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Merge pull request #339 from sanger-tol/dp24_module_update_3
Dp24 module update 3
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@@ -316,7 +316,7 @@ process { | |
| } | ||
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| withName: "BUSCO_BUSCO" { | ||
| ext.args = "--offline" | ||
| ext.args = "--offline --metaeuk" | ||
| } | ||
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25 changes: 10 additions & 15 deletions
25
modules/local/chunkfasta.nf → modules/local/seqkit/split/main.nf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,48 +1,43 @@ | ||
| process CHUNKFASTA { | ||
| process SEQKIT_SPLIT { | ||
| tag "${meta.id}" | ||
| label 'process_low' | ||
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| conda "conda-forge::pyfasta=0.5.2-1" | ||
| container "${ 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' }" | ||
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| input: | ||
| tuple val(meta), path('input.fasta') | ||
| val(number_of_chunks) | ||
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| 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 | ||
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| 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 | ||
| """ | ||
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| 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 | ||
| """ | ||
| } |
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