to gseagsea * Update input files * fix nftests * Address PR comments * Add seed setting parameter for stabilizing results * Fix linting * Add default random seed * Update datasets paths --------- Co-authored-by: Simon Pearce <[email protected]> * Bumped lima to 2.12.0 (#7294) * Update container version to 1.1.4 and modify test names for clarity * Remove obsolete test cases from fastqscatter and clean up pytest module configuration * Update wipertools version to 1.1.4 in environment.yml files for fastqgather, fastqscatter, fastqwiper, and reportgather * Update timestamps in fastqscatter test snapshots for consistency --------- Co-authored-by: Joris van Steenbrugge <[email protected]> Co-authored-by: Jorisvansteenbrugge <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Evangelos Karatzas <[email protected]> Co-authored-by: Jim Downie <[email protected]> Co-authored-by: Nicolás Schcolnicov <[email protected]> Co-authored-by: Usman Rashid <[email protected]>
nf-core · Jan 18, 2025 · e7f7c0f · e7f7c0f
1 parent 60645c2
commit e7f7c0f
Show file tree

Hide file tree

Showing 13 changed files with 54 additions and 54 deletions.
diff --git a/modules/nf-core/wipertools/fastqgather/environment.yml b/modules/nf-core/wipertools/fastqgather/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::wipertools=1.1.3"
+  - "bioconda::wipertools=1.1.4"
diff --git a/modules/nf-core/wipertools/fastqgather/main.nf b/modules/nf-core/wipertools/fastqgather/main.nf
@@ -4,8 +4,8 @@ process WIPERTOOLS_FASTQGATHER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/wipertools:1.1.3--pyhdfd78af_0':
-        'biocontainers/wipertools:1.1.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/wipertools:1.1.4--pyhdfd78af_0':
+        'biocontainers/wipertools:1.1.4--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)

diff --git a/modules/nf-core/wipertools/fastqgather/tests/main.nf.test.snap b/modules/nf-core/wipertools/fastqgather/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,291a2e6d58146bfcf57b4d9ef850cbd9"
+                    "versions.yml:md5,b4df541ef0f00762a863e9b88d620301"
                 ],
                 "gathered_fastq": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,291a2e6d58146bfcf57b4d9ef850cbd9"
+                    "versions.yml:md5,b4df541ef0f00762a863e9b88d620301"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-13T18:49:15.441781"
+        "timestamp": "2025-01-18T07:48:36.495342"
     },
     "merge two gzipped fastq - fastq.gz": {
         "content": [
@@ -40,29 +40,29 @@
                         {
                             "id": "fastq_chunks"
                         },
-                        "fastq_chunks_gather.fastq.gz:md5,eedbbe1317d4d464da30d56cff7d677e"
+                        "fastq_chunks_gather.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,291a2e6d58146bfcf57b4d9ef850cbd9"
+                    "versions.yml:md5,b4df541ef0f00762a863e9b88d620301"
                 ],
                 "gathered_fastq": [
                     [
                         {
                             "id": "fastq_chunks"
                         },
-                        "fastq_chunks_gather.fastq.gz:md5,eedbbe1317d4d464da30d56cff7d677e"
+                        "fastq_chunks_gather.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,291a2e6d58146bfcf57b4d9ef850cbd9"
+                    "versions.yml:md5,b4df541ef0f00762a863e9b88d620301"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-13T18:49:02.891972"
+        "timestamp": "2025-01-18T07:48:25.182554"
     }
 }
diff --git a/modules/nf-core/wipertools/fastqscatter/environment.yml b/modules/nf-core/wipertools/fastqscatter/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::wipertools=1.1.3"
+  - "bioconda::wipertools=1.1.4"
diff --git a/modules/nf-core/wipertools/fastqscatter/main.nf b/modules/nf-core/wipertools/fastqscatter/main.nf
@@ -4,8 +4,8 @@ process WIPERTOOLS_FASTQSCATTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/wipertools:1.1.3--pyhdfd78af_0':
-        'biocontainers/wipertools:1.1.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/wipertools:1.1.4--pyhdfd78af_0':
+        'biocontainers/wipertools:1.1.4--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)

diff --git a/modules/nf-core/wipertools/fastqscatter/tests/main.nf.test b/modules/nf-core/wipertools/fastqscatter/tests/main.nf.test
@@ -8,7 +8,7 @@ nextflow_process {
     tag "wipertools"
     tag "wipertools/fastqscatter"
 
-    test("3 reads, one truncated - fastq") {
+    test("test1 - fastq") {
         config "./nextflow.config"
 
         when {
@@ -34,7 +34,7 @@ nextflow_process {
         }
     }
 
-    test("3 reads, one truncated - fastq - stub") {
+    test("test1 - fastq - stub") {
         options "-stub"
         config "./nextflow.config"
 

