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fixed channel mixup and removed remnants of utility function #186

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merged 1 commit into from
Mar 15, 2024
Merged

fixed channel mixup and removed remnants of utility function #186

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36 changes: 0 additions & 36 deletions modules/local/liftoff_annotation/main.nf
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2 changes: 1 addition & 1 deletion modules/local/liftoff_cli_annotation/main.nf
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Expand Up @@ -20,7 +20,7 @@ process LIFTOFF_CLI {
}

input:
tuple val(meta), path(fasta)
tuple val(meta), path(fasta), path(fastq1), path(fastq2)
path ref_fasta_path
path ref_gff_path

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2 changes: 1 addition & 1 deletion modules/local/repeatmasker_annotation/main.nf
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Expand Up @@ -12,7 +12,7 @@ process REPEATMASKER {
'quay.io/biocontainers/repeatmasker:4.1.5--pl5321hdfd78af_0'}"

input:
tuple val(meta), path(fasta_path)
tuple val(meta), path(fasta_path), path(fast1), path(fastq2)
path repeat_library

script:
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2 changes: 1 addition & 1 deletion modules/local/vadr_annotation/main.nf
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Expand Up @@ -12,7 +12,7 @@ process VADR {
'staphb/vadr:latest' : 'staphb/vadr:latest' }"

input:
tuple val(meta), path(fasta_path)
tuple val(meta), path(fasta_path), path(fastq1), path(fastq2)
path vadr_models_dir

script:
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3 changes: 1 addition & 2 deletions modules/nf-core/bakta/bakta/main.nf
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Expand Up @@ -18,9 +18,8 @@ process BAKTA {
publishDir "$params.output_dir/$params.bakta_output_dir", mode: 'copy', overwrite: params.overwrite_output

input:
val signal
path db_path
tuple val(meta), path(fasta_path)
tuple val(meta), path(fasta_path), path(fastq1), path(fastq2)

script:
def args = task.ext.args ?: ''
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3 changes: 1 addition & 2 deletions modules/nf-core/bakta/baktadbdownload/main.nf
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Expand Up @@ -6,8 +6,7 @@ process BAKTADBDOWNLOAD {
'quay.io/biocontainers/bakta:1.8.2--pyhdfd78af_0' }"

input:
val signal


output:
path "bakta_db/*" , emit: db

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9 changes: 4 additions & 5 deletions workflows/tostadas.nf
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Expand Up @@ -79,6 +79,7 @@ workflow TOSTADAS {

// Create initial submission channel
submission_ch = metadata_ch.join(reads_ch)

// check if the user wants to skip annotation or not
if ( params.annotation ) {
if ( params.virus && !params.bacteria ) {
Expand All @@ -87,7 +88,7 @@ workflow TOSTADAS {
if ( params.repeatmasker_liftoff ) {
// run repeatmasker annotation on files
REPEATMASKER_LIFTOFF (
fasta_ch
reads_ch
)
repeatmasker_gff_ch = REPEATMASKER_LIFTOFF.out.gff.collect().flatten()
.map {
Expand All @@ -97,14 +98,13 @@ workflow TOSTADAS {
}

// set up submission channels
// submission_ch = metadata_ch.join(fasta_ch)
submission_ch = submission_ch.join(repeatmasker_gff_ch) // meta.id, fasta, fastq1, fastq2, gff
}

// run vadr processes
if ( params.vadr ) {
RUN_VADR (
fasta_ch
reads_ch
)
vadr_gff_ch = RUN_VADR.out.gff
.collect()
Expand All @@ -121,7 +121,7 @@ workflow TOSTADAS {
// run bakta annotation process
if ( params.bakta == true ) {
RUN_BAKTA(
fasta_ch
reads_ch
)
// set up submission channels
bakta_gff_ch = RUN_BAKTA.out.gff3
Expand All @@ -130,7 +130,6 @@ workflow TOSTADAS {
meta = [id:it.getSimpleName()]
[ meta, it ]
}
// submission_ch = metadata_ch.join(fasta_ch)
submission_ch = submission_ch.join(bakta_gff_ch) // meta.id, fasta, fastq1, fastq2, gff
}
}
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