Merge branch 'template_2024-07-10' into 'dev'

template update 2024-07-10

See merge request epi2melabs/workflows/wf-transcriptomes!178

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
         always_run: true
         pass_filenames: false
         additional_dependencies:
-          - epi2melabs==0.0.55
+          - epi2melabs==0.0.56
       - id: build_models
         name: build_models
         entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py

README.md

@@ -76,6 +76,7 @@ the following command:
 ```
 nextflow pull epi2me-labs/wf-transcriptomes
 ```
+
 A demo dataset is provided for testing of the workflow.
 It can be downloaded and unpacked using the following commands:
 ```
@@ -97,6 +98,7 @@ nextflow run epi2me-labs/wf-transcriptomes \
 	--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \
 	-profile standard
 ```
+
 For further information about running a workflow on
 the command line see https://labs.epi2me.io/wfquickstart/
 

bin/workflow_glue/check_bam_headers_in_dir.py

@@ -60,6 +60,6 @@ def main(args):
 
 def argparser():
     """Argument parser for entrypoint."""
-    parser = wf_parser("check_bam_headers")
+    parser = wf_parser("check_bam_headers_in_dir")
     parser.add_argument("input_path", type=Path, help="Path to target directory")
     return parser

bin/workflow_glue/check_xam_index.py

@@ -38,6 +38,6 @@ def main(args):
 
 def argparser():
     """Argument parser for entrypoint."""
-    parser = wf_parser("check_bam_headers")
+    parser = wf_parser("check_xam_index")
     parser.add_argument("input_xam", type=Path, help="Path to target XAM")
     return parser

bin/workflow_glue/get_max_depth_locus.py

@@ -49,7 +49,7 @@ def main(args):
 
 def argparser():
     """Argument parser for entrypoint."""
-    parser = wf_parser("check_bam_headers")
+    parser = wf_parser("get_max_depth_locus")
     parser.add_argument(
         "depths_bed",
         type=Path,

docs/04_install_and_run.md

@@ -36,6 +36,7 @@ the following command:
 ```
 nextflow pull epi2me-labs/wf-transcriptomes
 ```
+
 A demo dataset is provided for testing of the workflow.
 It can be downloaded and unpacked using the following commands:
 ```
@@ -57,5 +58,6 @@ nextflow run epi2me-labs/wf-transcriptomes \
 	--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \
 	-profile standard
 ```
+
 For further information about running a workflow on
 the command line see https://labs.epi2me.io/wfquickstart/