diff --git a/modules/nf-core/wipertools/fastqscatter/tests/main.nf.test.snap b/modules/nf-core/wipertools/fastqscatter/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "3 reads, one truncated - fastq": {
+    "test1 - fastq - stub": {
         "content": [
             {
                 "0": [
@@ -8,37 +8,37 @@
                             "id": "test"
                         },
                         [
-                            "test_000.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
-                            "test_001.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
+                            "test_1-of-2_suffix.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2-of-2_suffix.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                         ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c8e701c1048cc9ab79752d1bf631ad4b"
+                    "versions.yml:md5,48702abf648becf3110470614c556f1b"
                 ],
                 "fastq_chunks": [
                     [
                         {
                             "id": "test"
                         },
                         [
-                            "test_000.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
-                            "test_001.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
+                            "test_1-of-2_suffix.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2-of-2_suffix.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                         ]
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c8e701c1048cc9ab79752d1bf631ad4b"
+                    "versions.yml:md5,48702abf648becf3110470614c556f1b"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-13T18:41:58.317846"
+        "timestamp": "2025-01-18T17:33:01.715401"
     },
-    "3 reads, one truncated - fastq - stub": {
+    "test1 - fastq": {
         "content": [
             {
                 "0": [
@@ -47,34 +47,34 @@
                             "id": "test"
                         },
                         [
-                            "test_1-of-2_suffix.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_2-of-2_suffix.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                            "test_000.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
+                            "test_001.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
                         ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c8e701c1048cc9ab79752d1bf631ad4b"
+                    "versions.yml:md5,48702abf648becf3110470614c556f1b"
                 ],
                 "fastq_chunks": [
                     [
                         {
                             "id": "test"
                         },
                         [
-                            "test_1-of-2_suffix.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_2-of-2_suffix.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                            "test_000.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
+                            "test_001.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
                         ]
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c8e701c1048cc9ab79752d1bf631ad4b"
+                    "versions.yml:md5,48702abf648becf3110470614c556f1b"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-13T18:42:09.268891"
+        "timestamp": "2025-01-18T17:32:49.482796"
     }
 }
diff --git a/modules/nf-core/wipertools/fastqwiper/environment.yml b/modules/nf-core/wipertools/fastqwiper/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::wipertools=1.1.3"
+  - "bioconda::wipertools=1.1.4"
diff --git a/modules/nf-core/wipertools/fastqwiper/main.nf b/modules/nf-core/wipertools/fastqwiper/main.nf
@@ -4,8 +4,8 @@ process WIPERTOOLS_FASTQWIPER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/wipertools:1.1.3--pyhdfd78af_0':
-        'biocontainers/wipertools:1.1.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/wipertools:1.1.4--pyhdfd78af_0':
+        'biocontainers/wipertools:1.1.4--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)

diff --git a/modules/nf-core/wipertools/fastqwiper/tests/main.nf.test.snap b/modules/nf-core/wipertools/fastqwiper/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,0a814cc53368590314bd01d1b433b6fd"
+                    "versions.yml:md5,f736a990049d46418335d7e5b66e8569"
                 ],
                 "report": [
                     [
@@ -30,7 +30,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0a814cc53368590314bd01d1b433b6fd"
+                    "versions.yml:md5,f736a990049d46418335d7e5b66e8569"
                 ],
                 "wiped_fastq": [
                     [
@@ -46,7 +46,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-13T18:52:39.908974"
+        "timestamp": "2025-01-18T07:49:20.507561"
     },
     "Quality mismatch - fastq": {
         "content": [
@@ -68,7 +68,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,0a814cc53368590314bd01d1b433b6fd"
+                    "versions.yml:md5,f736a990049d46418335d7e5b66e8569"
                 ],
                 "report": [
                     [
@@ -79,7 +79,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0a814cc53368590314bd01d1b433b6fd"
+                    "versions.yml:md5,f736a990049d46418335d7e5b66e8569"
                 ],
                 "wiped_fastq": [
                     [
@@ -95,6 +95,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-13T18:52:27.962146"
+        "timestamp": "2025-01-18T07:49:09.920936"
     }
 }
diff --git a/modules/nf-core/wipertools/reportgather/environment.yml b/modules/nf-core/wipertools/reportgather/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::wipertools=1.1.3"
+  - "bioconda::wipertools=1.1.4"
diff --git a/modules/nf-core/wipertools/reportgather/main.nf b/modules/nf-core/wipertools/reportgather/main.nf
@@ -4,8 +4,8 @@ process WIPERTOOLS_REPORTGATHER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/wipertools:1.1.3--pyhdfd78af_0':
-        'biocontainers/wipertools:1.1.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/wipertools:1.1.4--pyhdfd78af_0':
+        'biocontainers/wipertools:1.1.4--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(report)

diff --git a/modules/nf-core/wipertools/reportgather/tests/main.nf.test.snap b/modules/nf-core/wipertools/reportgather/tests/main.nf.test.snap
@@ -17,8 +17,8 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8f315851a1d3b7a1bb186ab41e7675df",
-                    "versions.yml:md5,8f315851a1d3b7a1bb186ab41e7675df"
+                    "versions.yml:md5,6089d61842607d8760740fab8d1bfe02",
+                    "versions.yml:md5,6089d61842607d8760740fab8d1bfe02"
                 ],
                 "gathered_report": [
                     [
@@ -35,16 +35,16 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8f315851a1d3b7a1bb186ab41e7675df",
-                    "versions.yml:md5,8f315851a1d3b7a1bb186ab41e7675df"
+                    "versions.yml:md5,6089d61842607d8760740fab8d1bfe02",
+                    "versions.yml:md5,6089d61842607d8760740fab8d1bfe02"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-13T19:37:46.90862"
+        "timestamp": "2025-01-18T09:01:17.744913"
     },
     "merge two reports - .report": {
         "content": [
@@ -64,8 +64,8 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8f315851a1d3b7a1bb186ab41e7675df",
-                    "versions.yml:md5,8f315851a1d3b7a1bb186ab41e7675df"
+                    "versions.yml:md5,6089d61842607d8760740fab8d1bfe02",
+                    "versions.yml:md5,6089d61842607d8760740fab8d1bfe02"
                 ],
                 "gathered_report": [
                     [
@@ -82,15 +82,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8f315851a1d3b7a1bb186ab41e7675df",
-                    "versions.yml:md5,8f315851a1d3b7a1bb186ab41e7675df"
+                    "versions.yml:md5,6089d61842607d8760740fab8d1bfe02",
+                    "versions.yml:md5,6089d61842607d8760740fab8d1bfe02"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-13T19:37:34.849059"
+        "timestamp": "2025-01-18T07:49:32.055316"
     }
 }