Anaconda purge 2

CITATIONS.md

@@ -50,9 +50,9 @@
 
 ## 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://bioconda.github.io)
 

README.md

@@ -4,7 +4,7 @@
 [![GitHub Actions Linting Status](https://github.com/sanger-tol/blobtoolkit/workflows/nf-core%20linting/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions?query=workflow%3A%22nf-core+linting%22)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7949058-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7949058)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.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/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/sanger-tol/blobtoolkit)

conf/modules.config

@@ -96,8 +96,8 @@ process {
         ext.args = { 'test' in workflow.profile.tokenize(',') ?
                         // Additional configuration to speed processes up during testing.
                         // Note: BUSCO *must* see the double-quotes around the parameters
-                        '--force --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
-                    : '--force' }
+                        '--force --metaeuk --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
+                    : '--force --metaeuk'  }
     }
 
     withName: "RESTRUCTUREBUSCODIR" {

lib/Utils.groovy

@@ -22,7 +22,7 @@ class Utils {
 
         // Check that all channels are present
         // This channel list is ordered by required channel priority.
-        def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+        def required_channels_in_order = ['conda-forge', 'bioconda']
         def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
         // Check that they are in the right order

modules.json

@@ -7,83 +7,84 @@
                 "nf-core": {
                     "blast/blastn": {
                         "branch": "master",
-                        "git_sha": "209e5a3e2753c5e628736a662c877c20f341ee15",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/blast/blastn/blast-blastn.diff"
                     },
-                    "busco": {
+                    "busco/busco": {
                         "branch": "master",
-                        "git_sha": "e3126f437c336c826f242842fe51769cfce0ec2d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
-                        "patch": "modules/nf-core/busco/busco.diff"
+                        "patch": "modules/nf-core/busco/busco/busco-busco.diff"
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "diamond/blastp": {
                         "branch": "master",
-                        "git_sha": "b29f6beb86d1d24d680277fb1a3f4de7b8b8a92c",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/diamond/blastp/diamond-blastp.diff"
                     },
                     "diamond/blastx": {
                         "branch": "master",
-                        "git_sha": "b29f6beb86d1d24d680277fb1a3f4de7b8b8a92c",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/diamond/blastx/diamond-blastx.diff"
                     },
                     "fastawindows": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastawindows/fastawindows.diff"
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "2c2d1cf80866dbd6dd0ea5d61ddd59533a72d41e",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "pigz/compress": {
                         "branch": "master",
-                        "git_sha": "0eab94fc1e48703c1b0a8704bd665f554905c39d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb",
-                        "installed_by": ["modules"]
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/view/samtools-view.diff"
                     },
                     "seqtk/subseq": {
                         "branch": "master",
-                        "git_sha": "7f88aae93c69586c0789322b77743ee0ef469502",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/seqtk/subseq/seqtk-subseq.diff"
                     },
@@ -94,12 +95,12 @@
                     },
                     "windowmasker/mkcounts": {
                         "branch": "master",
-                        "git_sha": "32cac29d4a92220965dace68a1fb0bb2e3547cac",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "windowmasker/ustat": {
                         "branch": "master",
-                        "git_sha": "32cac29d4a92220965dace68a1fb0bb2e3547cac",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }