diff --git a/CHANGELOG.md b/CHANGELOG.md index 49528c1..f633651 100644 --- 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 old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/aav_structures.py b/bin/workflow_glue/aav_structures.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/check_bam_headers_in_dir.py b/bin/workflow_glue/check_bam_headers_in_dir.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/check_sample_sheet.py b/bin/workflow_glue/check_sample_sheet.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/check_xam_index.py b/bin/workflow_glue/check_xam_index.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/configure_igv.py b/bin/workflow_glue/configure_igv.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/contamination.py b/bin/workflow_glue/contamination.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/get_max_depth_locus.py b/bin/workflow_glue/get_max_depth_locus.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/mask_itrs.py b/bin/workflow_glue/mask_itrs.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/reheader_samstream.py b/bin/workflow_glue/reheader_samstream.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/report.py b/bin/workflow_glue/report.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/structure_definitions.py b/bin/workflow_glue/structure_definitions.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/tests/__init__.py b/bin/workflow_glue/tests/__init__.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/tests/data/AAV8_new.bed b/bin/workflow_glue/tests/data/AAV8_new.bed old mode 100755 new mode 100644 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 old mode 100755 new mode 100644 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 old mode 100755 new mode 100644 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 old mode 100755 new mode 100644 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 old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/tests/data/structures.yaml b/bin/workflow_glue/tests/data/structures.yaml old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/tests/test_aav_structures.py b/bin/workflow_glue/tests/test_aav_structures.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/tests/test_mask_itrs.py b/bin/workflow_glue/tests/test_mask_itrs.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/tests/test_test.py b/bin/workflow_glue/tests/test_test.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/tests/test_truncations.py b/bin/workflow_glue/tests/test_truncations.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/truncations.py b/bin/workflow_glue/truncations.py old mode 100755 new mode 100644 diff --git a/bin/workflow_glue/util.py b/bin/workflow_glue/util.py old mode 100755 new mode 100644 diff --git a/lib/common.nf b/lib/common.nf index 3a8568d..745b892 100644 --- 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 index 192f91c..dbc5875 100644 --- 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 index f317c03..da43086 100644 --- 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,