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Bugfix/path creation bug #385

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merged 2 commits into from
Nov 4, 2024
Merged

Bugfix/path creation bug #385

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79d0c26
Paths as string concetation bugfix (issue #379)
madeline-scyphers Nov 4, 2024
2a54af8
Remove not used genes param
madeline-scyphers Nov 4, 2024
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8 changes: 3 additions & 5 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -122,10 +122,8 @@ params.make_product_pkg = "dram_viz"
// Move to nextflow.config when ready
params.trees = 0
params.add_trees = 0
params.trees = 0
params.trees_list = "dmso"
//trees_list = "nar_nxr;dsr;mcra;amoa_pmoa;hydrogenase"
params.add_trees = ""
params.tree_data_files = "${projectDir}/assets/trees/"
params.trees_scripts = "${projectDir}/assets"

Expand Down Expand Up @@ -635,7 +633,7 @@ if( params.rename || params.call ){
// If calling genes, then create a channel called ch_input_fastas.
if ( params.input_fasta != "" ) {
ch_input_fastas = Channel
.fromPath(params.input_fasta + params.fasta_fmt, checkIfExists: true)
.fromPath(file(params.input_fasta) / params.fasta_fmt, checkIfExists: true)
.ifEmpty { exit 1, "Cannot find any fasta files matching: ${params.input_fasta}\nNB: Path needs to follow pattern: path/to/directory/" }
} else {
ch_input_fastas = Channel
Expand Down Expand Up @@ -664,7 +662,7 @@ if( params.annotate ){
if( params.call == 0 ){
// Set ch_input_genes
ch_called_proteins = Channel
.fromPath(params.input_genes + params.genes_fmt, checkIfExists: true)
.fromPath(file(params.input_genes) / params.genes_fmt, checkIfExists: true)
.ifEmpty { exit 1, "If you specify --annotate without --call, you must provide a fasta file of called genes using --input_genes. Cannot find any called gene fasta files matching: ${params.input_genes}\nNB: Path needs to follow pattern: path/to/directory/" }
.map {
sampleName = it.getName().replaceAll(/\.[^.]+$/, '').replaceAll(/\./, '-')
Expand Down Expand Up @@ -775,7 +773,7 @@ if( params.trees ) {
.ifEmpty { exit 1, "If you specify --distill_<topic|ecosystem|custom> without --annotate, you must provide an annotations TSV file (--annotations <path>) with approprite formatting. Cannot find any called gene fasta files matching: ${params.annotations}\nNB: Path needs to follow pattern: path/to/directory/" }

ch_collected_faa = Channel
.fromPath(params.input_genes + params.genes_fmt, checkIfExists: true)
.fromPath(file(params.input_genes) / params.genes_fmt, checkIfExists: true)
.ifEmpty { exit 1, "If you specify --annotations without --input_genes, with the desire to run trees, you must provide a fasta file of called genes using --input_genes. Cannot find any called gene fasta files matching: ${params.input_genes}\nNB: Path needs to follow pattern: path/to/directory/" }
.collect()
}
Expand Down
3 changes: 1 addition & 2 deletions nextflow.config
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Expand Up @@ -87,10 +87,9 @@ params {
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Input Called genes Directory
Input genes formats, DRAM will use either genes + genes_fmt or input_genes
Input genes formats, DRAM will use either input_genes + genes_fmt
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
genes = "${launchDir}/input_genes/*.faa"
genes_fmt = "*.faa"
input_genes = ""

Expand Down