Add support for presupplied annotation files (FAA + GFF or FAA + GBK) #340
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…e new columns not present)
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
…with gzip support
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…verison (as reported on antiSMASH github)
jasmezz
reviewed
Apr 10, 2024
jasmezz
reviewed
Apr 10, 2024
jasmezz
reviewed
Apr 10, 2024
jasmezz
reviewed
Apr 10, 2024
jasmezz
reviewed
Apr 10, 2024
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
jfy133
commented
Apr 10, 2024
Darcy220606
reviewed
Apr 25, 2024
workflows/funcscan.nf
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| meta, files -> | ||
| def fasta_found = files.find{it.toString().tokenize('.').last().matches('fasta|fas|fna|fa')} | ||
| def faa_found = files.find{it.toString().endsWith('.faa')} | ||
| def gbk_found = files.find{it.toString().tokenize('.').last().matches('gbk')} |
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Should also add 'gbk|gbff' also as that is the gbk extension output for bakta.
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Ill add it here as i couldnt comment on it for some reason :D
So in line 188
// TODO: Only NT at the moment. AA tax. classification will be added only when its PR is merged.
remove this because now that the user supllies always both fasta and gbk files for the preannotated track, we dont need to update the taxonomy workflow ;)
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Oooh that's a good question.. currently only FASTAs go to taxonomy... I can't remember if that's preanno ones too
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Wait, the user doesn't always supply GBK, I don't understand now...?
workflows/funcscan.nf
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| ch_versions = ch_versions.mix( SEQKIT_SEQ_LONG.out.versions ) | ||
| ch_versions = ch_versions.mix( SEQKIT_SEQ_SHORT.out.versions ) | ||
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| ch_prepped_input_long = SEQKIT_SEQ_LONG.out.fastx | ||
| ch_intermediate_input_long = SEQKIT_SEQ_LONG.out.fastx | ||
| .map{ meta, file -> [ meta + [id: meta.id + '_long', length: "long" ], file ] } |
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Did you check the actual final output files (.tsv) with the test_taxonomy.config ? Do please correct me if im wrong with understanding the workflow now, so we are now renaming the meta.ids with suffixes _longand _short, will that not interfere with adding the taxonomy to the right files because taxonomy is added according to not only contig but sample_id too which comes from the meta_id.
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No, which is why I asked you to test 😆
If I understand your question correctly:
meta.id indeeds comes from sample, so updating meta is replacing the sample_id with the suffix
But the taxonomy workflow takes input from after this renaming, so it should be OK i hope? Please run the branch and check 😬
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With regards to the summary and taxonomy :
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ampcombi: it doesnt output all samples (but that will be fixed when i put in the new ampcombi submodules). Taxonomy is merged
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combgc: it doesnt consider the samples_1 and 2 that are preannotated, only takes those from the annotatation step in the final report, which i dont understand why. Taxonomy is merged
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hamronization: Works perfectly.
So either therees a problem with this collectfile() function fro both ampcombi/combgc or somethings up with the publishdir path, that every time the pipeline stops and resumes it rewrites the final report.
jfy133
commented
Apr 26, 2024
workflows/funcscan.nf
Outdated
| ch_versions = ch_versions.mix( SEQKIT_SEQ_LONG.out.versions ) | ||
| ch_versions = ch_versions.mix( SEQKIT_SEQ_SHORT.out.versions ) | ||
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| ch_prepped_input_long = SEQKIT_SEQ_LONG.out.fastx | ||
| ch_intermediate_input_long = SEQKIT_SEQ_LONG.out.fastx | ||
| .map{ meta, file -> [ meta + [id: meta.id + '_long', length: "long" ], file ] } |
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No, which is why I asked you to test 😆
If I understand your question correctly:
meta.id indeeds comes from sample, so updating meta is replacing the sample_id with the suffix
But the taxonomy workflow takes input from after this renaming, so it should be OK i hope? Please run the branch and check 😬
workflows/funcscan.nf
Outdated
| meta, files -> | ||
| def fasta_found = files.find{it.toString().tokenize('.').last().matches('fasta|fas|fna|fa')} | ||
| def faa_found = files.find{it.toString().endsWith('.faa')} | ||
| def gbk_found = files.find{it.toString().tokenize('.').last().matches('gbk')} |
workflows/funcscan.nf
Outdated
| meta, files -> | ||
| def fasta_found = files.find{it.toString().tokenize('.').last().matches('fasta|fas|fna|fa')} | ||
| def faa_found = files.find{it.toString().endsWith('.faa')} | ||
| def gbk_found = files.find{it.toString().tokenize('.').last().matches('gbk')} |
There was a problem hiding this comment.
Oooh that's a good question.. currently only FASTAs go to taxonomy... I can't remember if that's preanno ones too
Darcy220606
reviewed
May 1, 2024
workflows/funcscan.nf
Outdated
Comment on lines
189
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| if ( params.run_taxa_classification ) { | ||
| TAXA_CLASS ( ch_prepped_input ) | ||
| TAXA_CLASS ( ch_prepped_input.fastas ) | ||
| ch_versions = ch_versions.mix( TAXA_CLASS.out.versions ) |
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Suggested change
| if ( params.run_taxa_classification ) { | |
| TAXA_CLASS ( ch_prepped_input ) | |
| TAXA_CLASS ( ch_prepped_input.fastas ) | |
| ch_versions = ch_versions.mix( TAXA_CLASS.out.versions ) | |
| ch_intermediate_fasta_for_taxa = ch_intermediate_input.fastas.map{ meta, fasta, faa, gbk -> [ meta, fasta ] } | |
| .mix(ch_intermediate_input.preannotated.map{ meta, fasta, faa, gbk -> [ meta, fasta ] }) | |
| if ( params.run_taxa_classification ) { | |
| TAXA_CLASS ( ch_intermediate_fasta_for_taxa ) | |
| ch_versions = ch_versions.mix( TAXA_CLASS.out.versions ) |
workflows/funcscan.nf
Outdated
| ch_versions = ch_versions.mix( SEQKIT_SEQ_LONG.out.versions ) | ||
| ch_versions = ch_versions.mix( SEQKIT_SEQ_SHORT.out.versions ) | ||
|
|
||
| ch_prepped_input_long = SEQKIT_SEQ_LONG.out.fastx | ||
| ch_intermediate_input_long = SEQKIT_SEQ_LONG.out.fastx | ||
| .map{ meta, file -> [ meta + [id: meta.id + '_long', length: "long" ], file ] } |
There was a problem hiding this comment.
With regards to the summary and taxonomy :
-
ampcombi: it doesnt output all samples (but that will be fixed when i put in the new ampcombi submodules). Taxonomy is merged
-
combgc: it doesnt consider the samples_1 and 2 that are preannotated, only takes those from the annotatation step in the final report, which i dont understand why. Taxonomy is merged
-
hamronization: Works perfectly.
So either therees a problem with this collectfile() function fro both ampcombi/combgc or somethings up with the publishdir path, that every time the pipeline stops and resumes it rewrites the final report.
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OK tests to run:
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…hannels for CREATETSV
…g fastas taxonom results to BGC
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PR checklist
nf-core lint).nextflow run . -profile 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).