Dp24 module update 3

CHANGELOG.md

@@ -13,11 +13,16 @@ Our 3rd release for sanger-tol/treeval.
 - Adds a JBrowse Only workflow (this will lead to an update to the FULL workflow which can now call JBROWSE_ONLY and RAPID).
 - Updates to containers (local modules) to remove Anaconda dependencies following policy changes.
 - Updates to modules to remove Anaconda dependencies following policy changes
+  - The majority of these updates only remove the `default` channel from the environment.yml
 - CONDA warnings for modules which cannot use CONDA.
 - Removable of a liberal use of spaces.
 - reformat_intersect was previously not outputing version data.
 - Adding arch specification to Pretext GitHub actions runner. Hopefully this will stop the spurious errors we see on there.
 - Addition of steps into schema.
+- Adds \*ktab as an output.
+- Updated singularity containers
+- Added `--metaeuk` to BUSCO_BUSCO, default was causing pipeline errors on Actions -- Needs more investigation.
+- Replaced Pyfasta split (depreciated 6 years ago) with Seqkit split which is frequently updated and very fast.
 
 ### Parameters
 
@@ -29,39 +34,43 @@ Our 3rd release for sanger-tol/treeval.
 
 Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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.
 
-| Module                                 | Old Version      | New Versions |
-| -------------------------------------- | ---------------- | ------------ |
-| bamtobed_sort ( bedtools + samtools )  | 2.31.0 + 1.17    |              |
-| bedtools                               | 2.31.1           |              |
-| busco                                  | 5.5.0            |              |
-| bwa-mem2                               | 2.2.1            |              |
-| cat                                    | 2.3.4            |              |
-| chunk_fasta ( pyfasta )                | 0.5.2-1          |              |
-| cooler                                 | 0.9.2            |              |
-| cram_filter_align_bwamem2_fixmate_sort | -                |              |
-| ^ ( samtools + bwamem2 ) ^             | 1.17 + 2.2.1     |              |
-| coreutils                              | 9.1              |              |
-| fastk                                  | 1.0.1            |              |
-| gcc                                    | 10.4.0           |              |
-| find_telomere_windows ( java-jdk )     | 8.0.112          |              |
-| generate_cram_csv ( samtools )         | 1.17             |              |
-| gnu-sort                               | 8.25             |              |
-| juicer_tools_pre ( java-jdk )          | 8.0.112          |              |
-| perl                                   | 5.26.2           |              |
-| merquryfk                              | 1.0.1            |              |
-| minimap2 + samtools                    | 2.24 + 1.14      |              |
-| miniprot                               | 0.11--he4a0461_2 |              |
-| mummer                                 | 3.23             |              |
-| paftools ( minimap2 + samtools )       | 2.24 + 1.14      |              |
-| pretextmap + samtools                  | 0.0.2 + 1.17     |              |
-| python                                 | 3.9              | -            |
-| - pandas                               | 1.5.2            | -            |
-| samtools                               | 1.18             | 1.21         |
-| selfcomp_splitfasta ( perl-bioperl )   | 1.7.8-1          |              |
-| seqtk                                  | 1.4              |              |
-| tabix                                  | 1.11             |              |
-| ucsc                                   | 377              |              |
-| windowmasker (blast)                   | 2.14.0           |              |
+| Module                                 | Old Version      | New Versions      |
+| -------------------------------------- | ---------------- | ----------------- |
+| bamtobed_sort ( bedtools + samtools )  | 2.31.0 + 1.17    |                   |
+| bedtools                               | 2.31.1           | -                 |
+| busco\*                                | 5.5.0            | -                 |
+| bwa-mem2                               | 2.2.1            |                   |
+| cat                                    | 2.3.4            |                   |
+| chunk_fasta ( pyfasta )                | 0.5.2-1          | REMOVED           |
+| cooler                                 | 0.9.2            |                   |
+| cram_filter_align_bwamem2_fixmate_sort | -                |                   |
+| ^ ( samtools + bwamem2 ) ^             | 1.17 + 2.2.1     |                   |
+| coreutils                              | 9.1              |                   |
+| fastk                                  | 1.0.1            |                   |
+| gcc                                    | 10.4.0           |                   |
+| find_telomere_windows ( java-jdk )     | 8.0.112          |                   |
+| generate_cram_csv ( samtools )         | 1.17             |                   |
+| gnu-sort                               | 8.25             | 9.3               |
+| juicer_tools_pre ( java-jdk )          | 8.0.112          |                   |
+| perl                                   | 5.26.2           |                   |
+| merquryfk                              | 1.0.1            |                   |
+| minimap2 + samtools                    | 2.24 + 1.14      |                   |
+| minimap2_index                         | 2.24             | 2.28              |
+| miniprot                               | 0.11--he4a0461_2 |                   |
+| mummer                                 | 3.23             |                   |
+| paftools ( minimap2 + samtools )       | 2.24 + 1.14      |                   |
+| pretextmap + samtools                  | 0.0.2 + 1.17     | 0.0.3 + 1.17      |
+| python                                 | 3.9              | -                 |
+| - pandas                               | 1.5.2            | -                 |
+| samtools                               | 1.18             | 1.21              |
+| selfcomp_splitfasta ( perl-bioperl )   | 1.7.8-1          |                   |
+| seqtk                                  | 1.4              |                   |
+| seqkit                                 | ADDED            | 2.9.0--h9ee0642_0 |
+| tabix                                  | 1.11             |                   |
+| ucsc                                   | 377              | 447               |
+| windowmasker (blast)                   | 2.14.0           | 2.15.0            |
+
+- busco is currently pinned to v5.5.0 - Upgrading v5.7.1 would cause github actions to crash. Further investigation needed.
 
