Release PR for 2.1.0 #456
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Release PR for 2.1.0 #456
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Post-release version bump
Update citations
Add InterProScan to Pipeline and integrate in AMPcombi
Co-authored-by: James A. Fellows Yates <[email protected]>
Add 2.1 metromap
Update documentaion and parameter schema
Set ampcombi2/parsetables resources
Release version bump to 2.1.0
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erikrikarddaniel
approved these changes
Feb 17, 2025
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Only a few very small suggestions, otherwise great!
I am a bit curious as to why you have so many resource specifications in the pipeline rather than letting the nf-core defaults shine through. Doesn't that defeat the purpose of using the labels? If I were to run the pipeline and reset e.g. process_high so it fits my HPC, many processes wouldn't get what I specify since it's overridden by withName: declarations. I'm not asking you to change this now, as this wasn't part of this release and has hence been accepted earlier. Just curious.
jasmezz
commented
Feb 18, 2025
Co-authored-by: Jasmin Frangenberg <[email protected]>
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@erikrikarddaniel Regarding your question of the very specific resource configurations: Would definitely be nice to use the labels; we found for some tools that they fail if certain resources are not given, so to prevent pipeline restarts, we decided to configure those minimums. Also, certain tools (e.g. for downloading databases) need only a single cpu and almost no memory, so also here we tried to be precise. We can revisit this question for a next release to check if some module configs can be replaced with "process_long" for example. |
Update interproscan resources
mashehu
approved these changes
Feb 20, 2025
| NFTEST_VER: "0.8.4" | ||
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | ||
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | ||
| NFTEST_VER: "0.9.0" |
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Suggested change
| NFTEST_VER: "0.9.0" | |
| NFTEST_VER: "0.9.2" |
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| pull_request_target: | ||
| branches: | ||
| - main | ||
| - master |
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remove pull_request_target, see nf-core/tools#3399
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| - [#421](https://github.com/nf-core/funcscan/pull/421) Updated to nf-core template 3.0.2. (by @jfy133) | ||
| - [#427](https://github.com/nf-core/funcscan/pull/427) AMPcombi now can use multiple other databases for classifications. (by @darcy220606) | ||
| - [#428](https://github.com/nf-core/funcscan/pull/428) Added InterProScan annotation workflow to the pipeline. The results are coupled to AMPcombi final table. (by @darcy220606) | ||
| - [#429](https://github.com/nf-core/funcscan/pull/429) Updated to nf-core template 3.1.0. (by @jfy133 and @jasmezz) | ||
| - [#433](https://github.com/nf-core/funcscan/pull/433) Updated to nf-core template 3.1.1. (by @jfy133) | ||
| - [#431](https://github.com/nf-core/funcscan/pull/431) Updated AMPcombi, Macrel, all MMseqs2 modules, MultiQC, Pyrodigal, and seqkit, added `--taxa_classification_mmseqs_compressed` parameter. (by @jasmezz) | ||
| - [#438](https://github.com/nf-core/funcscan/pull/438) Updated to nf-core template 3.1.2. (by @jfy133) | ||
| - [#441](https://github.com/nf-core/funcscan/pull/441) Updated to nf-core template 3.2.0, updated MultiQC. (by @jasmezz and @jfy133) | ||
| - [#440](https://github.com/nf-core/funcscan/pull/440) Updated Bakta and introduced new parameter `--annotation_bakta_hmms`. (by @jasmezz) |
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combine template updates to one bullet point
| "errorMessage": "Input file for peptide annotations has incorrect file format. File must end in `.fasta` or `.faa`", | ||
| "unique": true, | ||
| "dependentRequired": ["gbk"] | ||
| "errorMessage": "Input file for peptide annotations has incorrect file format. File must end in `.fasta` or `.faa`" |
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maybe call it test_minimal?
| }, | ||
| "protein_annotation_interproscan_applications": { | ||
| "type": "string", | ||
| "default": "PANTHER,ProSiteProfiles,ProSitePatterns,Pfam", |
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add a pattern to make sure you get it in the correct format.
