all modules updated, anaconda references removed

sanger-tol · Dec 3, 2024 · bccdc19 · bccdc19
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diff --git a/CITATION.cff b/CITATION.cff
@@ -16,6 +16,10 @@ authors:
       family-names: Surana
       orcid: "https://orcid.org/0000-0002-7167-0875"
       affiliation: Wellcome Sanger Institute
+    - given-names: Tyler
+      family-names: Chafin
+      orcid: "https://orcid.org/0000-0001-8687-5905"
+      affiliation: Wellcome Sanger Institute
 identifiers:
     - type: doi
       value: 10.5281/zenodo.7183379

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -20,9 +20,9 @@
 
 ## Software packaging/containerisation tools
 
-- [Anaconda](https://anaconda.com)
+- [Conda](https://conda.org/)
 
-  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+  > conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. https://github.com/conda/conda
 
 - [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
 

diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7183379-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7183379)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
+[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=conda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 
@@ -61,6 +61,7 @@ sanger-tol/ensemblrepeatdownload was originally written by [Matthieu Muffato](ht
 We thank the following people for their assistance in the development of this pipeline:
 
 - [Priyanka Surana](https://github.com/priyanka-surana) for providing reviews.
+- [Tyler Chafin](https://github.com/tkchafin) for updates.
 
 ## Contributions and Support
 

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/getchromsizes": {
@@ -17,22 +17,22 @@
                     },
                     "samtools/dict": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgzip": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -3,10 +3,10 @@ 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/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
diff --git a/modules/nf-core/samtools/dict/environment.yml b/modules/nf-core/samtools/dict/environment.yml
diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf
diff --git a/modules/nf-core/samtools/dict/meta.yml b/modules/nf-core/samtools/dict/meta.yml