Feature/prokka in annotation #171
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…e and replaces prodigal, annotation module now gets gtdb results for prokka call
…e and replaces prodigal, annotation module now gets gtdb results for prokka call
... that somehow got lost during a merge.
Leftover from testing.
Not needed anymore since prokka version now includes the partial genes option.
bosterholz
approved these changes
May 26, 2022
modules/annotation/module.nf
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| @@ -282,7 +231,7 @@ process pKEGGFromDiamond { | |||
| pattern: "{**.tsv}" | |||
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| // UID mapping does not work for some reason. Every time a database directory is created while running docker, | |||
| // the permissions are set to root. This leads to crashes later on. | |||
| // the permissions are set to root. This leasds to crashes later on. | |||
| * - "meta" for smaller contigs / metagenomes | ||
| * - "param" sets prodigalMode to whatever is defined as params.steps.annotation.prokka.prodigalMode | ||
| * Other input is a tuple consisting of sample, binID, path to fasta file and the domain (for gene prediction) | ||
| * locusTag setzen? Eindeutiger Tag den wir ersetzen koennen |
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Should we open an issue for this?
modules/annotation/module.nf
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| time '5h' | ||
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| publishDir params.output, saveAs: { filename -> getOutput("${sample}",params.runid ,"prokka", filename) }, \ | ||
| pattern: "{**.gff.gz,**.fna.gz,**.faa.gz,**.sqn.gz,**.txt,**.tsv,**.fsa.gz,**.ffn.gz,**.gbk.gz,**.tbl.gz}" |
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Is this pattern necessary. You need all outputs and you are forgetting the command files.
modules/annotation/module.nf
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| for f in out/* ; do suffix=$(echo "${f##*.}"); mv $f ${BIN_PREFIX}.${suffix}; done | ||
| sed -i -e "2,$ s/^/!{sample}\t${BIN_ID}\t/" -e "1,1 s/^/SAMPLE\tBIN_ID\t/g" *.tsv | ||
| mv *.tsv !{sample}_prokka_${BIN_ID}.tsv | ||
| gzip --best *gff *.faa *.fna *.ffn *.fsa *.gbk *.sqn *tbl |
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Should we use pigz because it ships with the toolkit?
There could also be a little speed boost if files get bigger.
pbelmann
pushed a commit
that referenced
this pull request
Jun 29, 2022
* feat(annotation): replaced prodigal with prokka in annotation module * feat(annotation): removed prokka, moved to annotation module * feat(annotation): prokka moved from magAttributes to annotation and replaces prodigal * feat(annotation): prokka moved from magAttributes to annotation and replaces prodigal * feat(annotation): removed duplicate prokka container and set to own container * feat(annotation): prokka moved from magAttributes to annotation module and replaces prodigal, annotation module now gets gtdb results for prokka call * feat(annotation): replaced prokka 1.12 with prokka 1.14.6 * feat(annotation): added tsv output which is available again in prokka 1.14.6 * feat(annotation): Re-added documentation for _wAnnotation ... that somehow got lost during a merge. * feat(annotation): Removed test output Leftover from testing. * fix(annotation): Removed containerOptions in pProkka Not needed anymore since prokka version now includes the partial genes option. * fix(annotation): correct indention * fix(annotation): _wAnnotation missed parameter in wAnnotateFile * fix(annotation): input.fasta should be removed after prokka execution * fix(annotation): typo + review changes Co-authored-by: bosterholz <[email protected]>
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Prokka is replaced by prodigal in the annotation module. In magAttributes, prokka is no longer used since the annotation of bins now takes place in the annotation module as well. The main workflow wPipeline is changed accordingly.
The Workflwo wCMSeqWorkflowFile in the magAttributes-module is also changed to use prokka, but there seems to be a problem with the CMSeq image. See Issue #170
Issue #164 has been resolved in this branch as well.
The prokka version that is used is a custom image that uses an older prokka version with a fix to support partialgenes. We should update the current prokka version with these changes and include that in our custom image and then evaluate, if we should replace prokka with bacta, which includes partialgenes support without further modifications to the source code.