Merge branch 'v1.2.0' into 'dev'

Bump v1.2.0 / xmas template update See merge request epi2melabs/workflows/wf-aav-qc!175
epi2me-labs · Dec 13, 2024 · 473a4f5 · 473a4f5
2 parents 26ab931 + d08916f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,11 +4,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html)
 
-## [Unrelease]
+## [v1.2.0]
 ### Updated
 - Diagrams in the README describing AAV genome types. 
-
-## [Unreleased]
 ### Fixed
 - Rounding issues in genome structures table.
 - ITR locations can be specified in a BED file with `--transgene_bed`.

diff --git a/bin/workflow_glue/__init__.py b/bin/workflow_glue/__init__.py
diff --git a/bin/workflow_glue/aav_structures.py b/bin/workflow_glue/aav_structures.py
diff --git a/bin/workflow_glue/check_bam_headers_in_dir.py b/bin/workflow_glue/check_bam_headers_in_dir.py
diff --git a/bin/workflow_glue/check_sample_sheet.py b/bin/workflow_glue/check_sample_sheet.py
diff --git a/bin/workflow_glue/check_xam_index.py b/bin/workflow_glue/check_xam_index.py
diff --git a/bin/workflow_glue/configure_igv.py b/bin/workflow_glue/configure_igv.py
diff --git a/bin/workflow_glue/contamination.py b/bin/workflow_glue/contamination.py
diff --git a/bin/workflow_glue/get_max_depth_locus.py b/bin/workflow_glue/get_max_depth_locus.py
diff --git a/bin/workflow_glue/mask_itrs.py b/bin/workflow_glue/mask_itrs.py
diff --git a/bin/workflow_glue/reheader_samstream.py b/bin/workflow_glue/reheader_samstream.py
diff --git a/bin/workflow_glue/report.py b/bin/workflow_glue/report.py
diff --git a/bin/workflow_glue/structure_definitions.py b/bin/workflow_glue/structure_definitions.py
diff --git a/bin/workflow_glue/tests/__init__.py b/bin/workflow_glue/tests/__init__.py
diff --git a/bin/workflow_glue/tests/data/AAV8_new.bed b/bin/workflow_glue/tests/data/AAV8_new.bed
diff --git a/bin/workflow_glue/tests/data/AAV8_rep2_transgene_plasmid_ITR-ITR_orientations.fasta b/bin/workflow_glue/tests/data/AAV8_rep2_transgene_plasmid_ITR-ITR_orientations.fasta
diff --git a/bin/workflow_glue/tests/data/AAV8_rep2_transgene_plasmid_ITR-ITR_orientations.fasta.fai b/bin/workflow_glue/tests/data/AAV8_rep2_transgene_plasmid_ITR-ITR_orientations.fasta.fai
diff --git a/bin/workflow_glue/tests/data/AAV8_transgene_fixed_ITR1_no_3bp_del.fasta b/bin/workflow_glue/tests/data/AAV8_transgene_fixed_ITR1_no_3bp_del.fasta
diff --git a/bin/workflow_glue/tests/data/AAV8_transgene_fixed_ITR1_no_3bp_del.fasta.fai b/bin/workflow_glue/tests/data/AAV8_transgene_fixed_ITR1_no_3bp_del.fasta.fai
diff --git a/bin/workflow_glue/tests/data/structures.yaml b/bin/workflow_glue/tests/data/structures.yaml
diff --git a/bin/workflow_glue/tests/test_aav_structures.py b/bin/workflow_glue/tests/test_aav_structures.py
diff --git a/bin/workflow_glue/tests/test_mask_itrs.py b/bin/workflow_glue/tests/test_mask_itrs.py
diff --git a/bin/workflow_glue/tests/test_test.py b/bin/workflow_glue/tests/test_test.py
diff --git a/bin/workflow_glue/tests/test_truncations.py b/bin/workflow_glue/tests/test_truncations.py
diff --git a/bin/workflow_glue/truncations.py b/bin/workflow_glue/truncations.py
diff --git a/bin/workflow_glue/util.py b/bin/workflow_glue/util.py
diff --git a/lib/common.nf b/lib/common.nf
@@ -2,6 +2,8 @@ import groovy.json.JsonBuilder
 
 process getParams {
     label "wf_common"
+    publishDir "${params.out_dir}", mode: 'copy', pattern: "params.json"
+    cache false
     cpus 1
     memory "2 GB"
     output:

diff --git a/main.nf b/main.nf
@@ -60,6 +60,7 @@ process get_ref_names {
 
 process getParams {
     label "wf_aav"
+    cache false
     cpus 1
     memory "2 GB"
     output:

diff --git a/nextflow.config b/nextflow.config
@@ -60,7 +60,7 @@ params {
             "--ref_transgene_plasmid 'wf-aav-qc-demo/transgene.fasta'"
         ]
         container_sha = "sha9b4b07df083ba71262da90933ce692b9ae0154ee"
-        common_sha = "shad28e55140f75a68f59bbecc74e880aeab16ab158"
+        common_sha = "shabadd33adae761be6f2d59c6ecfb44b19cf472cfc"
         container_sha_medaka = "sha3486abaab0d3b90351617eb8622acf2028edb154"
         agent = null
     }
@@ -73,7 +73,7 @@ manifest {
     description     = 'AAV plasmid quality control workflow'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.1.2'
+    version         = 'v1.2.0'
 }
 
 // used by default for "standard" (docker) and singularity profiles,