Merge pull request #124 from tkchafin/anaconda_purge_2

Anaconda purge 2
sanger-tol · Nov 25, 2024 · 000b442 · 000b442
2 parents 6fe1861 + 15974b4
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,9 +19,13 @@ The pipeline is now considered to be a complete and suitable replacement for the
 
 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 |
-| ----------- | ----------- | ----------- |
-| blobtoolkit | 4.3.9       | 4.3.13      |
+| Dependency  | Old version       | New version     |
+| ----------- | ----------------- | --------------- |
+| blast       | 2.14.1 and 2.15.0 | only 2.15.0     |
+| blobtoolkit | 4.3.9             | 4.4.0           |
+| busco       | 5.5.0             | 5.7.1           |
+| multiqc     | 1.20 and 1.21     | 1.20 and 1.25.1 |
+| samtools    | 1.18 and 1.19.2   | 1.20 and 1.21   |
 
 ## [[0.6.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.6.0)] – Bellsprout – [2024-09-13]
 
@@ -112,7 +116,7 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 | blobtoolkit | 4.3.3         | 4.3.9             |
 | blast       | 2.14.0        | 2.15.0 and 2.14.1 |
 | multiqc     | 1.17 and 1.18 | 1.20 and 1.21     |
-| samtools    | 1.18          | 1.19.2            |
+| samtools    | 1.18          | 1.18 and 1.19.2   |
 | seqtk       | 1.3           | 1.4               |
 
 > **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.

diff --git a/CITATIONS.md b/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)
 

diff --git a/README.md b/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)

diff --git a/conf/modules.config b/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" {

diff --git a/docs/usage.md b/docs/usage.md
@@ -272,7 +272,7 @@ List of tools for any given dataset can be fetched from the API, for example htt
 
 | Dependency        | Snakemake | Nextflow |
 | ----------------- | --------- | -------- |
-| blobtoolkit       | 4.3.2     | 4.3.13   |
+| blobtoolkit       | 4.3.2     | 4.4.0    |
 | blast             | 2.12.0    | 2.14.1   |
 | blobtk            | 0.5.0     | 0.5.1    |
 | busco             | 5.3.2     | 5.5.0    |

diff --git a/lib/Utils.groovy b/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

diff --git a/modules.json b/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"]
                     }
                 }

diff --git a/modules/local/blobtoolkit/chunk.nf b/modules/local/blobtoolkit/chunk.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_CHUNK {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_CHUNK module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta) , path(fasta)

diff --git a/modules/local/blobtoolkit/countbuscos.nf b/modules/local/blobtoolkit/countbuscos.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_COUNTBUSCOS {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_COUNTBUSCOS module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(table, stageAs: 'dir??/*')

diff --git a/modules/local/blobtoolkit/createblobdir.nf b/modules/local/blobtoolkit/createblobdir.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_CREATEBLOBDIR {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_BLOBDIR module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(window, stageAs: 'windowstats/*')

diff --git a/modules/local/blobtoolkit/extractbuscos.nf b/modules/local/blobtoolkit/extractbuscos.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_EXTRACTBUSCOS {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_EXTRACTBUSCOS module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/local/blobtoolkit/summary.nf b/modules/local/blobtoolkit/summary.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_SUMMARY {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_SUMMARY module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(blobdir)

diff --git a/modules/local/blobtoolkit/unchunk.nf b/modules/local/blobtoolkit/unchunk.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_UNCHUNK {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_UNCHUNK module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(blast_table)

diff --git a/modules/local/blobtoolkit/updateblobdir.nf b/modules/local/blobtoolkit/updateblobdir.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_UPDATEBLOBDIR {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_BLOBDIR module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(input, stageAs: "input_blobdir")

diff --git a/modules/local/blobtoolkit/updatemeta.nf b/modules/local/blobtoolkit/updatemeta.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_UPDATEMETA {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_UPDATEMETA module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/local/blobtoolkit/windowstats.nf b/modules/local/blobtoolkit/windowstats.nf
@@ -4,7 +4,7 @@ process BLOBTOOLKIT_WINDOWSTATS {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_WINDOWSTATS module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(tsv)

diff --git a/modules/local/generate_config.nf b/modules/local/generate_config.nf
@@ -3,7 +3,7 @@ process GENERATE_CONFIG {
     label 'process_single'
 
     conda "conda-forge::requests=2.28.1 conda-forge::pyyaml=6.0"
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), val(fasta)

diff --git a/modules/nf-core/blast/blastn/blast-blastn.diff b/modules/nf-core/blast/blastn/blast-blastn.diff
diff --git a/modules/nf-core/blast/blastn/environment.yml b/modules/nf-core/blast/blastn/environment.yml
diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf