Merge pull request #86 from tkchafin/anaconda_purge

Anaconda purge
sanger-tol · Dec 5, 2024 · 6d05467 · 6d05467
2 parents 8025881 + e56e007
commit 6d05467
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -44,4 +44,4 @@ jobs:
 
       - name: Run pipeline with unaligned test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_align,docker --outdir ./results --align
+          nextflow run ${GITHUB_WORKSPACE} -profile test_align,docker --outdir ./results
diff --git a/.github/workflows/sanger_test.yml b/.github/workflows/sanger_test.yml
@@ -18,8 +18,7 @@ jobs:
           workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}",
-              "align":  true
+              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}"
             }
           profiles: test_align,sanger,singularity,cleanup
 

diff --git a/.github/workflows/sanger_test_full.yml b/.github/workflows/sanger_test_full.yml
@@ -31,8 +31,7 @@ jobs:
           workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }}
           parameters: |
             {
-              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
-              "align":  true,
+              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}"
             }
           profiles: test_full_align,sanger,singularity,cleanup
 

diff --git a/CHANGELOG.md b/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 3) - [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

diff --git a/CITATION.cff b/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

diff --git a/README.md b/README.md
@@ -45,7 +45,7 @@ Steps involved:
    nextflow run sanger-tol/variantcalling -profile test,YOURPROFILE --outdir <OUTDIR>
 
    # for unaligned reads
-   nextflow run sanger-tol/variantcalling -profile test_align,YOURPROFILE --align --outdir <OUTDIR>
+   nextflow run sanger-tol/variantcalling -profile test_align,YOURPROFILE --outdir <OUTDIR>
 
    ```
 

diff --git a/conf/test_align.config b/conf/test_align.config
@@ -21,6 +21,7 @@ params {
 
     // Input data
     input  = "${projectDir}/assets/samplesheet_test_align.csv"
+    align  = true
 
     // Fasta references
     fasta = "https://tolit.cog.sanger.ac.uk/test-data/Cantharis_rufa/assembly/GCA_947369205.1_OX376310.1_CANBKR010000003.1.fasta.gz"

diff --git a/conf/test_full_align.config b/conf/test_full_align.config
@@ -18,6 +18,7 @@ params {
 
     // Input data for full size test
     input = "${projectDir}/assets/samplesheet_test_full_align.csv"
+    align = true
 
     // Fasta references
     fasta = "/lustre/scratch124/tol/projects/darwin/data/insects/Polyommatus_icarus/assembly/release/ilPolIcar1.1/insdc/GCA_937595015.1.fasta.gz"

diff --git a/modules.json b/modules.json
@@ -7,104 +7,140 @@
                 "nf-core": {
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "blast/blastn": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
-                        "installed_by": ["modules"]
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
-                    "deepvariant": {
+                    "deepvariant/rundeepvariant": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
-                        "installed_by": ["modules"]
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/collate": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
-                        "installed_by": ["modules"]
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/fasta": {
                         "branch": "master",
-                        "git_sha": "6f4299292ef2c5b66e6829527b2647c301b77cc9",
-                        "installed_by": ["modules"]
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/fastq": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "63e817de8c617131447192ab2c4e70b4ed4071f7",
-                        "installed_by": ["modules"]
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "63e817de8c617131447192ab2c4e70b4ed4071f7",
-                        "installed_by": ["modules"]
+                        "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",
-                        "installed_by": ["modules"]
+                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"],
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/samtools/view/samtools-view.diff"
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "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"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/modules/local/samplesheet_check.nf b/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

diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml
diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf