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Seqera suggestions #184

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merged 3 commits into from
Mar 14, 2024
Merged

Seqera suggestions #184

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3b34a43
Generate fasta and fastq in a single map operation
robsyme Mar 13, 2024
cacae99
Map closure cleanup
robsyme Mar 13, 2024
1f04a58
Consistent style
robsyme Mar 13, 2024
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59 changes: 27 additions & 32 deletions workflows/tostadas.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -67,35 +67,28 @@ workflow TOSTADAS {
params.meta_path
)
// todo: the names of these tsv_Files need to be from sample name not fasta file name
metadata_ch = METADATA_VALIDATION.out.tsv_Files.flatten()
.map {
def meta = [:]
meta['id'] = it.getSimpleName()
[ meta, it ]
}
metadata_ch = METADATA_VALIDATION.out.tsv_Files
.flatten()
.map {
meta = [id:it.getSimpleName()]
[ meta, it ]
}

// Generate the fasta and fastq paths
fasta_ch =
METADATA_VALIDATION.out.csv_Files.flatten()
| splitCsv(header: true)
| map { row ->
reads_ch =
METADATA_VALIDATION.out.csv_Files
.flatten()
.splitCsv(header: true)
.map { row ->
meta = [id:row.sequence_name]
fasta_path = row.fasta_path ? file(row.fasta_path) : null
[meta, fasta_path]
}

fastq_ch =
METADATA_VALIDATION.out.csv_Files.flatten()
| splitCsv(header: true)
| map { row ->
meta = [id:row.sequence_name]
fastq1 = row.fastq_path_1 ? file(row.fastq_path_1) : null
fastq2 = row.fastq_path_2 ? file(row.fastq_path_2) : null
[meta, fastq1, fastq2]
[meta, fasta_path, fastq1, fastq2]
}

// Create initial submission channel
submission_ch = metadata_ch.join(fasta_ch)
submission_ch = submission_ch.join(fastq_ch)
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 @@ -109,7 +102,7 @@ workflow TOSTADAS {
)
repeatmasker_gff_ch = REPEATMASKER_LIFTOFF.out.gff.collect().flatten()
.map {
def meta = [:]
meta = [:]
meta['id'] = it.getSimpleName().replaceAll('_reformatted', '')
[ meta, it ]
}
Expand All @@ -125,12 +118,14 @@ workflow TOSTADAS {
RUN_UTILITY.out,
fasta_ch
)
vadr_gff_ch = RUN_VADR.out.gff.collect().flatten()
.map {
def meta = [:]
meta['id'] = it.getSimpleName().replaceAll('_reformatted', '')
[ meta, it ]
}
vadr_gff_ch = RUN_VADR.out.gff
.collect()
.flatten()
.map {
meta = [:]
meta['id'] = it.getSimpleName().replaceAll('_reformatted', '')
[ meta, it ]
}
submission_ch = submission_ch.join(vadr_gff_ch) // meta.id, fasta, fastq1, fastq2, gff
}
}
Expand All @@ -142,12 +137,12 @@ workflow TOSTADAS {
fasta_ch
)
// set up submission channels
bakta_gff_ch = RUN_BAKTA.out.gff3.flatten()
bakta_gff_ch = RUN_BAKTA.out.gff3
.flatten()
.map {
def meta = [:]
meta['id'] = it.getSimpleName()
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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