 ## [1.1.1] - Ancient Aurora (H1) - [2024-04-26]
 

CITATIONS.md

@@ -112,9 +112,9 @@
 
 ## Software packaging/containerisation tools
 
-- [Anaconda](https://anaconda.com)
+- [Conda](https://conda.org/)
 
-  > Anaconda Software Distribution. 2016. Computer software. Vers. 2-2.4.0. Anaconda, 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/)
 

README.md

@@ -1,6 +1,6 @@
 [![Cite with Zenodo](https://zenodo.org/badge/509096312.svg)](https://zenodo.org/doi/10.5281/zenodo.10047653)
 [![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/treeval)

conf/modules.config

@@ -316,7 +316,7 @@ process {
     }
 
     withName: "BUSCO_BUSCO" {
-        ext.args        = "--offline"
+        ext.args        = "--offline --metaeuk"
     }
 
 

modules.json

@@ -12,7 +12,7 @@
                     },
                     "bedtools/genomecov": {
                         "branch": "master",
-                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
+                        "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963",
                         "installed_by": ["modules"]
                     },
                     "bedtools/intersect": {
@@ -27,7 +27,7 @@
                     },
                     "bedtools/map": {
                         "branch": "master",
-                        "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bedtools/merge": {
@@ -58,12 +58,12 @@
                     },
                     "cooler/cload": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "cooler/zoomify": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
@@ -94,7 +94,7 @@
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
                     },
@@ -115,9 +115,8 @@
                     },
                     "mummer": {
                         "branch": "master",
-                        "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/mummer/mummer.diff"
+                        "git_sha": "a15872dde4c4affaac2dfee6c3c65fadab4719bd",
+                        "installed_by": ["modules"]
                     },
                     "paftools/sam2paf": {
                         "branch": "master",

modules/local/pretext_graph.nf

@@ -2,7 +2,7 @@ process PRETEXT_GRAPH {
     tag "$meta.id"
     label 'process_single'
 
-    container "quay.io/sanger-tol/pretext:0.0.2-yy5-c3"
+    container "quay.io/sanger-tol/pretext:0.0.3-yy5-c1"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/local/chunkfasta.nf → modules/local/seqkit/split/main.nf

@@ -1,48 +1,43 @@
-process CHUNKFASTA {
+process SEQKIT_SPLIT {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::pyfasta=0.5.2-1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pyfasta:0.5.2--py_1' :
-        'biocontainers/pyfasta:0.5.2--py_1' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path('input.fasta')
     val(number_of_chunks)
 
     output:
-    tuple val(meta), path('*.fasta'), emit: fasta
-    path "versions.yml"             , emit: versions
+    tuple val(meta), path('*.fa'),  emit: fasta
+    path "versions.yml",            emit: versions
 
     script:
-    def VERSION = '0.5.2' // Tool does not report version
     // This should be abstracted outside of the container to
     // stop it spinning up in the first place,
     // however dsl2 can't do comparisons with channels which makes it harder
     """
     if [ $number_of_chunks -le 1 ]; then
-        mv input.fasta ${meta.id}_whole.fasta
+        mv input.fasta ${meta.id}_whole.fa
     else
-        pyfasta split -n $number_of_chunks input.fasta
+        seqkit split input.fasta -p $number_of_chunks -O ./
     fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-        pyfasta: $VERSION
+        seqkit: \$(seqkit version | sed -e "s/seqkit v//g")
     END_VERSIONS
     """
 
     stub:
-    def VERSION = '0.5.2' // Tool does not report version
     """
-    touch ${meta.id}.fa
+    touch ${prefix}.fa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-        pyfasta: $VERSION
+        seqkit: \$(seqkit version | sed -e "s/seqkit v//g")
     END_VERSIONS
     """
 }