Merge pull request #156 from tkchafin/1.2.3

Anaconda purge (1.2.3)
sanger-tol · Dec 5, 2024 · 61c56e4 · 61c56e4
2 parents 2208ff8 + da38725
commit 61c56e4
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diff --git a/CITATIONS.md b/CITATIONS.md
@@ -48,9 +48,9 @@
 
 ## 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 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7949384-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7949384)
 
 [![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/)
 [![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/genomenote)

diff --git a/conf/base.config b/conf/base.config
@@ -81,6 +81,7 @@ process {
 
     withName: MULTIQC {
         memory = { check_max( 150.MB  * task.attempt, 'memory'  ) }
+        time   = { check_max( 1.hour * task.attempt, 'time' ) }
     }
 
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {

diff --git a/conf/modules.config b/conf/modules.config
@@ -49,14 +49,14 @@ process {
         ]
     }
 
-    withName: BUSCO {
+    withName: "BUSCO|BUSCO_BUSCO" {
         // Obey "use_work_dir_as_temp", except for large genomes
         scratch = { !params.use_work_dir_as_temp || (meta.genome_size < 2000000000) }
         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
-                        '--mode genome --tar --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
-                    : '--mode genome --tar' }
+                        '--tar --metaeuk --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
+                    : '--tar --metaeuk ' }
     }
 
     withName: "RESTRUCTUREBUSCODIR" {

diff --git a/conf/test_full.config b/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'

diff --git a/modules.json b/modules.json
@@ -7,65 +7,65 @@
                 "nf-core": {
                     "bedtools/bamtobed": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "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"
                     },
                     "cooler/cload": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "cooler/dump": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "cooler/zoomify": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "fastk/fastk": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff"
                     },
                     "gnu/sort": {
                         "branch": "master",
-                        "git_sha": "88f6e982fb8bd40488d837b3b08a65008e602840",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "merquryfk/merquryfk": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff"
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/busco/environment.yml → ...nf-core/bedtools/bamtobed/environment.yml b/modules/nf-core/busco/environment.yml → ...nf-core/bedtools/bamtobed/environment.yml
diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf
diff --git a/modules/nf-core/bedtools/bamtobed/meta.yml b/modules/nf-core/bedtools/bamtobed/meta.yml
diff --git a/modules/nf-core/bedtools/bamtobed/tests/main.nf.test b/modules/nf-core/bedtools/bamtobed/tests/main.nf.test
diff --git a/modules/nf-core/bedtools/bamtobed/tests/main.nf.test.snap b/modules/nf-core/bedtools/bamtobed/tests/main.nf.test.snap
diff --git a/modules/nf-core/bedtools/bamtobed/tests/tags.yml b/modules/nf-core/bedtools/bamtobed/tests/tags.yml
diff --git a/modules/nf-core/busco/busco.diff → modules/nf-core/busco/busco/busco-busco.diff b/modules/nf-core/busco/busco.diff → modules/nf-core/busco/busco/busco-busco.diff
diff --git a/modules/nf-core/busco/busco/environment.yml b/modules/nf-core/busco/busco/environment.yml