| "protein_annotation_tool": { | ||
| "type": "string", | ||
| "default": "InterProScan", | ||
| "help_text": "This flag specifies which tool for protein annotation should be activated.\nAt the moment only [InterProScan](https://github.com/ebi-pf-team/interproscan) is incorporated in the pipeline. This annotates the locus tags to protein and domain levels according to the InterPro databases.\n\nMore details can be found in the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/index.html).", |
| "type": "integer", | ||
| "default": 0, | ||
| "enum": [0, 1], | ||
| "help_text": "To compress MMseqs2 output files, choose 1, otherwise leave to 0. Compressing output files can lead to errors when the output is actually empty. In that case, just leave this parameter to default. More details can be found in the [documentation (GitHub)](https://github.com/soedinglab/MMseqs2?tab=readme-ov-file#memory-requirements).\n\n> Modifies tool parameter(s):\n> - mmseqs createdb --compressed <0|1>\n> - mmseqs createtsv --compressed <0|1>\n> - mmseqs databases --compressed <0|1>\n> - mmseqs taxonomy --compressed <0|1>", |
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| "help_text": "To compress MMseqs2 output files, choose 1, otherwise leave to 0. Compressing output files can lead to errors when the output is actually empty. In that case, just leave this parameter to default. More details can be found in the [documentation (GitHub)](https://github.com/soedinglab/MMseqs2?tab=readme-ov-file#memory-requirements).\n\n> Modifies tool parameter(s):\n> - mmseqs createdb --compressed <0|1>\n> - mmseqs createtsv --compressed <0|1>\n> - mmseqs databases --compressed <0|1>\n> - mmseqs taxonomy --compressed <0|1>", | |
| "help_text": "To compress MMseqs2 output files, choose `1`, otherwise `0`. Compressing output files can lead to errors when the output is actually empty. In that case, just leave this parameter to its default value. More details can be found in the [documentation (GitHub)](https://github.com/soedinglab/MMseqs2?tab=readme-ov-file#memory-requirements).\n\n> Modifies tool parameter(s):\n> - mmseqs createdb --compressed <0|1>\n> - mmseqs createtsv --compressed <0|1>\n> - mmseqs databases --compressed <0|1>\n> - mmseqs taxonomy --compressed <0|1>", |
| }, | ||
| "protein_annotation_interproscan_db": { | ||
| "type": "string", | ||
| "help_text": "Use this to supply the path to a pre-downloaded InterProScan database. This can be any unzipped InterProScan version. By default the database version '5.72-103.0' is downloaded.\n\nFor more details on where to find different InterProScan databases see tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/UserDocs.html#obtaining-a-copy-of-interproscan).\n", |
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| "help_text": "Use this to supply the path to a pre-downloaded InterProScan database. This can be any unzipped InterProScan version. By default the database version '5.72-103.0' is downloaded.\n\nFor more details on where to find different InterProScan databases see tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/UserDocs.html#obtaining-a-copy-of-interproscan).\n", | |
| "help_text": "Use this to supply the path to a pre-downloaded InterProScan database. This can be any unzipped InterProScan version.\n\nFor more details on where to find different InterProScan databases see tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/UserDocs.html#obtaining-a-copy-of-interproscan).\n", |
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any reason why this is not an nf-core subworkflow?
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WE WILL IGNORE CONDA CI TEST FAILURES TO THEM BEING A CONDA OVERLAPPING LOCK ERROR RELATED TO NEXTFLOW
Added--taxa_classification_mmseqs_compressedparameter. (by @jasmezz)--annotation_bakta_hmms. (by @jasmezz)Fixedrgi/mainmodule to fix incorrect variable name. (by @amizeranschi and @jasmezz)--annotation_pyrodigal_usespecialstopcharacterparameter to improve AMPlify screening. (by @jasmezz)ampcombi2/parsetables. (by @jasmezz)DependenciesDeprecatedPR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).