Update ci.yml

.github/workflows/ci.yml

@@ -31,7 +31,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 

CHANGELOG.md

@@ -3,6 +3,26 @@
 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).
 
+## [[1.1.4](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.4)] - Shang Tang (patch 4) - [2024-12-05]
+
+### Enhancements & fixes
+
+- Module updates and remove Anaconda references
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| bcftools    | 1.17        | 1.20        |
+| blastn      | 2.14.1      | 2.15.0      |
+| deepvariant | 1.5.0       | 1.6.1       |
+| Python      | 3.8.3       | 3.9.1       |
+| samtools    | 1.17        | 1.21        |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
+
 ## [[1.1.3](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.3)] - Shang Tang (patch 3) - [2024-05-24]
 
 ### Enhancements & fixes

CITATION.cff

@@ -20,6 +20,10 @@ authors:
       family-names: Muffato
       affiliation: Wellcome Sanger Institute
       orcid: "https://orcid.org/0000-0002-7860-3560"
+    - given-names: Tyler
+      family-names: Chafin
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0001-8687-5905"
 identifiers:
     - type: doi
       value: 10.5281/zenodo.7890528

conf/test_full.config

@@ -10,8 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-cleanup = true
-
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'

conf/test_full_align.config

@@ -10,8 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-cleanup = true
-
 params {
     config_profile_name        = 'Full test profile with alignment'
     config_profile_description = 'Full non-aligned test dataset to check pipeline function'

modules.json

@@ -7,100 +7,99 @@
                 "nf-core": {
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
                         "installed_by": ["modules"]
                     },
                     "blast/blastn": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "deepvariant": {
+                    "deepvariant/rundeepvariant": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "samtools/collate": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/fasta": {
                         "branch": "master",
-                        "git_sha": "6f4299292ef2c5b66e6829527b2647c301b77cc9",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/fastq": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "63e817de8c617131447192ab2c4e70b4ed4071f7",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "63e817de8c617131447192ab2c4e70b4ed4071f7",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "e7ce60acc8a33fa17429e966364657a63016e870",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/samtools/merge/samtools-merge.diff"
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
+                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91",
-                        "installed_by": ["modules"]
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/view/samtools-view.diff"
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "vcftools": {
                         "branch": "master",
-                        "git_sha": "485558b40040fc3ace093d9084210125d8ba4c97",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/vcftools/vcftools.diff"
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
                     }
                 }
             }

modules/local/samplesheet_check.nf

@@ -2,10 +2,10 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda "conda-forge::python=3.8.3"
+    conda "conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'biocontainers/python:3.8.3' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'quay.io/biocontainers/python:3.9--1' }"
 
     input:
     path samplesheet